RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep']
Forking launchpad-buildd slave process...
Kernel version: Linux lgw01-16 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64
Buildd toolchain package versions: launchpad-buildd_139 python-lpbuildd_139 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa8 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.5 git-build-recipe_0.3~git201603101733.90b6821~ubuntu14.04.2 git_1:1.9.1-1ubuntu0.3 dpkg-dev_1.17.5ubuntu5.6 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1 qemu-user-static_2.0.0+dfsg-2ubuntu1.22.
Syncing the system clock with the buildd NTP service...
27 Apr 04:26:52 ntpdate[1668]: adjust time server 10.211.37.1 offset -0.000374 sec
RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-9645758', '/home/buildd/filecache-default/063eeb43ee0a3186cd7a3c6a3a452f2f4c9a8d95']
Unpacking chroot for build PACKAGEBUILD-9645758
RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-9645758']
Mounting chroot for build PACKAGEBUILD-9645758
RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-9645758', 'deb http://ftpmaster.internal/ubuntu yakkety main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-security main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-proposed main universe']
Overriding sources.list in build-PACKAGEBUILD-9645758
RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-9645758', 'amd64']
Updating debian chroot for build PACKAGEBUILD-9645758
Get:1 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB]
Get:2 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB]
Get:3 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB]
Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed InRelease [95.7 kB]
Get:5 http://ftpmaster.internal/ubuntu yakkety/main amd64 Packages [1207 kB]
Get:6 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [568 kB]
Get:7 http://ftpmaster.internal/ubuntu yakkety/universe amd64 Packages [7540 kB]
Get:8 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4355 kB]
Get:9 http://ftpmaster.internal/ubuntu yakkety-security/main amd64 Packages [64 B]
Get:10 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B]
Get:11 http://ftpmaster.internal/ubuntu yakkety-security/universe amd64 Packages [64 B]
Get:12 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B]
Get:13 http://ftpmaster.internal/ubuntu yakkety-updates/main amd64 Packages [64 B]
Get:14 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B]
Get:15 http://ftpmaster.internal/ubuntu yakkety-updates/universe amd64 Packages [64 B]
Get:16 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B]
Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 Packages [146 kB]
Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main Translation-en [61.0 kB]
Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/universe amd64 Packages [316 kB]
Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/universe Translation-en [246 kB]
Fetched 15.0 MB in 3s (4534 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following NEW packages will be installed:
  libpng16-16
The following packages will be upgraded:
  apt apt-transport-https bash binutils cpp-5 g++-5 gcc-5 gcc-5-base
  gcc-6-base grep hostname init init-system-helpers initscripts libapt-pkg5.0
  libasan2 libatomic1 libcc1-0 libcilkrts5 libgcc-5-dev libgcc1 libgomp1
  libitm1 liblsan0 libmpx0 libperl5.22 libpng12-0 libquadmath0 libsasl2-2
  libsasl2-modules-db libsemanage-common libsemanage1 libsepol1 libslang2
  libstdc++-5-dev libstdc++6 libsystemd0 libtsan0 libubsan0 libudev1
  linux-libc-dev make optipng perl perl-base perl-modules-5.22
  policyrcd-script-zg2 sed systemd systemd-sysv sysv-rc sysvinit-utils tzdata
53 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 95.2 MB of archives.
After this operation, 243 MB of additional disk space will be used.
Get:1 http://ftpmaster.internal/ubuntu yakkety/main amd64 bash amd64 4.3-14ubuntu2 [593 kB]
Get:2 http://ftpmaster.internal/ubuntu yakkety/main amd64 grep amd64 2.25-1 [153 kB]
Get:3 http://ftpmaster.internal/ubuntu yakkety/main amd64 hostname amd64 3.17ubuntu1 [11.7 kB]
Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libperl5.22 amd64 5.22.1-10 [3367 kB]
Get:5 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 perl amd64 5.22.1-10 [237 kB]
Get:6 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 perl-base amd64 5.22.1-10 [1298 kB]
Get:7 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 perl-modules-5.22 all 5.22.1-10 [2640 kB]
Get:8 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 init-system-helpers all 1.31ubuntu1 [31.9 kB]
Get:9 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 init amd64 1.31ubuntu1 [4568 B]
Get:10 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 sed amd64 4.2.2-7.1 [140 kB]
Get:11 http://ftpmaster.internal/ubuntu yakkety/main amd64 gcc-6-base amd64 6.0.1-2ubuntu13 [15.8 kB]
Get:12 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgcc1 amd64 1:6.0.1-2ubuntu13 [38.6 kB]
Get:13 http://ftpmaster.internal/ubuntu yakkety/main amd64 libstdc++6 amd64 6.0.1-2ubuntu13 [399 kB]
Get:14 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libapt-pkg5.0 amd64 1.2.11 [698 kB]
Get:15 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 apt amd64 1.2.11 [1036 kB]
Get:16 http://ftpmaster.internal/ubuntu yakkety/main amd64 sysvinit-utils amd64 2.88dsf-59.3ubuntu4 [21.5 kB]
Get:17 http://ftpmaster.internal/ubuntu yakkety/main amd64 sysv-rc all 2.88dsf-59.3ubuntu4 [18.2 kB]
Get:18 http://ftpmaster.internal/ubuntu yakkety/main amd64 initscripts amd64 2.88dsf-59.3ubuntu4 [24.4 kB]
Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libsystemd0 amd64 229-5ubuntu1 [210 kB]
Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 systemd amd64 229-5ubuntu1 [3643 kB]
Get:21 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 systemd-sysv amd64 229-5ubuntu1 [17.8 kB]
Get:22 http://ftpmaster.internal/ubuntu yakkety/main amd64 libsepol1 amd64 2.5-1 [216 kB]
Get:23 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libsemanage-common all 2.4-3build2 [6558 B]
Get:24 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libsemanage1 amd64 2.4-3build2 [79.3 kB]
Get:25 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libudev1 amd64 229-5ubuntu1 [60.4 kB]
Get:26 http://ftpmaster.internal/ubuntu yakkety/main amd64 tzdata all 2016d-2 [168 kB]
Get:27 http://ftpmaster.internal/ubuntu yakkety/main amd64 g++-5 amd64 5.3.1-16ubuntu2 [32.4 MB]
Get:28 http://ftpmaster.internal/ubuntu yakkety/main amd64 gcc-5 amd64 5.3.1-16ubuntu2 [8564 kB]
Get:29 http://ftpmaster.internal/ubuntu yakkety/main amd64 cpp-5 amd64 5.3.1-16ubuntu2 [30.1 MB]
Get:30 http://ftpmaster.internal/ubuntu yakkety/main amd64 libcc1-0 amd64 6.0.1-2ubuntu13 [31.2 kB]
Get:31 http://ftpmaster.internal/ubuntu yakkety/main amd64 binutils amd64 2.26-8ubuntu3 [2441 kB]
Get:32 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgomp1 amd64 6.0.1-2ubuntu13 [74.0 kB]
Get:33 http://ftpmaster.internal/ubuntu yakkety/main amd64 libitm1 amd64 6.0.1-2ubuntu13 [28.0 kB]
Get:34 http://ftpmaster.internal/ubuntu yakkety/main amd64 libatomic1 amd64 6.0.1-2ubuntu13 [9160 B]
Get:35 http://ftpmaster.internal/ubuntu yakkety/main amd64 libasan2 amd64 5.3.1-16ubuntu2 [269 kB]
Get:36 http://ftpmaster.internal/ubuntu yakkety/main amd64 liblsan0 amd64 6.0.1-2ubuntu13 [116 kB]
Get:37 http://ftpmaster.internal/ubuntu yakkety/main amd64 libtsan0 amd64 6.0.1-2ubuntu13 [260 kB]
Get:38 http://ftpmaster.internal/ubuntu yakkety/main amd64 libubsan0 amd64 6.0.1-2ubuntu13 [107 kB]
Get:39 http://ftpmaster.internal/ubuntu yakkety/main amd64 libcilkrts5 amd64 6.0.1-2ubuntu13 [40.9 kB]
Get:40 http://ftpmaster.internal/ubuntu yakkety/main amd64 libmpx0 amd64 5.3.1-16ubuntu2 [9754 B]
Get:41 http://ftpmaster.internal/ubuntu yakkety/main amd64 libquadmath0 amd64 6.0.1-2ubuntu13 [132 kB]
Get:42 http://ftpmaster.internal/ubuntu yakkety/main amd64 libstdc++-5-dev amd64 5.3.1-16ubuntu2 [1407 kB]
Get:43 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgcc-5-dev amd64 5.3.1-16ubuntu2 [2238 kB]
Get:44 http://ftpmaster.internal/ubuntu yakkety/main amd64 gcc-5-base amd64 5.3.1-16ubuntu2 [17.2 kB]
Get:45 http://ftpmaster.internal/ubuntu yakkety/universe amd64 libpng12-0 amd64 1.2.54-6ubuntu1 [116 kB]
Get:46 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libslang2 amd64 2.3.0-2.3ubuntu1 [414 kB]
Get:47 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 apt-transport-https amd64 1.2.11 [25.7 kB]
Get:48 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [14.5 kB]
Get:49 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [48.7 kB]
Get:50 http://ftpmaster.internal/ubuntu yakkety/main amd64 libpng16-16 amd64 1.6.21-4 [172 kB]
Get:51 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 linux-libc-dev amd64 4.4.0-22.38 [839 kB]
Get:52 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 make amd64 4.1-9 [154 kB]
Get:53 http://ftpmaster.internal/ubuntu yakkety/main amd64 optipng amd64 0.7.6-1build1 [81.9 kB]
Get:54 http://ftpmaster.internal/ubuntu yakkety/main amd64 policyrcd-script-zg2 all 0.1-3 [5610 B]
debconf: delaying package configuration, since apt-utils is not installed
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Current default time zone: 'Etc/UTC'
Local time is now:      Wed Apr 27 04:27:43 UTC 2016.
Universal Time is now:  Wed Apr 27 04:27:43 UTC 2016.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-9645758', 'amd64', 'yakkety-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=yakkety-proposed', '--purge=never', '--nolog', '-A', 'picard-tools_2.1.1+dfsg-1.dsc']
Initiating build PACKAGEBUILD-9645758 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lgw01-16.buildd

╔══════════════════════════════════════════════════════════════════════════════╗
║ picard-tools 2.1.1+dfsg-1 (amd64)                          27 Apr 2016 04:27 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: picard-tools
Version: 2.1.1+dfsg-1
Source Version: 2.1.1+dfsg-1
Distribution: yakkety-proposed
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64

I: NOTICE: Log filtering will replace 'build/picard-tools-Jcekps/picard-tools-2.1.1+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/picard-tools-Jcekps' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-9645758/chroot-autobuild' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘


Local sources
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picard-tools_2.1.1+dfsg-1.dsc exists in .; copying to chroot

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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver)                         │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
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Building dependency tree...
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Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), ant, default-jdk (>= 2:1.8), debhelper (>= 9), javahelper, maven-repo-helper, libhtsjdk-java (>= 2.1.1), libguava-java, testng, libjcommander-java, r-base-core, ant-optional, default-jdk-doc, libhtsjdk-java-doc, libguava-java-doc
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), ant, default-jdk (>= 2:1.8), debhelper (>= 9), javahelper, maven-repo-helper, libhtsjdk-java (>= 2.1.1), libguava-java, testng, libjcommander-java, r-base-core, ant-optional, default-jdk-doc, libhtsjdk-java-doc, libguava-java-doc
dpkg-deb: building package 'sbuild-build-depends-picard-tools-dummy' in '/«BUILDDIR»/resolver-neO8eM/apt_archive/sbuild-build-depends-picard-tools-dummy.deb'.
Ign:1 copy:/«BUILDDIR»/resolver-neO8eM/apt_archive ./ InRelease
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Get:4 copy:/«BUILDDIR»/resolver-neO8eM/apt_archive ./ Sources [515 B]
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Fetched 3418 B in 0s (262 kB/s)
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install picard-tools build dependencies (apt-based resolver)                 │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  ant ant-optional autoconf automake autopoint autotools-dev bsdmainutils
  ca-certificates-java dctrl-tools debhelper default-jdk default-jdk-doc
  default-jdk-headless default-jre default-jre-headless devscripts
  dh-autoreconf dh-python dh-strip-nondeterminism file fontconfig
  fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
  intltool-debian java-common javahelper libapache-pom-java
  libarchive-zip-perl libasound2 libasound2-data libasprintf0v5 libasyncns0
  libatinject-jsr330-api-java libatk1.0-0 libatk1.0-data libavahi-client3
  libavahi-common-data libavahi-common3 libblas-common libblas3 libbsd0
  libbsh-java libcairo2 libcommons-compress-java libcommons-jexl2-java
  libcommons-logging-java libcommons-parent-java libcroco3 libcups2 libcurl3
  libdatrie1 libdbus-1-3 libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2
  libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1
  libfile-stripnondeterminism-perl libflac8 libfontconfig1 libfreetype6
  libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran3 libgif7
  libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3
  libgtk2.0-0 libgtk2.0-common libguava-java libguava-java-doc libharfbuzz0b
  libhtsjdk-java libhtsjdk-java-doc libice6 libicu57 libjaxp1.3-java libjbig0
  libjbzip2-java libjcommander-java libjpeg-turbo8 libjpeg8 libjson-c2
  libjsr305-java liblapack3 liblcms2-2 libllvm3.8 libmagic1 libmpdec2 libnspr4
  libnss3 libnss3-nssdb libogg0 libpango-1.0-0 libpangocairo-1.0-0
  libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1
  libpipeline1 libpixman-1-0 libpulse0 libpython3-stdlib libpython3.5-minimal
  libpython3.5-stdlib libsigsegv2 libsm6 libsnappy-java libsnappy-jni
  libsnappy1v5 libsndfile1 libstax-java libtcl8.6 libthai-data libthai0
  libtiff5 libtimedate-perl libtk8.6 libtool libunistring0 libvorbis0a
  libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6
  libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0
  libxcb-shm0 libxcb-sync1 libxcb1 libxcomposite1 libxcursor1 libxdamage1
  libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxrandr2
  libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 m4 man-db
  maven-repo-helper mime-support openjdk-8-doc openjdk-8-jdk
  openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless po-debconf
  python3 python3-minimal python3.5 python3.5-minimal r-base-core
  shared-mime-info testng ucf unzip x11-common xdg-utils zip
Suggested packages:
  ant-doc ant-gcj ant-optional-gcj antlr javacc junit jython libbcel-java
  libbsf-java libcommons-net-java libgnumail-java libjdepend-java libjsch-java
  liblog4j1.2-java liboro-java libregexp-java libxalan2-java
  libxml-commons-resolver1.1-java autoconf-archive gnu-standards autoconf-doc
  wamerican | wordlist whois vacation debtags dh-make default-java-plugin
  bsd-mailx | mailx cvs-buildpackage diffoscope devscripts-el dose-extra
  gnuplot libauthen-sasl-perl libfile-desktopentry-perl libnet-smtp-ssl-perl
  libterm-size-perl libyaml-syck-perl mozilla-devscripts mutt ssh-client
  svn-buildpackage w3m debian-keyring equivs liblwp-protocol-https-perl
  libsoap-lite-perl gettext-doc groff cvs gawk tofrodos libasound2-plugins
  alsa-utils libatinject-jsr330-api-java-doc libxz-java
  libcommons-jexl2-java-doc libavalon-framework-java
  libcommons-logging-java-doc libexcalibur-logkit-java cups-common
  librsvg2-common gvfs picard-tools python libjaxp1.3-java-gcj
  libjcommander-java-doc libjsr305-java-doc liblcms2-utils pciutils pcscd
  pulseaudio libstax-java-doc tcl8.6 tk8.6 libtool-doc gfortran
  | fortran95-compiler gcj-jdk less www-browser maven-debian-helper
  openjdk-8-demo openjdk-8-source visualvm icedtea-8-plugin
  openjdk-8-jre-jamvm libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic
  fonts-ipafont-mincho ttf-wqy-microhei | ttf-wqy-zenhei fonts-indic
  libmail-box-perl python3-doc python3-tk python3-venv python3.5-venv
  python3.5-doc binfmt-support ess r-doc-info | r-doc-pdf r-mathlib
  r-base-html gvfs-bin
Recommended packages:
  at dput | dupload libdistro-info-perl libencode-locale-perl liburi-perl
  libwww-perl lintian patchutils python3-debian python3-magic strace wdiff
  wget | curl curl | wget | lynx-cur libasprintf-dev libgettextpo-dev dbus
  libtxc-dxtn-s2tc0 | libtxc-dxtn0 libglib2.0-data xdg-user-dirs
  hicolor-icon-theme libgtk2.0-bin libltdl-dev tcpd xml-core libxt-dev
  libgnome-2-0 libgnomevfs2-0 libgconf-2-4 fonts-dejavu-extra
  libmail-sendmail-perl r-recommended r-base-dev r-doc-html junit4
  libyaml-snake-java libfile-mimeinfo-perl libnet-dbus-perl
  libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  ant ant-optional autoconf automake autopoint autotools-dev bsdmainutils
  ca-certificates-java dctrl-tools debhelper default-jdk default-jdk-doc
  default-jdk-headless default-jre default-jre-headless devscripts
  dh-autoreconf dh-python dh-strip-nondeterminism file fontconfig
  fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
  intltool-debian java-common javahelper libapache-pom-java
  libarchive-zip-perl libasound2 libasound2-data libasprintf0v5 libasyncns0
  libatinject-jsr330-api-java libatk1.0-0 libatk1.0-data libavahi-client3
  libavahi-common-data libavahi-common3 libblas-common libblas3 libbsd0
  libbsh-java libcairo2 libcommons-compress-java libcommons-jexl2-java
  libcommons-logging-java libcommons-parent-java libcroco3 libcups2 libcurl3
  libdatrie1 libdbus-1-3 libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2
  libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1
  libfile-stripnondeterminism-perl libflac8 libfontconfig1 libfreetype6
  libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran3 libgif7
  libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3
  libgtk2.0-0 libgtk2.0-common libguava-java libguava-java-doc libharfbuzz0b
  libhtsjdk-java libhtsjdk-java-doc libice6 libicu57 libjaxp1.3-java libjbig0
  libjbzip2-java libjcommander-java libjpeg-turbo8 libjpeg8 libjson-c2
  libjsr305-java liblapack3 liblcms2-2 libllvm3.8 libmagic1 libmpdec2 libnspr4
  libnss3 libnss3-nssdb libogg0 libpango-1.0-0 libpangocairo-1.0-0
  libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1
  libpipeline1 libpixman-1-0 libpulse0 libpython3-stdlib libpython3.5-minimal
  libpython3.5-stdlib libsigsegv2 libsm6 libsnappy-java libsnappy-jni
  libsnappy1v5 libsndfile1 libstax-java libtcl8.6 libthai-data libthai0
  libtiff5 libtimedate-perl libtk8.6 libtool libunistring0 libvorbis0a
  libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6
  libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0
  libxcb-shm0 libxcb-sync1 libxcb1 libxcomposite1 libxcursor1 libxdamage1
  libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxrandr2
  libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 m4 man-db
  maven-repo-helper mime-support openjdk-8-doc openjdk-8-jdk
  openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless po-debconf
  python3 python3-minimal python3.5 python3.5-minimal r-base-core
  sbuild-build-depends-picard-tools-dummy shared-mime-info testng ucf unzip
  x11-common xdg-utils zip
0 upgraded, 185 newly installed, 0 to remove and 0 not upgraded.
Need to get 130 MB of archives.
After this operation, 818 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
  sbuild-build-depends-picard-tools-dummy
Authentication warning overridden.
Get:1 copy:/«BUILDDIR»/resolver-neO8eM/apt_archive ./ sbuild-build-depends-picard-tools-dummy 0.invalid.0 [1026 B]
Get:2 http://ftpmaster.internal/ubuntu yakkety/main amd64 libjson-c2 amd64 0.11-4ubuntu2 [22.3 kB]
Get:3 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libpython3.5-minimal amd64 3.5.1-11 [522 kB]
Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libexpat1 amd64 2.1.1-1 [70.9 kB]
Get:5 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 python3.5-minimal amd64 3.5.1-11 [1626 kB]
Get:6 http://ftpmaster.internal/ubuntu yakkety/main amd64 python3-minimal amd64 3.5.1-3 [23.3 kB]
Get:7 http://ftpmaster.internal/ubuntu yakkety/main amd64 mime-support all 3.59ubuntu1 [31.0 kB]
Get:8 http://ftpmaster.internal/ubuntu yakkety/main amd64 libmpdec2 amd64 2.4.2-1 [82.6 kB]
Get:9 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libpython3.5-stdlib amd64 3.5.1-11 [2122 kB]
Get:10 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 python3.5 amd64 3.5.1-11 [159 kB]
Get:11 http://ftpmaster.internal/ubuntu yakkety/main amd64 libpython3-stdlib amd64 3.5.1-3 [6818 B]
Get:12 http://ftpmaster.internal/ubuntu yakkety/main amd64 dh-python all 2.20151103ubuntu1 [74.4 kB]
Get:13 http://ftpmaster.internal/ubuntu yakkety/main amd64 python3 amd64 3.5.1-3 [8710 B]
Get:14 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B]
Get:15 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [11.0 kB]
Get:16 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcb1 amd64 1.11.1-1ubuntu1 [40.0 kB]
Get:17 http://ftpmaster.internal/ubuntu yakkety/main amd64 libx11-data all 2:1.6.3-1ubuntu2 [113 kB]
Get:18 http://ftpmaster.internal/ubuntu yakkety/main amd64 libx11-6 amd64 2:1.6.3-1ubuntu2 [571 kB]
Get:19 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB]
Get:20 http://ftpmaster.internal/ubuntu yakkety/main amd64 groff-base amd64 1.22.3-7 [1151 kB]
Get:21 http://ftpmaster.internal/ubuntu yakkety/main amd64 bsdmainutils amd64 9.0.6ubuntu3 [174 kB]
Get:22 http://ftpmaster.internal/ubuntu yakkety/main amd64 libpipeline1 amd64 1.4.1-2 [24.6 kB]
Get:23 http://ftpmaster.internal/ubuntu yakkety/main amd64 man-db amd64 2.7.5-1 [854 kB]
Get:24 http://ftpmaster.internal/ubuntu yakkety/main amd64 fonts-dejavu-core all 2.35-1 [1039 kB]
Get:25 http://ftpmaster.internal/ubuntu yakkety/main amd64 ucf all 3.0036 [52.9 kB]
Get:26 http://ftpmaster.internal/ubuntu yakkety/main amd64 fontconfig-config all 2.11.94-0ubuntu1 [49.9 kB]
Get:27 http://ftpmaster.internal/ubuntu yakkety/main amd64 libfreetype6 amd64 2.6.1-0.1ubuntu3 [316 kB]
Get:28 http://ftpmaster.internal/ubuntu yakkety/main amd64 libfontconfig1 amd64 2.11.94-0ubuntu1 [131 kB]
Get:29 http://ftpmaster.internal/ubuntu yakkety/main amd64 fontconfig amd64 2.11.94-0ubuntu1 [178 kB]
Get:30 http://ftpmaster.internal/ubuntu yakkety/main amd64 libasyncns0 amd64 0.8-5build1 [12.3 kB]
Get:31 http://ftpmaster.internal/ubuntu yakkety/main amd64 x11-common all 1:7.7+13ubuntu3 [22.4 kB]
Get:32 http://ftpmaster.internal/ubuntu yakkety/main amd64 libice6 amd64 2:1.0.9-1 [39.2 kB]
Get:33 http://ftpmaster.internal/ubuntu yakkety/main amd64 libjpeg-turbo8 amd64 1.4.2-0ubuntu3 [111 kB]
Get:34 http://ftpmaster.internal/ubuntu yakkety/main amd64 liblcms2-2 amd64 2.6-3ubuntu2 [137 kB]
Get:35 http://ftpmaster.internal/ubuntu yakkety/main amd64 libogg0 amd64 1.3.2-1 [17.2 kB]
Get:36 http://ftpmaster.internal/ubuntu yakkety/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB]
Get:37 http://ftpmaster.internal/ubuntu yakkety/main amd64 libunistring0 amd64 0.9.3-5.2ubuntu1 [279 kB]
Get:38 http://ftpmaster.internal/ubuntu yakkety/main amd64 libwrap0 amd64 7.6.q-25 [46.2 kB]
Get:39 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcomposite1 amd64 1:0.4.4-1 [7714 B]
Get:40 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxfixes3 amd64 1:5.0.1-2 [11.1 kB]
Get:41 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxrender1 amd64 1:0.9.9-0ubuntu1 [18.5 kB]
Get:42 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcursor1 amd64 1:1.1.14-1 [22.8 kB]
Get:43 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxdamage1 amd64 1:1.1.4-2 [6946 B]
Get:44 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxft2 amd64 2.3.2-1 [36.1 kB]
Get:45 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxinerama1 amd64 2:1.1.3-1 [7908 B]
Get:46 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxshmfence1 amd64 1.2-1 [5042 B]
Get:47 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxss1 amd64 1:1.2.2-1 [8582 B]
Get:48 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxtst6 amd64 2:1.2.2-1 [14.1 kB]
Get:49 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxxf86vm1 amd64 1:1.1.4-1 [10.6 kB]
Get:50 http://ftpmaster.internal/ubuntu yakkety/main amd64 java-common all 0.56ubuntu2 [7742 B]
Get:51 http://ftpmaster.internal/ubuntu yakkety/main amd64 default-jre-headless amd64 2:1.8-56ubuntu2 [4380 B]
Get:52 http://ftpmaster.internal/ubuntu yakkety/main amd64 libnspr4 amd64 2:4.11-1ubuntu1 [112 kB]
Get:53 http://ftpmaster.internal/ubuntu yakkety/main amd64 libnss3-nssdb all 2:3.21-1ubuntu4 [10.6 kB]
Get:54 http://ftpmaster.internal/ubuntu yakkety/main amd64 libnss3 amd64 2:3.21-1ubuntu4 [1129 kB]
Get:55 http://ftpmaster.internal/ubuntu yakkety/main amd64 ca-certificates-java all 20160321 [12.9 kB]
Get:56 http://ftpmaster.internal/ubuntu yakkety/main amd64 libavahi-common-data amd64 0.6.32~rc+dfsg-1ubuntu2 [21.7 kB]
Get:57 http://ftpmaster.internal/ubuntu yakkety/main amd64 libavahi-common3 amd64 0.6.32~rc+dfsg-1ubuntu2 [21.6 kB]
Get:58 http://ftpmaster.internal/ubuntu yakkety/main amd64 libdbus-1-3 amd64 1.10.6-1ubuntu3 [161 kB]
Get:59 http://ftpmaster.internal/ubuntu yakkety/main amd64 libavahi-client3 amd64 0.6.32~rc+dfsg-1ubuntu2 [25.1 kB]
Get:60 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libcups2 amd64 2.1.3-5 [197 kB]
Get:61 http://ftpmaster.internal/ubuntu yakkety/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B]
Get:62 http://ftpmaster.internal/ubuntu yakkety/main amd64 libpcsclite1 amd64 1.8.14-1ubuntu1 [21.4 kB]
Get:63 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxi6 amd64 2:1.7.6-1 [28.6 kB]
Get:64 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 openjdk-8-jre-headless amd64 8u91-b14-2ubuntu1 [26.9 MB]
Get:65 http://ftpmaster.internal/ubuntu yakkety/main amd64 libjbig0 amd64 2.1-3.1 [26.6 kB]
Get:66 http://ftpmaster.internal/ubuntu yakkety/main amd64 libmagic1 amd64 1:5.25-2ubuntu1 [216 kB]
Get:67 http://ftpmaster.internal/ubuntu yakkety/main amd64 file amd64 1:5.25-2ubuntu1 [21.2 kB]
Get:68 http://ftpmaster.internal/ubuntu yakkety/main amd64 libbsd0 amd64 0.8.2-1 [41.7 kB]
Get:69 http://ftpmaster.internal/ubuntu yakkety/main amd64 libasprintf0v5 amd64 0.19.7-2ubuntu3 [6412 B]
Get:70 http://ftpmaster.internal/ubuntu yakkety/main amd64 gettext-base amd64 0.19.7-2ubuntu3 [47.9 kB]
Get:71 http://ftpmaster.internal/ubuntu yakkety/main amd64 libdrm2 amd64 2.4.67-1 [28.3 kB]
Get:72 http://ftpmaster.internal/ubuntu yakkety/main amd64 libedit2 amd64 3.1-20150325-1ubuntu2 [76.5 kB]
Get:73 http://ftpmaster.internal/ubuntu yakkety/main amd64 libelf1 amd64 0.165-3ubuntu1 [42.5 kB]
Get:74 http://ftpmaster.internal/ubuntu yakkety/main amd64 libglib2.0-0 amd64 2.48.0-1ubuntu4 [1117 kB]
Get:75 http://ftpmaster.internal/ubuntu yakkety/main amd64 libicu57 amd64 57.1-1 [7690 kB]
Get:76 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxml2 amd64 2.9.3+dfsg1-1build1 [695 kB]
Get:77 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 shared-mime-info amd64 1.6-1 [405 kB]
Get:78 http://ftpmaster.internal/ubuntu yakkety/universe amd64 ant all 1.9.6-1ubuntu1 [1892 kB]
Get:79 http://ftpmaster.internal/ubuntu yakkety/universe amd64 ant-optional all 1.9.6-1ubuntu1 [313 kB]
Get:80 http://ftpmaster.internal/ubuntu yakkety/main amd64 libsigsegv2 amd64 2.10-5 [14.1 kB]
Get:81 http://ftpmaster.internal/ubuntu yakkety/main amd64 m4 amd64 1.4.17-5 [195 kB]
Get:82 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 autoconf all 2.69-10 [321 kB]
Get:83 http://ftpmaster.internal/ubuntu yakkety/main amd64 autotools-dev all 20150820.1 [39.8 kB]
Get:84 http://ftpmaster.internal/ubuntu yakkety/main amd64 automake all 1:1.15-4ubuntu1 [510 kB]
Get:85 http://ftpmaster.internal/ubuntu yakkety/main amd64 autopoint all 0.19.7-2ubuntu3 [406 kB]
Get:86 http://ftpmaster.internal/ubuntu yakkety/main amd64 dctrl-tools amd64 2.24-2 [59.1 kB]
Get:87 http://ftpmaster.internal/ubuntu yakkety/main amd64 libcroco3 amd64 0.6.11-1 [81.6 kB]
Get:88 http://ftpmaster.internal/ubuntu yakkety/main amd64 gettext amd64 0.19.7-2ubuntu3 [1076 kB]
Get:89 http://ftpmaster.internal/ubuntu yakkety/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB]
Get:90 http://ftpmaster.internal/ubuntu yakkety/main amd64 po-debconf all 1.0.19 [234 kB]
Get:91 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libarchive-zip-perl all 1.57-1 [84.0 kB]
Get:92 http://ftpmaster.internal/ubuntu yakkety/main amd64 libfile-stripnondeterminism-perl all 0.016-1 [11.0 kB]
Get:93 http://ftpmaster.internal/ubuntu yakkety/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB]
Get:94 http://ftpmaster.internal/ubuntu yakkety/main amd64 dh-strip-nondeterminism all 0.016-1 [4858 B]
Get:95 http://ftpmaster.internal/ubuntu yakkety/main amd64 libtool all 2.4.6-0.1 [193 kB]
Get:96 http://ftpmaster.internal/ubuntu yakkety/main amd64 dh-autoreconf all 12 [15.8 kB]
Get:97 http://ftpmaster.internal/ubuntu yakkety/main amd64 debhelper all 9.20160403ubuntu1 [711 kB]
Get:98 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgtk2.0-common all 2.24.30-1ubuntu1 [123 kB]
Get:99 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libatk1.0-data all 2.20.0-1 [17.5 kB]
Get:100 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libatk1.0-0 amd64 2.20.0-1 [57.6 kB]
Get:101 http://ftpmaster.internal/ubuntu yakkety/main amd64 libpixman-1-0 amd64 0.33.6-1 [231 kB]
Get:102 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcb-render0 amd64 1.11.1-1ubuntu1 [11.4 kB]
Get:103 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcb-shm0 amd64 1.11.1-1ubuntu1 [5588 B]
Get:104 http://ftpmaster.internal/ubuntu yakkety/main amd64 libcairo2 amd64 1.14.6-1build1 [555 kB]
Get:105 http://ftpmaster.internal/ubuntu yakkety/main amd64 libtiff5 amd64 4.0.6-1 [144 kB]
Get:106 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgdk-pixbuf2.0-common all 2.34.0-1ubuntu1 [10.3 kB]
Get:107 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgdk-pixbuf2.0-0 amd64 2.34.0-1ubuntu1 [159 kB]
Get:108 http://ftpmaster.internal/ubuntu yakkety/main amd64 libthai-data all 0.1.24-2 [131 kB]
Get:109 http://ftpmaster.internal/ubuntu yakkety/main amd64 libdatrie1 amd64 0.2.10-2 [17.3 kB]
Get:110 http://ftpmaster.internal/ubuntu yakkety/main amd64 libthai0 amd64 0.1.24-2 [17.3 kB]
Get:111 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libpango-1.0-0 amd64 1.40.1-1 [149 kB]
Get:112 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgraphite2-3 amd64 1.3.6-1ubuntu1 [70.8 kB]
Get:113 http://ftpmaster.internal/ubuntu yakkety/main amd64 libharfbuzz0b amd64 1.2.6-2 [180 kB]
Get:114 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libpangoft2-1.0-0 amd64 1.40.1-1 [33.1 kB]
Get:115 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 libpangocairo-1.0-0 amd64 1.40.1-1 [20.6 kB]
Get:116 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxrandr2 amd64 2:1.5.0-1 [17.6 kB]
Get:117 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgtk2.0-0 amd64 2.24.30-1ubuntu1 [1777 kB]
Get:118 http://ftpmaster.internal/ubuntu yakkety/main amd64 libglapi-mesa amd64 11.2.0-1ubuntu2 [22.8 kB]
Get:119 http://ftpmaster.internal/ubuntu yakkety/main amd64 libx11-xcb1 amd64 2:1.6.3-1ubuntu2 [8956 B]
Get:120 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcb-dri2-0 amd64 1.11.1-1ubuntu1 [6882 B]
Get:121 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcb-dri3-0 amd64 1.11.1-1ubuntu1 [5218 B]
Get:122 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcb-glx0 amd64 1.11.1-1ubuntu1 [20.9 kB]
Get:123 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcb-present0 amd64 1.11.1-1ubuntu1 [5218 B]
Get:124 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxcb-sync1 amd64 1.11.1-1ubuntu1 [8324 B]
Get:125 http://ftpmaster.internal/ubuntu yakkety/main amd64 libdrm-amdgpu1 amd64 2.4.67-1 [16.4 kB]
Get:126 http://ftpmaster.internal/ubuntu yakkety/main amd64 libpciaccess0 amd64 0.13.4-1 [18.1 kB]
Get:127 http://ftpmaster.internal/ubuntu yakkety/main amd64 libdrm-intel1 amd64 2.4.67-1 [55.9 kB]
Get:128 http://ftpmaster.internal/ubuntu yakkety/main amd64 libdrm-nouveau2 amd64 2.4.67-1 [16.3 kB]
Get:129 http://ftpmaster.internal/ubuntu yakkety/main amd64 libdrm-radeon1 amd64 2.4.67-1 [21.5 kB]
Get:130 http://ftpmaster.internal/ubuntu yakkety/main amd64 libllvm3.8 amd64 1:3.8-2ubuntu3 [10.3 MB]
Get:131 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgl1-mesa-dri amd64 11.2.0-1ubuntu2 [4655 kB]
Get:132 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgl1-mesa-glx amd64 11.2.0-1ubuntu2 [127 kB]
Get:133 http://ftpmaster.internal/ubuntu yakkety/main amd64 libasound2-data all 1.1.0-0ubuntu1 [29.4 kB]
Get:134 http://ftpmaster.internal/ubuntu yakkety/main amd64 libasound2 amd64 1.1.0-0ubuntu1 [350 kB]
Get:135 http://ftpmaster.internal/ubuntu yakkety/main amd64 libgif7 amd64 5.1.4-0.1 [30.7 kB]
Get:136 http://ftpmaster.internal/ubuntu yakkety/main amd64 libflac8 amd64 1.3.1-4 [210 kB]
Get:137 http://ftpmaster.internal/ubuntu yakkety/main amd64 libvorbis0a amd64 1.3.5-3 [86.8 kB]
Get:138 http://ftpmaster.internal/ubuntu yakkety/main amd64 libvorbisenc2 amd64 1.3.5-3 [70.7 kB]
Get:139 http://ftpmaster.internal/ubuntu yakkety/main amd64 libsndfile1 amd64 1.0.25-10 [137 kB]
Get:140 http://ftpmaster.internal/ubuntu yakkety/main amd64 libpulse0 amd64 1:8.0-0ubuntu3 [247 kB]
Get:141 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 openjdk-8-jre amd64 8u91-b14-2ubuntu1 [69.7 kB]
Get:142 http://ftpmaster.internal/ubuntu yakkety/main amd64 default-jre amd64 2:1.8-56ubuntu2 [980 B]
Get:143 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 openjdk-8-jdk-headless amd64 8u91-b14-2ubuntu1 [8166 kB]
Get:144 http://ftpmaster.internal/ubuntu yakkety/main amd64 default-jdk-headless amd64 2:1.8-56ubuntu2 [986 B]
Get:145 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 openjdk-8-jdk amd64 8u91-b14-2ubuntu1 [429 kB]
Get:146 http://ftpmaster.internal/ubuntu yakkety/main amd64 default-jdk amd64 2:1.8-56ubuntu2 [968 B]
Get:147 http://ftpmaster.internal/ubuntu yakkety-proposed/main amd64 openjdk-8-doc all 8u91-b14-2ubuntu1 [12.1 MB]
Get:148 http://ftpmaster.internal/ubuntu yakkety/main amd64 default-jdk-doc amd64 2:1.8-56ubuntu2 [4346 B]
Get:149 http://ftpmaster.internal/ubuntu yakkety/main amd64 devscripts amd64 2.16.2ubuntu3 [848 kB]
Get:150 http://ftpmaster.internal/ubuntu yakkety/universe amd64 javahelper all 0.54ubuntu1 [77.4 kB]
Get:151 http://ftpmaster.internal/ubuntu yakkety/universe amd64 libapache-pom-java all 10-2build1 [4022 B]
Get:152 http://ftpmaster.internal/ubuntu yakkety/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-2 [22.7 kB]
Get:153 http://ftpmaster.internal/ubuntu yakkety/main amd64 libblas-common amd64 3.6.0-2ubuntu2 [5342 B]
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Get:182 http://ftpmaster.internal/ubuntu yakkety/main amd64 zip amd64 3.0-11 [158 kB]
Get:183 http://ftpmaster.internal/ubuntu yakkety/main amd64 unzip amd64 6.0-20ubuntu1 [158 kB]
Get:184 http://ftpmaster.internal/ubuntu yakkety/main amd64 xdg-utils all 1.1.1-1ubuntu1 [59.9 kB]
Get:185 http://ftpmaster.internal/ubuntu yakkety/universe amd64 r-base-core amd64 3.2.5-1 [20.5 MB]
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Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libtool (2.4.6-0.1) ...
Setting up libgtk2.0-common (2.24.30-1ubuntu1) ...
Setting up libatk1.0-data (2.20.0-1) ...
Setting up libatk1.0-0:amd64 (2.20.0-1) ...
Setting up libpixman-1-0:amd64 (0.33.6-1) ...
Setting up libxcb-render0:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-shm0:amd64 (1.11.1-1ubuntu1) ...
Setting up libcairo2:amd64 (1.14.6-1build1) ...
Setting up libtiff5:amd64 (4.0.6-1) ...
Setting up libgdk-pixbuf2.0-common (2.34.0-1ubuntu1) ...
Setting up libgdk-pixbuf2.0-0:amd64 (2.34.0-1ubuntu1) ...
Setting up libthai-data (0.1.24-2) ...
Setting up libdatrie1:amd64 (0.2.10-2) ...
Setting up libthai0:amd64 (0.1.24-2) ...
Setting up libpango-1.0-0:amd64 (1.40.1-1) ...
Setting up libgraphite2-3:amd64 (1.3.6-1ubuntu1) ...
Setting up libharfbuzz0b:amd64 (1.2.6-2) ...
Setting up libpangoft2-1.0-0:amd64 (1.40.1-1) ...
Setting up libpangocairo-1.0-0:amd64 (1.40.1-1) ...
Setting up libxrandr2:amd64 (2:1.5.0-1) ...
Setting up libgtk2.0-0:amd64 (2.24.30-1ubuntu1) ...
Setting up libglapi-mesa:amd64 (11.2.0-1ubuntu2) ...
Setting up libx11-xcb1:amd64 (2:1.6.3-1ubuntu2) ...
Setting up libxcb-dri2-0:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-dri3-0:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-glx0:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-present0:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-sync1:amd64 (1.11.1-1ubuntu1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.67-1) ...
Setting up libpciaccess0:amd64 (0.13.4-1) ...
Setting up libdrm-intel1:amd64 (2.4.67-1) ...
Setting up libdrm-nouveau2:amd64 (2.4.67-1) ...
Setting up libdrm-radeon1:amd64 (2.4.67-1) ...
Setting up libllvm3.8:amd64 (1:3.8-2ubuntu3) ...
Setting up libgl1-mesa-dri:amd64 (11.2.0-1ubuntu2) ...
Setting up libgl1-mesa-glx:amd64 (11.2.0-1ubuntu2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/mesa/ld.so.conf to provide /etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf (x86_64-linux-gnu_gl_conf) in auto mode
Setting up libasound2-data (1.1.0-0ubuntu1) ...
Setting up libasound2:amd64 (1.1.0-0ubuntu1) ...
Setting up libgif7:amd64 (5.1.4-0.1) ...
Setting up libflac8:amd64 (1.3.1-4) ...
Setting up libvorbis0a:amd64 (1.3.5-3) ...
Setting up libvorbisenc2:amd64 (1.3.5-3) ...
Setting up libsndfile1:amd64 (1.0.25-10) ...
Setting up libpulse0:amd64 (1:8.0-0ubuntu3) ...
Setting up openjdk-8-doc (8u91-b14-2ubuntu1) ...
Setting up default-jdk-doc (2:1.8-56ubuntu2) ...
Setting up libapache-pom-java (10-2build1) ...
Setting up libatinject-jsr330-api-java (1.0+ds1-2) ...
Setting up libblas-common (3.6.0-2ubuntu2) ...
Setting up libblas3 (3.6.0-2ubuntu2) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libbsh-java (2.0b4-17ubuntu1) ...
Setting up libcommons-compress-java (1.10-2) ...
Setting up libcommons-parent-java (39-3) ...
Setting up libcommons-logging-java (1.2-1+build1) ...
Setting up libcommons-jexl2-java (2.1.1-3) ...
Setting up libcurl3:amd64 (7.47.0-1ubuntu2) ...
Setting up libgfortran3:amd64 (6.0.1-2ubuntu13) ...
Setting up libjsr305-java (0.1~+svn49-9) ...
Setting up libguava-java (19.0-1) ...
Setting up libguava-java-doc (19.0-1) ...
Setting up libjbzip2-java (0.9.1-3) ...
Setting up libsnappy1v5:amd64 (1.1.3-3) ...
Setting up libsnappy-jni (1.1.2.1-2) ...
Setting up libsnappy-java (1.1.2.1-2) ...
Setting up libjcommander-java (1.48-1) ...
Setting up testng (6.9.5-1) ...
Setting up libhtsjdk-java (2.1.1+dfsg.1-1) ...
Setting up libhtsjdk-java-doc (2.1.1+dfsg.1-1) ...
Setting up libjaxp1.3-java (1.3.05-2ubuntu3) ...
Setting up liblapack3 (3.6.0-2ubuntu2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libpaper1:amd64 (1.1.24+nmu4ubuntu1) ...

Creating config file /etc/papersize with new version
Setting up libpaper-utils (1.1.24+nmu4ubuntu1) ...
Setting up libstax-java (1.2.0-3build1) ...
Setting up libtcl8.6:amd64 (8.6.5+dfsg-2) ...
Setting up libtk8.6:amd64 (8.6.5-1) ...
Setting up libxt6:amd64 (1:1.1.5-0ubuntu1) ...
Setting up zip (3.0-11) ...
Setting up unzip (6.0-20ubuntu1) ...
Setting up xdg-utils (1.1.1-1ubuntu1) ...
Setting up r-base-core (3.2.5-1) ...

Creating config file /etc/R/Renviron with new version
Setting up dh-python (2.20151103ubuntu1) ...
Setting up python3 (3.5.1-3) ...
Setting up libnss3-nssdb (2:3.21-1ubuntu4) ...
Setting up dh-autoreconf (12) ...
Setting up devscripts (2.16.2ubuntu3) ...
Setting up libnss3:amd64 (2:3.21-1ubuntu4) ...
Setting up openjdk-8-jre-headless:amd64 (8u91-b14-2ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up ca-certificates-java (20160321) ...
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:NetLock_Business_=Class_B=_Root.pem
Adding debian:Sonera_Class_1_Root_CA.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:ComSign_CA.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:GeoTrust_Global_CA_2.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Certigna.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:RSA_Security_2048_v3.pem
Adding debian:StartCom_Certification_Authority_G2.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:EC-ACC.pem
Adding debian:ApplicationCA_-_Japanese_Government.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Certification_Authority_of_WoSign_G2.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem
Adding debian:Juur-SK.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:Camerfirma_Global_Chambersign_Root.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:StartCom_Certification_Authority.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:NetLock_Notary_=Class_A=_Root.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:Swisscom_Root_CA_2.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
Adding debian:Equifax_Secure_Global_eBusiness_CA.pem
Adding debian:NetLock_Express_=Class_C=_Root.pem
Adding debian:WoSign_China.pem
Adding debian:AddTrust_Low-Value_Services_Root.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
Adding debian:Security_Communication_EV_RootCA1.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:TC_TrustCenter_Class_3_CA_II.pem
Adding debian:ACEDICOM_Root.pem
Adding debian:AddTrust_Qualified_Certificates_Root.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:CNNIC_ROOT.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:PSCProcert.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:ACCVRAIZ1.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:Visa_eCommerce_Root.pem
Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem
Adding debian:UTN_USERFirst_Hardware_Root_CA.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:AC_Raíz_Certicámara_S.A..pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:NetLock_Qualified_=Class_QA=_Root.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:DST_ACES_CA_X6.pem
Adding debian:Secure_Global_CA.pem
Adding debian:S-TRUST_Universal_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:CA_Disig_Root_R1.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:Root_CA_Generalitat_Valenciana.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:Comodo_Trusted_Services_root.pem
Adding debian:Certum_Root_CA.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem
Adding debian:IGC_A.pem
Adding debian:SwissSign_Platinum_CA_-_G2.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:StartCom_Certification_Authority_2.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:Certinomis_-_Autorité_Racine.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:CA_WoSign_ECC_Root.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:UTN_USERFirst_Email_Root_CA.pem
Adding debian:EE_Certification_Centre_Root_CA.pem
Adding debian:Comodo_Secure_Services_root.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:Equifax_Secure_eBusiness_CA_1.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem
Adding debian:Equifax_Secure_CA.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem
Adding debian:CA_Disig.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:SecureTrust_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:Swisscom_Root_EV_CA_2.pem
Adding debian:Buypass_Class_2_CA_1.pem
Adding debian:AddTrust_Public_Services_Root.pem
Adding debian:Staat_der_Nederlanden_Root_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:Microsec_e-Szigno_Root_CA.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:Swisscom_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:WoSign.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:QuoVadis_Root_CA.pem
done.
Setting up default-jre-headless (2:1.8-56ubuntu2) ...
Setting up ant (1.9.6-1ubuntu1) ...
Setting up ant-optional (1.9.6-1ubuntu1) ...
Setting up debhelper (9.20160403ubuntu1) ...
Setting up openjdk-8-jre:amd64 (8u91-b14-2ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode
Setting up default-jre (2:1.8-56ubuntu2) ...
Setting up openjdk-8-jdk-headless:amd64 (8u91-b14-2ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
Setting up default-jdk-headless (2:1.8-56ubuntu2) ...
Setting up openjdk-8-jdk:amd64 (8u91-b14-2ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up default-jdk (2:1.8-56ubuntu2) ...
Setting up javahelper (0.54ubuntu1) ...
Setting up maven-repo-helper (1.8.12) ...
Setting up sbuild-build-depends-picard-tools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.23-0ubuntu3) ...
Processing triggers for systemd (229-5ubuntu1) ...
Processing triggers for ca-certificates (20160104ubuntu1) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...

done.
done.

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 3.13.0-85-generic amd64 (x86_64)
Toolchain package versions: binutils_2.26-8ubuntu3 dpkg-dev_1.18.4ubuntu1 g++-5_5.3.1-16ubuntu2 gcc-5_5.3.1-16ubuntu2 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-16ubuntu2 libstdc++6_6.0.1-2ubuntu13 linux-libc-dev_4.4.0-22.38
Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 ant_1.9.6-1ubuntu1 ant-optional_1.9.6-1ubuntu1 apt_1.2.11 apt-transport-https_1.2.11 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.7-2ubuntu3 autotools-dev_20150820.1 base-files_9.6ubuntu1 base-passwd_3.5.39 bash_4.3-14ubuntu2 binutils_2.26-8ubuntu3 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20160104ubuntu1 ca-certificates-java_20160321 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-16ubuntu2 dash_0.5.8-2.1ubuntu2 dctrl-tools_2.24-2 debconf_1.5.58ubuntu1 debhelper_9.20160403ubuntu1 debianutils_4.7 default-jdk_2:1.8-56ubuntu2 default-jdk-doc_2:1.8-56ubuntu2 default-jdk-headless_2:1.8-56ubuntu2 default-jre_2:1.8-56ubuntu2 default-jre-headless_2:1.8-56ubuntu2 devscripts_2.16.2ubuntu3 dh-autoreconf_12 dh-python_2.20151103ubuntu1 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.110-1ubuntu10 dpkg_1.18.4ubuntu1 dpkg-dev_1.18.4ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.6.0+git+20160126-2 fontconfig_2.11.94-0ubuntu1 fontconfig-config_2.11.94-0ubuntu1 fonts-dejavu-core_2.35-1 g++_4:5.3.1-1ubuntu1 g++-5_5.3.1-16ubuntu2 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-16ubuntu2 gcc-5-base_5.3.1-16ubuntu2 gcc-6-base_6.0.1-2ubuntu13 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 hostname_3.17ubuntu1 init_1.31ubuntu1 init-system-helpers_1.31ubuntu1 initscripts_2.88dsf-59.3ubuntu4 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 java-common_0.56ubuntu2 javahelper_0.54ubuntu1 libacl1_2.2.52-3 libapache-pom-java_10-2build1 libapparmor1_2.10.95-0ubuntu2 libapt-pkg5.0_1.2.11 libarchive-zip-perl_1.57-1 libasan2_5.3.1-16ubuntu2 libasn1-8-heimdal_1.7~git20150920+dfsg-4ubuntu1 libasound2_1.1.0-0ubuntu1 libasound2-data_1.1.0-0ubuntu1 libasprintf0v5_0.19.7-2ubuntu3 libasyncns0_0.8-5build1 libatinject-jsr330-api-java_1.0+ds1-2 libatk1.0-0_2.20.0-1 libatk1.0-data_2.20.0-1 libatomic1_6.0.1-2ubuntu13 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu2 libaudit1_1:2.4.5-1ubuntu2 libavahi-client3_0.6.32~rc+dfsg-1ubuntu2 libavahi-common-data_0.6.32~rc+dfsg-1ubuntu2 libavahi-common3_0.6.32~rc+dfsg-1ubuntu2 libblas-common_3.6.0-2ubuntu2 libblas3_3.6.0-2ubuntu2 libblkid1_2.27.1-6ubuntu3 libbsd0_0.8.2-1 libbsh-java_2.0b4-17ubuntu1 libbz2-1.0_1.0.6-8 libc-bin_2.23-0ubuntu3 libc-dev-bin_2.23-0ubuntu3 libc6_2.23-0ubuntu3 libc6-dev_2.23-0ubuntu3 libcairo2_1.14.6-1build1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_6.0.1-2ubuntu13 libcilkrts5_6.0.1-2ubuntu13 libcomerr2_1.42.13-1ubuntu1 libcommons-compress-java_1.10-2 libcommons-jexl2-java_2.1.1-3 libcommons-logging-java_1.2-1+build1 libcommons-parent-java_39-3 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcups2_2.1.3-5 libcurl3_7.47.0-1ubuntu2 libcurl3-gnutls_7.47.0-1ubuntu2 libdatrie1_0.2.10-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu3 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.110-1ubuntu10 libdpkg-perl_1.18.4ubuntu1 libdrm-amdgpu1_2.4.67-1 libdrm-intel1_2.4.67-1 libdrm-nouveau2_2.4.67-1 libdrm-radeon1_2.4.67-1 libdrm2_2.4.67-1 libedit2_3.1-20150325-1ubuntu2 libelf1_0.165-3ubuntu1 libexpat1_2.1.1-1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-6ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libflac8_1.3.1-4 libfontconfig1_2.11.94-0ubuntu1 libfreetype6_2.6.1-0.1ubuntu3 libgcc-5-dev_5.3.1-16ubuntu2 libgcc1_1:6.0.1-2ubuntu13 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libgdk-pixbuf2.0-0_2.34.0-1ubuntu1 libgdk-pixbuf2.0-common_2.34.0-1ubuntu1 libgfortran3_6.0.1-2ubuntu13 libgif7_5.1.4-0.1 libgl1-mesa-dri_11.2.0-1ubuntu2 libgl1-mesa-glx_11.2.0-1ubuntu2 libglapi-mesa_11.2.0-1ubuntu2 libglib2.0-0_2.48.0-1ubuntu4 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.10-4ubuntu1 libgomp1_6.0.1-2ubuntu13 libgpg-error0_1.21-2ubuntu1 libgraphite2-3_1.3.6-1ubuntu1 libgssapi-krb5-2_1.13.2+dfsg-5 libgssapi3-heimdal_1.7~git20150920+dfsg-4ubuntu1 libgtk2.0-0_2.24.30-1ubuntu1 libgtk2.0-common_2.24.30-1ubuntu1 libguava-java_19.0-1 libguava-java-doc_19.0-1 libharfbuzz0b_1.2.6-2 libhcrypto4-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimbase1-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimntlm0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhogweed4_3.2-1 libhtsjdk-java_2.1.1+dfsg.1-1 libhtsjdk-java-doc_2.1.1+dfsg.1-1 libhx509-5-heimdal_1.7~git20150920+dfsg-4ubuntu1 libice6_2:1.0.9-1 libicu57_57.1-1 libidn11_1.32-3ubuntu1 libisl15_0.16.1-1 libitm1_6.0.1-2ubuntu13 libjaxp1.3-java_1.3.05-2ubuntu3 libjbig0_2.1-3.1 libjbzip2-java_0.9.1-3 libjcommander-java_1.48-1 libjpeg-turbo8_1.4.2-0ubuntu3 libjpeg8_8c-2ubuntu8 libjson-c2_0.11-4ubuntu2 libjsr305-java_0.1~+svn49-9 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8ubuntu1 libkmod2_22-1ubuntu4 libkrb5-26-heimdal_1.7~git20150920+dfsg-4ubuntu1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 liblapack3_3.6.0-2ubuntu2 liblcms2-2_2.6-3ubuntu2 libldap-2.4-2_2.4.42+dfsg-2ubuntu3 libllvm3.8_1:3.8-2ubuntu3 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblsan0_6.0.1-2ubuntu13 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-6ubuntu3 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.4-1 libmpx0_5.3.1-16ubuntu2 libncurses5_6.0+20160213-1ubuntu1 libncursesw5_6.0+20160213-1ubuntu1 libnettle6_3.2-1 libnspr4_2:4.11-1ubuntu1 libnss3_2:3.21-1ubuntu4 libnss3-nssdb_2:3.21-1ubuntu4 libogg0_1.3.2-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpango-1.0-0_1.40.1-1 libpangocairo-1.0-0_1.40.1-1 libpangoft2-1.0-0_1.40.1-1 libpaper-utils_1.1.24+nmu4ubuntu1 libpaper1_1.1.24+nmu4ubuntu1 libpciaccess0_0.13.4-1 libpcre3_2:8.38-3.1 libpcsclite1_1.8.14-1ubuntu1 libperl5.22_5.22.1-10 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpng12-0_1.2.54-6ubuntu1 libpng16-16_1.6.21-4 libprocps4_2:3.3.10-4ubuntu2 libpulse0_1:8.0-0ubuntu3 libpython3-stdlib_3.5.1-3 libpython3.5-minimal_3.5.1-11 libpython3.5-stdlib_3.5.1-11 libquadmath0_6.0.1-2ubuntu13 libreadline6_6.3-8ubuntu2 libroken18-heimdal_1.7~git20150920+dfsg-4ubuntu1 librtmp1_2.4+20151223.gitfa8646d-1build1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.2.3-3ubuntu3 libselinux1_2.4-3build2 libsemanage-common_2.4-3build2 libsemanage1_2.4-3build2 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsm6_2:1.2.2-1 libsmartcols1_2.27.1-6ubuntu3 libsnappy-java_1.1.2.1-2 libsnappy-jni_1.1.2.1-2 libsnappy1v5_1.1.3-3 libsndfile1_1.0.25-10 libsqlite3-0_3.11.0-1ubuntu1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2g-1ubuntu4 libstax-java_1.2.0-3build1 libstdc++-5-dev_5.3.1-16ubuntu2 libstdc++6_6.0.1-2ubuntu13 libsystemd0_229-5ubuntu1 libtasn1-6_4.7-3 libtcl8.6_8.6.5+dfsg-2 libthai-data_0.1.24-2 libthai0_0.1.24-2 libtiff5_4.0.6-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1ubuntu1 libtk8.6_8.6.5-1 libtool_2.4.6-0.1 libtsan0_6.0.1-2ubuntu13 libubsan0_6.0.1-2ubuntu13 libudev1_229-5ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6ubuntu3 libvorbis0a_1.3.5-3 libvorbisenc2_1.3.5-3 libwind0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libwrap0_7.6.q-25 libx11-6_2:1.6.3-1ubuntu2 libx11-data_2:1.6.3-1ubuntu2 libx11-xcb1_2:1.6.3-1ubuntu2 libxau6_1:1.0.8-1 libxcb-dri2-0_1.11.1-1ubuntu1 libxcb-dri3-0_1.11.1-1ubuntu1 libxcb-glx0_1.11.1-1ubuntu1 libxcb-present0_1.11.1-1ubuntu1 libxcb-render0_1.11.1-1ubuntu1 libxcb-shm0_1.11.1-1ubuntu1 libxcb-sync1_1.11.1-1ubuntu1 libxcb1_1.11.1-1ubuntu1 libxcomposite1_1:0.4.4-1 libxcursor1_1:1.1.14-1 libxdamage1_1:1.1.4-2 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxfixes3_1:5.0.1-2 libxft2_2.3.2-1 libxi6_2:1.7.6-1 libxinerama1_2:1.1.3-1 libxml2_2.9.3+dfsg1-1build1 libxrandr2_2:1.5.0-1 libxrender1_1:0.9.9-0ubuntu1 libxshmfence1_1.2-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-0ubuntu1 libxtst6_2:1.2.2-1 libxxf86vm1_1:1.1.4-1 linux-libc-dev_4.4.0-22.38 lockfile-progs_0.1.17 login_1:4.2-3.1ubuntu5 lsb-base_9.20160110 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 maven-repo-helper_1.8.12 mawk_1.3.3-17ubuntu2 mime-support_3.59ubuntu1 mount_2.27.1-6ubuntu3 multiarch-support_2.23-0ubuntu3 ncurses-base_6.0+20160213-1ubuntu1 ncurses-bin_6.0+20160213-1ubuntu1 openjdk-8-doc_8u91-b14-2ubuntu1 openjdk-8-jdk_8u91-b14-2ubuntu1 openjdk-8-jdk-headless_8u91-b14-2ubuntu1 openjdk-8-jre_8u91-b14-2ubuntu1 openjdk-8-jre-headless_8u91-b14-2ubuntu1 openssl_1.0.2g-1ubuntu4 optipng_0.7.6-1build1 passwd_1:4.2-3.1ubuntu5 patch_2.7.5-1 perl_5.22.1-10 perl-base_5.22.1-10 perl-modules-5.22_5.22.1-10 pkg-create-dbgsym_0.72 pkgbinarymangler_129 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.10-4ubuntu2 python3_3.5.1-3 python3-minimal_3.5.1-3 python3.5_3.5.1-11 python3.5-minimal_3.5.1-11 r-base-core_3.2.5-1 readline-common_6.3-8ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-picard-tools-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 shared-mime-info_1.6-1 systemd_229-5ubuntu1 systemd-sysv_229-5ubuntu1 sysv-rc_2.88dsf-59.3ubuntu4 sysvinit-utils_2.88dsf-59.3ubuntu4 tar_1.28-2.1 testng_6.9.5-1 tzdata_2016d-2 ubuntu-keyring_2012.05.19 ucf_3.0036 unzip_6.0-20ubuntu1 util-linux_2.27.1-6ubuntu3 x11-common_1:7.7+13ubuntu3 xdg-utils_1.1.1-1ubuntu1 xz-utils_5.1.1alpha+20120614-2ubuntu2 zip_3.0-11 zlib1g_1:1.2.8.dfsg-2ubuntu4

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build                                                                        │
└──────────────────────────────────────────────────────────────────────────────┘


Unpack source
─────────────

gpgv: Signature made Tue Apr  5 08:19:18 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./picard-tools_2.1.1+dfsg-1.dsc
dpkg-source: info: extracting picard-tools in picard-tools-2.1.1+dfsg
dpkg-source: info: unpacking picard-tools_2.1.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking picard-tools_2.1.1+dfsg-1.debian.tar.xz
dpkg-source: info: applying 10-build.xml

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

DEB_BUILD_OPTIONS=parallel=4
HOME=/home/buildd
LANG=C.UTF-8
LOGNAME=buildd
MAIL=/var/mail/buildd
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
PWD=/«BUILDDIR»/picard-tools-2.1.1+dfsg
SHELL=/bin/sh
SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/picard-tools-2.1.1+dfsg' && 'env'
SUDO_GID=2501
SUDO_UID=2001
SUDO_USER=buildd
TERM=unknown
USER=buildd
USERNAME=root

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package picard-tools
dpkg-buildpackage: source version 2.1.1+dfsg-1
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build picard-tools-2.1.1+dfsg
dpkg-buildpackage: host architecture amd64
 fakeroot debian/rules clean
dh  clean --with javahelper
   dh_testdir
   dh_auto_clean
	ant clean
Buildfile: /«BUILDDIR»/picard-tools-2.1.1+dfsg/build.xml

clean-jar-opt:
    [mkdir] Created dir: /«BUILDDIR»/picard-tools-2.1.1+dfsg/.jar_opt

clean-local:

clean:

BUILD SUCCESSFUL
Total time: 0 seconds
   jh_clean
	rm -fr debian/.eclipse-build
	rm -f debian/orbitdeps.debhelper
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -f debian/picard-tools.substvars
	rm -f debian/picard-tools.*.debhelper
	rm -rf debian/picard-tools/
	rm -f debian/libpicard-java.substvars
	rm -f debian/libpicard-java.*.debhelper
	rm -rf debian/libpicard-java/
	rm -f debian/libpicard-java-doc.substvars
	rm -f debian/libpicard-java-doc.*.debhelper
	rm -rf debian/libpicard-java-doc/
	rm -rf debian/.debhelper/
	rm -f debian/*.debhelper.log
	rm -f debian/files
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
	rm -f *-stamp
 debian/rules build
dh  build --with javahelper
   dh_testdir
   dh_update_autotools_config
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
[ -d lib ] || mkdir lib # This empty directory is lost in the packages's Git clone.
dh_auto_configure
make[1]: Leaving directory '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
   jh_linkjars
   debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
dh_auto_build -- \
	-Dant.build.javac.source=1.8 \
	-Dant.build.javac.target=1.8 \
	-Djavac.target=1.8 \
	-Ddebug=true \
	picard-jar javadoc
	ant -Dant.build.javac.source=1.8 -Dant.build.javac.target=1.8 -Djavac.target=1.8 -Ddebug=true picard-jar javadoc
Buildfile: /«BUILDDIR»/picard-tools-2.1.1+dfsg/build.xml

init:

compile-picard:
    [mkdir] Created dir: /«BUILDDIR»/picard-tools-2.1.1+dfsg/classes
    [javac] /«BUILDDIR»/picard-tools-2.1.1+dfsg/build.xml:526: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 337 source files to /«BUILDDIR»/picard-tools-2.1.1+dfsg/classes
    [javac] /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java:35: warning: '_' used as an identifier
    [javac]                 public AtomicInteger make(final Byte _) {
    [javac]                                                      ^
    [javac]   (use of '_' as an identifier might not be supported in releases after Java SE 8)
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-src:

compile-picard-tests:
    [mkdir] Created dir: /«BUILDDIR»/picard-tools-2.1.1+dfsg/testclasses
    [javac] /«BUILDDIR»/picard-tools-2.1.1+dfsg/build.xml:547: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 121 source files to /«BUILDDIR»/picard-tools-2.1.1+dfsg/testclasses
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
     [copy] Copying 2 files to /«BUILDDIR»/picard-tools-2.1.1+dfsg/testclasses

compile-tests:

compile:

clean-jar-opt:
   [delete] Deleting directory /«BUILDDIR»/picard-tools-2.1.1+dfsg/.jar_opt
    [mkdir] Created dir: /«BUILDDIR»/picard-tools-2.1.1+dfsg/.jar_opt

maybe-add-gatk-tools-java:

process-external-jars:

set-htsjdk-version:

picard-jar:
    [mkdir] Created dir: /«BUILDDIR»/picard-tools-2.1.1+dfsg/dist
    [mkdir] Created dir: /«BUILDDIR»/picard-tools-2.1.1+dfsg/dist/tmp
      [jar] Building jar: /«BUILDDIR»/picard-tools-2.1.1+dfsg/dist/picard.jar
   [delete] Deleting directory /«BUILDDIR»/picard-tools-2.1.1+dfsg/dist/tmp

init:

javadoc:
  [javadoc] Generating Javadoc
  [javadoc] Javadoc execution
  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/PicardException.java...
  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/Test.java...
  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/analysis/AdapterUtility.java...
  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/analysis/AlignmentSummaryMetrics.java...
  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/analysis/AlignmentSummaryMetricsCollector.java...
  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/analysis/BaseDistributionByCycleMetrics.java...
  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/analysis/ChimeraUtil.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/RevertSam.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/EstimateLibraryComplexity.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/MarkDuplicates.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/MarkDuplicatesWithMateCigar.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/MarkDuplicatesWithMateCigarIterator.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/AbstractOpticalDuplicateFinderCommandLineProgram.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/DiskBasedReadEndsForMarkDuplicatesMap.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/LibraryIdGenerator.java...
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  [javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/MarkQueue.java...
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  [javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/ExecutorProcessing picard.analysis.AlignmentSummaryMetrics
  [javadoc] Processing picard.analysis.BaseDistributionByCycleMetrics
  [javadoc] Processing picard.analysis.CollectOxoGMetrics.CpcgMetrics
  [javadoc] Processing picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
  [javadoc] Processing picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
  [javadoc] Processing picard.analysis.CollectWgsMetrics.WgsMetrics
  [javadoc] Processing picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
  [javadoc] Processing picard.analysis.CollectWgsMetricsFromSampledSites.SampledWgsMetrics
  [javadoc] Processing picard.analysis.FingerprintingDetailMetrics
  [javadoc] Processing picard.analysis.FingerprintingSummaryMetrics
  [javadoc] Processing picard.analysis.GcBiasDetailMetrics
  [javadoc] Processing picard.analysis.GcBiasSummaryMetrics
  [javadoc] Processing picard.analysis.InsertSizeMetrics
  [javadoc] Processing picard.analysis.JumpingLibraryMetrics
  [javadoc] Processing picard.analysis.RnaSeqMetrics
  [javadoc] Processing picard.analysis.RrbsCpgDetailMetrics
  [javadoc] Processing picard.analysis.RrbsSummaryMetrics
  [javadoc] Processing picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
  [javadoc] Processing picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
  [javadoc] Processing picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
  [javadoc] Processing picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
  [javadoc] Processing picard.analysis.directed.HsMetrics
  [javadoc] Processing picard.analysis.directed.TargetedPcrMetrics
  [javadoc] Processing picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
  [javadoc] Processing picard.illumina.IlluminaBasecallingMetrics
  [javadoc] Processing picard.illumina.IlluminaLaneMetrics
  [javadoc] Processing picard.illumina.IlluminaPhasingMetrics
  [javadoc] Processing picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
  [javadoc] Processing picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
  [javadoc] Processing picard.metrics.GcBiasMetrics
  [javadoc] Processing picard.metrics.MultilevelMetrics
  [javadoc] Processing picard.sam.DuplicationMetrics
  [javadoc] Processing picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
  [javadoc] Processing picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
  [javadoc] Processing picard.vcf.GenotypeConcordanceContingencyMetrics
  [javadoc] Processing picard.vcf.GenotypeConcordanceDetailMetrics
  [javadoc] Processing picard.vcf.GenotypeConcordanceSummaryMetrics
  [javadoc] s.class)]]
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  [javadoc] 1 warning

BUILD SUCCESSFUL
Total time: 21 seconds
make[1]: Leaving directory '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
   jh_build
   debian/rules override_dh_auto_test
make[1]: Entering directory '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
# Tests do not work with locales with a different decimal separator
# (for example ',') 
env LC_ALL=C && \
dh_auto_build -- \
	-Dant.build.javac.source=1.8 \
	-Dant.build.javac.target=1.8 \
	-Djavac.target=1.8 \
	-Ddebug=true \
	test
DEB_HOST_GNU_SYSTEM=linux-gnu
SUDO_GID=2501
DEB_TARGET_GNU_CPU=x86_64
DEB_BUILD_ARCH_BITS=64
MAIL=/var/mail/buildd
DEB_HOST_ARCH_OS=linux
USER=buildd
CXXFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security
DEB_TARGET_MULTIARCH=x86_64-linux-gnu
DEB_BUILD_GNU_TYPE=x86_64-linux-gnu
OBJCFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security
DEB_BUILD_ARCH_CPU=amd64
DH_INTERNAL_OPTIONS=
HOME=/home/buildd
OLDPWD=/
DH_OPTIONS=
LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro
DEB_BUILD_ARCH_ENDIAN=little
DEB_TARGET_ARCH_BITS=64
MAKEFLAGS=w
DEB_BUILD_GNU_SYSTEM=linux-gnu
DEB_BUILD_ARCH_OS=linux
DEB_TARGET_GNU_TYPE=x86_64-linux-gnu
DEB_TARGET_ARCH_CPU=amd64
SUDO_UID=2001
LOGNAME=buildd
DEB_TARGET_ARCH_ENDIAN=little
USERNAME=root
DH_INTERNAL_OVERRIDE=dh_auto_test
DEB_HOST_ARCH=amd64
TERM=unknown
DEB_TARGET_GNU_SYSTEM=linux-gnu
DEB_HOST_GNU_CPU=x86_64
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
ANT_HOME=/usr/share/ant
CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security
DEB_TARGET_ARCH_OS=linux
MAKELEVEL=2
SOURCE_DATE_EPOCH=1459843167
FCFLAGS=-g -O2 -fstack-protector-strong
DEB_HOST_MULTIARCH=x86_64-linux-gnu
DH_VERBOSE=1
OBJCXXFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security
LANG=C.UTF-8
DH_INTERNAL_BUILDFLAGS=1
CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2
SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/picard-tools-2.1.1+dfsg' && 'dpkg-buildpackage' '-us' '-uc' '-mLaunchpad Build Daemon <buildd@lgw01-16.buildd>' '-b' '-rfakeroot'
DEB_BUILD_OPTIONS=parallel=4
SHELL=/bin/sh
DEB_HOST_ARCH_BITS=64
DEB_BUILD_ARCH=amd64
SUDO_USER=buildd
DEB_BUILD_GNU_CPU=x86_64
DEB_HOST_GNU_TYPE=x86_64-linux-gnu
DEB_HOST_ARCH_CPU=amd64
PWD=/«BUILDDIR»/picard-tools-2.1.1+dfsg
JAVA_HOME=
FFLAGS=-g -O2 -fstack-protector-strong
DEB_BUILD_MULTIARCH=x86_64-linux-gnu
GCJFLAGS=-g -O2 -fstack-protector-strong
MFLAGS=-w
DEB_HOST_ARCH_ENDIAN=little
DEB_TARGET_ARCH=amd64
LC_ALL=C
	ant -Dant.build.javac.source=1.8 -Dant.build.javac.target=1.8 -Djavac.target=1.8 -Ddebug=true test
Buildfile: /«BUILDDIR»/picard-tools-2.1.1+dfsg/build.xml

init:

compile-picard:
    [javac] /«BUILDDIR»/picard-tools-2.1.1+dfsg/build.xml:526: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds

compile-src:

compile-picard-tests:
    [javac] /«BUILDDIR»/picard-tools-2.1.1+dfsg/build.xml:547: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds

compile-tests:

compile:

set_excluded_test_groups_unix:

set_excluded_test_groups_non_unix:

set_excluded_test_groups:

test:
   [testng] [TestNG] Running:
   [testng]   picard-tests
   [testng] 
   [testng] [Wed Apr 27 04:29:18 UTC 2016] picard.sam.SortSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias4772326791706556795.bam OUTPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias6341430291923854.bam SORT_ORDER=coordinate    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:18 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:18	SortSam	Finished reading inputs, merging and writing to output now.
   [testng] [Wed Apr 27 04:29:18 UTC 2016] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=78643200
   [testng] [Wed Apr 27 04:29:18 UTC 2016] picard.sam.SortSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias4772326791706556795.bam OUTPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias5302657445652836493.bam SORT_ORDER=coordinate    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:18 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:18	SortSam	Finished reading inputs, merging and writing to output now.
   [testng] [Wed Apr 27 04:29:18 UTC 2016] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=78643200
   [testng] [Wed Apr 27 04:29:18 UTC 2016] picard.sam.SortSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias8404518665331074880.bam OUTPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias3118674105087030414.bam SORT_ORDER=coordinate    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:18 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:18	SortSam	Finished reading inputs, merging and writing to output now.
   [testng] [Wed Apr 27 04:29:18 UTC 2016] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=111149056
   [testng] [Wed Apr 27 04:29:19 UTC 2016] picard.sam.SortSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics8318008126110933495.bam OUTPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics7542775965639816387.bam SORT_ORDER=coordinate    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:19 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:20	SortSam	Finished reading inputs, merging and writing to output now.
   [testng] [Wed Apr 27 04:29:20 UTC 2016] picard.sam.SortSam done. Elapsed time: 0.02 minutes.
   [testng] Runtime.totalMemory()=204996608
   [testng] [Wed Apr 27 04:29:21 UTC 2016] picard.sam.SortSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectWgsMetrics5452173142895248403.bam OUTPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectWgsMetrics9132011334233881654.bam SORT_ORDER=coordinate    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:21 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:22	SortSam	Finished reading inputs, merging and writing to output now.
   [testng] [Wed Apr 27 04:29:22 UTC 2016] picard.sam.SortSam done. Elapsed time: 0.02 minutes.
   [testng] Runtime.totalMemory()=285736960
   [testng] [Wed Apr 27 04:29:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.820186065016189716.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.820186065016189716.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.820186065016189716.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:23 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:23	MarkDuplicates	Start of doWork freeMemory: 304440112; totalMemory: 335020032; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:23	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:23	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:23	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:23	MarkDuplicates	Read 10000 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 259314632; totalMemory: 339738624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	After generateDuplicateIndexes freeMemory: 312712272; totalMemory: 819986432; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	Before output close freeMemory: 707830760; totalMemory: 738197504; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:24	MarkDuplicates	After output close freeMemory: 785949672; totalMemory: 816316416; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
   [testng] Runtime.totalMemory()=816316416
   [testng] [Wed Apr 27 04:29:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4079958302464710254.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4079958302464710254.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4079958302464710254.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:25 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:25	MarkDuplicates	Start of doWork freeMemory: 713219496; totalMemory: 763887616; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:25	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:25	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:25	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:25	MarkDuplicates	Read 50000 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:25	MarkDuplicates	After buildSortedReadEndLists freeMemory: 709538696; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:25	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:26	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:26	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:26	MarkDuplicates	After generateDuplicateIndexes freeMemory: 330655592; totalMemory: 859308032; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:26	MarkDuplicates	Marking 40000 records as duplicates.
   [testng] INFO	2016-04-27 04:29:26	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:26	MarkDuplicates	Before output close freeMemory: 807570112; totalMemory: 859308032; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:26	MarkDuplicates	After output close freeMemory: 723684264; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.368497977187522063.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.368497977187522063.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.368497977187522063.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:27 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Start of doWork freeMemory: 828818240; totalMemory: 854589440; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	After buildSortedReadEndLists freeMemory: 781325248; totalMemory: 856686592; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	After generateDuplicateIndexes freeMemory: 353151184; totalMemory: 856162304; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Before output close freeMemory: 749321104; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	After output close freeMemory: 823770232; totalMemory: 849870848; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=849870848
   [testng] [Wed Apr 27 04:29:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2629951007443142243.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2629951007443142243.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2629951007443142243.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:27 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Start of doWork freeMemory: 749649784; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:27	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:27	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 767827712; totalMemory: 843055104; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 346993528; totalMemory: 849870848; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Before output close freeMemory: 821149160; totalMemory: 847249408; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	After output close freeMemory: 749321936; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7755060194444130424.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7755060194444130424.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7755060194444130424.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:28 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Start of doWork freeMemory: 814135800; totalMemory: 839909376; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:28	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 768216808; totalMemory: 843579392; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 341615536; totalMemory: 844627968; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:29:28	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Before output close freeMemory: 749320240; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	After output close freeMemory: 811710512; totalMemory: 837812224; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=837812224
   [testng] [Wed Apr 27 04:29:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5916942048982753018.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5916942048982753018.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5916942048982753018.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:29 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Start of doWork freeMemory: 749647504; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:29	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 754235136; totalMemory: 829423616; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 335498184; totalMemory: 838336512; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Before output close freeMemory: 810661176; totalMemory: 836763648; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	After output close freeMemory: 749319712; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6958258768127193366.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6958258768127193366.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6958258768127193366.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:29 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Start of doWork freeMemory: 805218952; totalMemory: 830996480; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:29	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 758775240; totalMemory: 834142208; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	After generateDuplicateIndexes freeMemory: 334271360; totalMemory: 837287936; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Before output close freeMemory: 749315712; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	After output close freeMemory: 804890240; totalMemory: 830996480; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=830996480
   [testng] [Wed Apr 27 04:29:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5172193356092681821.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5172193356092681821.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5172193356092681821.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:30 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Start of doWork freeMemory: 749642304; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:30	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	After buildSortedReadEndLists freeMemory: 745347504; totalMemory: 820510720; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	After generateDuplicateIndexes freeMemory: 328183656; totalMemory: 830996480; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	Before output close freeMemory: 805936848; totalMemory: 832045056; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:30	MarkDuplicates	After output close freeMemory: 749313744; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.921071336631839143.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.921071336631839143.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.921071336631839143.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:30 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Start of doWork freeMemory: 799971072; totalMemory: 825753600; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:31	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 753527584; totalMemory: 828899328; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	After generateDuplicateIndexes freeMemory: 330072200; totalMemory: 833093632; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Before output close freeMemory: 749310856; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	After output close freeMemory: 801215600; totalMemory: 827326464; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=827326464
   [testng] [Wed Apr 27 04:29:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.837691038947052734.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.837691038947052734.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.837691038947052734.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:31 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Start of doWork freeMemory: 749638376; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:31	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 741159632; totalMemory: 816316416; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:31	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 324519152; totalMemory: 827326464; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Before output close freeMemory: 802786168; totalMemory: 828899328; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	After output close freeMemory: 749309024; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:32 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:32 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8176472633771926716.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8176472633771926716.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8176472633771926716.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:32 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Start of doWork freeMemory: 797346632; totalMemory: 823132160; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:32	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	After buildSortedReadEndLists freeMemory: 750903152; totalMemory: 826277888; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 329020632; totalMemory: 832045056; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:32	MarkDuplicates	Before output close freeMemory: 749307864; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	After output close freeMemory: 799115224; totalMemory: 825229312; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=825229312
   [testng] [Wed Apr 27 04:29:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3385179709016631864.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3385179709016631864.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3385179709016631864.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:33 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Start of doWork freeMemory: 749635344; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:33	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	After buildSortedReadEndLists freeMemory: 739583584; totalMemory: 814743552; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	After generateDuplicateIndexes freeMemory: 322944040; totalMemory: 825753600; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Before output close freeMemory: 801735504; totalMemory: 827850752; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	After output close freeMemory: 749306936; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3068739269188033332.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3068739269188033332.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3068739269188033332.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:33 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Start of doWork freeMemory: 796294856; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:33	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:33	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749851192; totalMemory: 825229312; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327444304; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Before output close freeMemory: 749304424; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	After output close freeMemory: 798587728; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2715309219295293583.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2715309219295293583.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2715309219295293583.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:34 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Start of doWork freeMemory: 749632048; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:34	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 739056240; totalMemory: 814219264; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:34	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 322416520; totalMemory: 825229312; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Before output close freeMemory: 801208024; totalMemory: 827326464; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	After output close freeMemory: 749303512; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5430390858598486458.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5430390858598486458.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5430390858598486458.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:35 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Start of doWork freeMemory: 795768584; totalMemory: 821559296; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:35	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749325496; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 326918448; totalMemory: 829947904; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Before output close freeMemory: 749303160; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	After output close freeMemory: 798062176; totalMemory: 824180736; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824180736
   [testng] [Wed Apr 27 04:29:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4390423780031964319.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4390423780031964319.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4390423780031964319.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:35 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Start of doWork freeMemory: 749629472; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:35	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738015688; totalMemory: 813170688; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:35	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321900096; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Before output close freeMemory: 801730360; totalMemory: 827850752; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	After output close freeMemory: 749301792; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:36 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:36 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1927694564229032484.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1927694564229032484.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1927694564229032484.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:36 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Start of doWork freeMemory: 796288600; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749320664; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327438232; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	Before output close freeMemory: 749298256; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:36	MarkDuplicates	After output close freeMemory: 798057272; totalMemory: 824180736; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:36 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824180736
   [testng] [Wed Apr 27 04:29:36 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9030054452083496270.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9030054452083496270.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9030054452083496270.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:36 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Start of doWork freeMemory: 749625760; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738525424; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321885944; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Before output close freeMemory: 801725928; totalMemory: 827850752; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	After output close freeMemory: 749297128; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:37 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:37 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2991199333579597992.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2991199333579597992.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2991199333579597992.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:37 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Start of doWork freeMemory: 796286184; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749318256; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327435896; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:37	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Before output close freeMemory: 749295920; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	After output close freeMemory: 798054704; totalMemory: 824180736; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824180736
   [testng] [Wed Apr 27 04:29:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1176614058907218161.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1176614058907218161.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1176614058907218161.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:38 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Start of doWork freeMemory: 749622344; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738522000; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321882448; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Before output close freeMemory: 801722496; totalMemory: 827850752; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	After output close freeMemory: 749293928; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7302583729677074217.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7302583729677074217.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7302583729677074217.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:38 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Start of doWork freeMemory: 796282376; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749314440; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:38	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327432008; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Before output close freeMemory: 749291544; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	After output close freeMemory: 798574848; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1308704745450050720.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1308704745450050720.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1308704745450050720.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Start of doWork freeMemory: 749618328; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738517120; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321877704; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	Before output close freeMemory: 800669240; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:39	MarkDuplicates	After output close freeMemory: 749289248; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4006707889744555563.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4006707889744555563.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4006707889744555563.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Start of doWork freeMemory: 796279320; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749311384; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327428952; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Before output close freeMemory: 749289016; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	After output close freeMemory: 798572320; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:40 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:40 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7239492019211476121.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7239492019211476121.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7239492019211476121.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:40 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Start of doWork freeMemory: 749617384; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:40	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738517280; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:40	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321877560; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Before output close freeMemory: 800669016; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	After output close freeMemory: 749289024; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:41 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:41 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4277067310234823885.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4277067310234823885.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4277067310234823885.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Start of doWork freeMemory: 796278896; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Read 1 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749311520; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327428760; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Before output close freeMemory: 749289192; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	After output close freeMemory: 798572496; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:41 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:41 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2145295504529620149.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2145295504529620149.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2145295504529620149.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Start of doWork freeMemory: 749614960; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738514776; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:41	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321875136; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Before output close freeMemory: 800666704; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	After output close freeMemory: 749286712; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:42 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:42 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3180589149006020940.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3180589149006020940.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3180589149006020940.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:42 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Start of doWork freeMemory: 796274344; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:42	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749306328; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327424048; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Marking 3 records as duplicates.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Before output close freeMemory: 749284232; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	After output close freeMemory: 798567536; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:42 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:42 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5917946139275526600.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5917946139275526600.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5917946139275526600.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:42 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Start of doWork freeMemory: 749613592; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:42	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:42	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738513488; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321873768; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Before output close freeMemory: 800665336; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	After output close freeMemory: 749285344; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:43 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:43 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5938803249009221565.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5938803249009221565.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5938803249009221565.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:43 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Start of doWork freeMemory: 796274952; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749307768; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327424928; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Before output close freeMemory: 749285792; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	After output close freeMemory: 798569096; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:43 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:43 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9064625790499732061.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9064625790499732061.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9064625790499732061.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:43 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Start of doWork freeMemory: 749611888; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:43	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738512296; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321872336; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Before output close freeMemory: 800664584; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	After output close freeMemory: 749278896; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:44 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:44 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8334371966973230056.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8334371966973230056.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8334371966973230056.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Start of doWork freeMemory: 796118064; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749106360; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327223928; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	Before output close freeMemory: 748994480; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:44	MarkDuplicates	After output close freeMemory: 798277784; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:44 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:44 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6317634868608849009.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6317634868608849009.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6317634868608849009.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Start of doWork freeMemory: 749590232; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:45	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Read 18 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738487896; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321850096; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Marking 12 records as duplicates.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Before output close freeMemory: 800641664; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	After output close freeMemory: 749261672; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:45 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:45 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8227119436896783818.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8227119436896783818.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8227119436896783818.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Start of doWork freeMemory: 796258280; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:45	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749290104; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327407984; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:29:45	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Before output close freeMemory: 749268168; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	After output close freeMemory: 798551472; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4391172526841084798.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4391172526841084798.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4391172526841084798.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:46 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Start of doWork freeMemory: 749595408; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:46	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738494832; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321855592; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Before output close freeMemory: 801695648; totalMemory: 827850752; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	After output close freeMemory: 749267080; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8115972034117252558.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8115972034117252558.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8115972034117252558.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:46 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Start of doWork freeMemory: 796252120; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:46	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Read 12 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749283064; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:46	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327401664; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Marking 8 records as duplicates.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Before output close freeMemory: 749261848; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	After output close freeMemory: 798545152; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:47 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:47 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1747877303160634525.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1747877303160634525.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1747877303160634525.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:47 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Start of doWork freeMemory: 749594176; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:47	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738494152; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321854512; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	Before output close freeMemory: 800646496; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:47	MarkDuplicates	After output close freeMemory: 749266440; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:47 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:47 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2332348603382409185.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2332348603382409185.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2332348603382409185.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:47 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Start of doWork freeMemory: 796251920; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:48	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Read 8 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749283344; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327401464; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Before output close freeMemory: 749257040; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	After output close freeMemory: 798540112; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:48 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:48 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4778802107344546377.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4778802107344546377.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4778802107344546377.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Start of doWork freeMemory: 749588504; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:48	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738488640; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321848840; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:29:48	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Before output close freeMemory: 800640648; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	After output close freeMemory: 749260656; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:49 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:49 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8832172568607753741.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8832172568607753741.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8832172568607753741.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Start of doWork freeMemory: 796248176; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:49	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749280240; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327397392; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Before output close freeMemory: 749257488; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	After output close freeMemory: 798540792; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:49 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:49 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5953865439841493095.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5953865439841493095.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5953865439841493095.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Start of doWork freeMemory: 749584960; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:49	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738484616; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:49	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321845136; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Before output close freeMemory: 800636672; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	After output close freeMemory: 749256680; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:50 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:50 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2170710694869911821.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2170710694869911821.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2170710694869911821.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:50 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Start of doWork freeMemory: 796245672; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:50	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749277736; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327395376; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Before output close freeMemory: 749255528; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	After output close freeMemory: 798538832; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:50 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:50 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9037766155608550494.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9037766155608550494.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9037766155608550494.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:50 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Start of doWork freeMemory: 749582800; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:50	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:50	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738482456; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321842976; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Before output close freeMemory: 800634544; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	After output close freeMemory: 749254552; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:51 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:51 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3498203046054469064.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3498203046054469064.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3498203046054469064.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:51 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Start of doWork freeMemory: 796242976; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:51	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749274904; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327392544; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:51	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Before output close freeMemory: 749252928; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	After output close freeMemory: 798536232; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:52 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:52 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5769378234140635147.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5769378234140635147.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5769378234140635147.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:52 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Start of doWork freeMemory: 749580336; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:52	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738479992; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321840512; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Before output close freeMemory: 800632552; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	After output close freeMemory: 749252560; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:52 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:52 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3725081762352947383.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3725081762352947383.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3725081762352947383.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:52 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Start of doWork freeMemory: 796240616; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:52	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749272680; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:52	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327390320; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Before output close freeMemory: 749250384; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	After output close freeMemory: 798533688; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:53 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:53 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1547503714903715889.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1547503714903715889.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1547503714903715889.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:53 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Start of doWork freeMemory: 749578424; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:53	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738478088; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321838608; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Before output close freeMemory: 800630112; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	After output close freeMemory: 749250120; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:53 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:53 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2863590241543882505.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2863590241543882505.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2863590241543882505.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:53 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Start of doWork freeMemory: 796238976; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:53	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749271040; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:53	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327388680; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Before output close freeMemory: 749248776; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	After output close freeMemory: 798531848; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:54 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:54 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.332664797377899173.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.332664797377899173.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.332664797377899173.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:54 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Start of doWork freeMemory: 749576152; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:54	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738475040; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321835560; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Before output close freeMemory: 800627040; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	After output close freeMemory: 749247048; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:54 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:54 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1612124303693655226.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1612124303693655226.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1612124303693655226.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:54 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Start of doWork freeMemory: 796235968; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:54	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749268032; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:54	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327385672; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Before output close freeMemory: 749245792; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	After output close freeMemory: 798528864; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:55 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:55 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6759052904013550056.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6759052904013550056.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6759052904013550056.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Start of doWork freeMemory: 749573360; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:55	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738472936; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321833456; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	Before output close freeMemory: 800624928; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:55	MarkDuplicates	After output close freeMemory: 749244936; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:55 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:55 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6905821330100875312.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6905821330100875312.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6905821330100875312.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Start of doWork freeMemory: 796235080; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:56	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Read 2 records. 2 pairs never matched.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 749267464; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 327384784; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Before output close freeMemory: 749245104; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	After output close freeMemory: 798528408; totalMemory: 824705024; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:56 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=824705024
   [testng] [Wed Apr 27 04:29:56 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5375876690772473106.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5375876690772473106.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5375876690772473106.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:56 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Start of doWork freeMemory: 749572848; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738473280; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 321833320; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:56	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Before output close freeMemory: 800625568; totalMemory: 826802176; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	After output close freeMemory: 749245576; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:57 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:29:57 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.3374440351923123266.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.3374440351923123266.tmp/MarkDuplicates.duplicate_metrics    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:57 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Start of doWork freeMemory: 796237744; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:57	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	After buildSortedReadEndLists freeMemory: 740090112; totalMemory: 824705024; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	After generateDuplicateIndexes freeMemory: 320023120; totalMemory: 823132160; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Before output close freeMemory: 749123304; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	After output close freeMemory: 791591328; totalMemory: 817889280; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:57 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=817889280
   [testng] [Wed Apr 27 04:29:57 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.5071944980729590208.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.5071944980729590208.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:57 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Start of doWork freeMemory: 749552080; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:57	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
   [testng] INFO	2016-04-27 04:29:57	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	After buildSortedReadEndLists freeMemory: 728134552; totalMemory: 812646400; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	After generateDuplicateIndexes freeMemory: 314882248; totalMemory: 817889280; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Before output close freeMemory: 788969760; totalMemory: 815267840; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	After output close freeMemory: 749123872; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:58 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Start of doWork freeMemory: 785739376; totalMemory: 811597824; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	After buildSortedReadEndLists freeMemory: 729095712; totalMemory: 813694976; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	After generateDuplicateIndexes freeMemory: 311648352; totalMemory: 814743552; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	Before output close freeMemory: 749240400; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:58	MarkDuplicates	After output close freeMemory: 784367928; totalMemory: 810549248; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Start of doWork freeMemory: 749563496; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	After buildSortedReadEndLists freeMemory: 720293808; totalMemory: 804782080; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 307565040; totalMemory: 810549248; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Before output close freeMemory: 783841200; totalMemory: 810024960; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	After output close freeMemory: 749238192; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:29:59 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4058752121378458524.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4058752121378458524.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4058752121378458524.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:29:59 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Start of doWork freeMemory: 780474040; totalMemory: 806354944; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:29:59	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Read 2 records. 2 pairs never matched.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	After buildSortedReadEndLists freeMemory: 732980984; totalMemory: 808452096; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 306379712; totalMemory: 809500672; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:29:59	MarkDuplicates	Before output close freeMemory: 749211336; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	After output close freeMemory: 779620272; totalMemory: 805830656; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:00 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=805830656
   [testng] [Wed Apr 27 04:30:00 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1367316928513675396.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1367316928513675396.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1367316928513675396.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:00 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Start of doWork freeMemory: 749534760; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	After buildSortedReadEndLists freeMemory: 724689640; totalMemory: 800063488; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 302283232; totalMemory: 805306368; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Before output close freeMemory: 778566120; totalMemory: 804782080; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	After output close freeMemory: 749206224; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:00 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:30:00 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2929565121694684405.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2929565121694684405.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2929565121694684405.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:00 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Start of doWork freeMemory: 776274016; totalMemory: 802160640; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	After buildSortedReadEndLists freeMemory: 728257504; totalMemory: 803733504; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 302705128; totalMemory: 805830656; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:00	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Before output close freeMemory: 749206464; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	After output close freeMemory: 775945152; totalMemory: 802160640; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=802160640
   [testng] [Wed Apr 27 04:30:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2783386637206490849.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2783386637206490849.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2783386637206490849.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:01 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Start of doWork freeMemory: 749534776; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:01	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	After buildSortedReadEndLists freeMemory: 721544552; totalMemory: 796917760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	After generateDuplicateIndexes freeMemory: 299137584; totalMemory: 802160640; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Before output close freeMemory: 775945312; totalMemory: 802160640; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	After output close freeMemory: 749206624; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:30:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6718845593836790303.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6718845593836790303.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6718845593836790303.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:01 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Start of doWork freeMemory: 774171744; totalMemory: 800063488; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	After buildSortedReadEndLists freeMemory: 726154992; totalMemory: 801636352; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:01	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	After generateDuplicateIndexes freeMemory: 300602856; totalMemory: 803733504; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Before output close freeMemory: 749201160; totalMemory: 775421952; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	After output close freeMemory: 774367216; totalMemory: 800587776; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:02 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=800587776
   [testng] [Wed Apr 27 04:30:02 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2883866998564252344.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2883866998564252344.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2883866998564252344.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Start of doWork freeMemory: 749226128; totalMemory: 780140544; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:02	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Read 10000 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	After buildSortedReadEndLists freeMemory: 704909392; totalMemory: 785907712; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:02	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	After generateDuplicateIndexes freeMemory: 292739448; totalMemory: 800587776; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Before output close freeMemory: 779374928; totalMemory: 810549248; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	After output close freeMemory: 744520240; totalMemory: 775421952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:03 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
   [testng] Runtime.totalMemory()=775421952
   [testng] [Wed Apr 27 04:30:03 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4810167957950145420.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4810167957950145420.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4810167957950145420.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Start of doWork freeMemory: 754923184; totalMemory: 806354944; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:03	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:03	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	Read 50000 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	After buildSortedReadEndLists freeMemory: 750288584; totalMemory: 856162304; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	After generateDuplicateIndexes freeMemory: 330308360; totalMemory: 859832320; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	Marking 40000 records as duplicates.
   [testng] INFO	2016-04-27 04:30:04	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Before output close freeMemory: 806158176; totalMemory: 858783744; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	After output close freeMemory: 764487520; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4154351743781667120.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4154351743781667120.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4154351743781667120.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:05 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Start of doWork freeMemory: 828942240; totalMemory: 855638016; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	After buildSortedReadEndLists freeMemory: 780924888; totalMemory: 857210880; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	After generateDuplicateIndexes freeMemory: 352751360; totalMemory: 856686592; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Before output close freeMemory: 789865496; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	After output close freeMemory: 825789968; totalMemory: 852492288; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=852492288
   [testng] [Wed Apr 27 04:30:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.654324634700968247.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.654324634700968247.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.654324634700968247.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:05 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Start of doWork freeMemory: 790144872; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:05	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:05	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	After buildSortedReadEndLists freeMemory: 773133256; totalMemory: 849346560; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	After generateDuplicateIndexes freeMemory: 349153344; totalMemory: 853016576; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Before output close freeMemory: 823944696; totalMemory: 850919424; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	After output close freeMemory: 790138616; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:06 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:06 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8335626199594074059.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8335626199594074059.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8335626199594074059.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:06 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Start of doWork freeMemory: 820552400; totalMemory: 847249408; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:06	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	After buildSortedReadEndLists freeMemory: 773060336; totalMemory: 849346560; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	After generateDuplicateIndexes freeMemory: 345934776; totalMemory: 849870848; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Before output close freeMemory: 789864888; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	After output close freeMemory: 820546248; totalMemory: 847249408; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:06 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=847249408
   [testng] [Wed Apr 27 04:30:06 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6286132064093064884.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6286132064093064884.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6286132064093064884.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:06 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Start of doWork freeMemory: 790142976; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:06	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:07	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765297824; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	After generateDuplicateIndexes freeMemory: 342890856; totalMemory: 846725120; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Before output close freeMemory: 819748584; totalMemory: 846725120; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	After output close freeMemory: 790136824; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:07 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:07 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10259721504253425.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10259721504253425.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10259721504253425.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Start of doWork freeMemory: 816879800; totalMemory: 843579392; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:07	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	After buildSortedReadEndLists freeMemory: 768863048; totalMemory: 845152256; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	After generateDuplicateIndexes freeMemory: 343310592; totalMemory: 847249408; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	Before output close freeMemory: 789861944; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:07	MarkDuplicates	After output close freeMemory: 816873256; totalMemory: 843579392; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:07 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=843579392
   [testng] [Wed Apr 27 04:30:07 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7050849726288296949.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7050849726288296949.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7050849726288296949.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Start of doWork freeMemory: 790140184; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:08	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	After buildSortedReadEndLists freeMemory: 761634800; totalMemory: 837812224; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	After generateDuplicateIndexes freeMemory: 339752360; totalMemory: 843579392; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Before output close freeMemory: 817648208; totalMemory: 844627968; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	After output close freeMemory: 790133800; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:08 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:08 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3445490308685099499.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3445490308685099499.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3445490308685099499.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:08 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Start of doWork freeMemory: 814781240; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:08	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	After buildSortedReadEndLists freeMemory: 766764568; totalMemory: 843055104; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:08	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	After generateDuplicateIndexes freeMemory: 341212032; totalMemory: 845152256; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Before output close freeMemory: 789860536; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	After output close freeMemory: 816347792; totalMemory: 843055104; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=843055104
   [testng] [Wed Apr 27 04:30:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4367225672787457423.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4367225672787457423.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4367225672787457423.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Start of doWork freeMemory: 790138824; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:09	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	After buildSortedReadEndLists freeMemory: 761099056; totalMemory: 837287936; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	After generateDuplicateIndexes freeMemory: 338692248; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Before output close freeMemory: 816598352; totalMemory: 843579392; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	After output close freeMemory: 790132520; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5490951132618327240.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5490951132618327240.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5490951132618327240.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Start of doWork freeMemory: 813730912; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:09	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765714240; totalMemory: 842006528; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:09	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340685992; totalMemory: 844627968; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Before output close freeMemory: 789858784; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	After output close freeMemory: 814773176; totalMemory: 841482240; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:10 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=841482240
   [testng] [Wed Apr 27 04:30:10 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4892216511964598968.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4892216511964598968.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4892216511964598968.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Start of doWork freeMemory: 790137112; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:10	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	After buildSortedReadEndLists freeMemory: 760572888; totalMemory: 836763648; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	After generateDuplicateIndexes freeMemory: 338166240; totalMemory: 842006528; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Before output close freeMemory: 816072344; totalMemory: 843055104; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	After output close freeMemory: 790130800; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:10 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:10 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8416771810107457343.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8416771810107457343.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8416771810107457343.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Start of doWork freeMemory: 813205952; totalMemory: 839909376; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:10	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:10	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765189360; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340161032; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Before output close freeMemory: 789858112; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	After output close freeMemory: 815296792; totalMemory: 842006528; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:11 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=842006528
   [testng] [Wed Apr 27 04:30:11 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2743559109930140779.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2743559109930140779.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2743559109930140779.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Start of doWork freeMemory: 790136400; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:11	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759534096; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337651496; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Before output close freeMemory: 815547344; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	After output close freeMemory: 790130088; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:11 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:11 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.482150185656533903.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.482150185656533903.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.482150185656533903.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Start of doWork freeMemory: 813204312; totalMemory: 839909376; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:11	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:11	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765188040; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340159552; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Before output close freeMemory: 789856800; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	After output close freeMemory: 815295312; totalMemory: 842006528; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:12 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=842006528
   [testng] [Wed Apr 27 04:30:12 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3357019318519788445.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3357019318519788445.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3357019318519788445.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Start of doWork freeMemory: 790134464; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:12	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759532480; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337649720; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	Before output close freeMemory: 815545936; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:12	MarkDuplicates	After output close freeMemory: 790128312; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:12 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:12 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8959166407178879446.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8959166407178879446.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8959166407178879446.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Start of doWork freeMemory: 813200960; totalMemory: 839909376; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765184128; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340155968; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Before output close freeMemory: 789853016; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	After output close freeMemory: 814242920; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:13 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:13 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4010005840256889953.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4010005840256889953.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4010005840256889953.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:13 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Start of doWork freeMemory: 790131408; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759528864; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337646504; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:13	MarkDuplicates	Before output close freeMemory: 815542320; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	After output close freeMemory: 790125096; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:14 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:14 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4657451138905382856.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4657451138905382856.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4657451138905382856.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:14 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Start of doWork freeMemory: 813723488; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765182368; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340154280; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Before output close freeMemory: 789851328; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	After output close freeMemory: 814241464; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:14 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:14 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5940315781747947518.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5940315781747947518.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5940315781747947518.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:14 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Start of doWork freeMemory: 790129696; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759527160; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:14	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337644728; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Before output close freeMemory: 815540584; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	After output close freeMemory: 790123320; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:15 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:15 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8869925820585235434.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8869925820585235434.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8869925820585235434.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Start of doWork freeMemory: 813720936; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765179816; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340151656; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Before output close freeMemory: 789848704; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	After output close freeMemory: 814238840; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:15 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:15 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7345807268082783712.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7345807268082783712.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7345807268082783712.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Start of doWork freeMemory: 790125920; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759523136; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:15	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337640944; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Before output close freeMemory: 815536816; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	After output close freeMemory: 790119536; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:16 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:16 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.66584819847715174.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.66584819847715174.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.66584819847715174.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:16 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Start of doWork freeMemory: 813719048; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765177928; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340149768; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Before output close freeMemory: 789846856; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	After output close freeMemory: 814236952; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:16 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:16 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.594224191137026681.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.594224191137026681.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.594224191137026681.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:16 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Start of doWork freeMemory: 790126040; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:16	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759523736; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:16	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337641136; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Before output close freeMemory: 815536896; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	After output close freeMemory: 790119640; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:17 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:17 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4321234551387789813.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4321234551387789813.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4321234551387789813.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:17 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Start of doWork freeMemory: 813718816; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:17	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Read 1 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765178256; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340149768; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Before output close freeMemory: 789847096; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	After output close freeMemory: 814236952; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:17 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:17 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6125512355878280884.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6125512355878280884.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6125512355878280884.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:17 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Start of doWork freeMemory: 790123784; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:17	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759521400; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:17	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337638880; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Before output close freeMemory: 815534768; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	After output close freeMemory: 790117472; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:18 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:18 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4132919683452663128.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4132919683452663128.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4132919683452663128.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:18 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Start of doWork freeMemory: 813714528; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:18	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765173328; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340145320; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Marking 3 records as duplicates.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Before output close freeMemory: 789842440; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	After output close freeMemory: 814232504; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:18 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:18 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6994797965774091721.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6994797965774091721.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6994797965774091721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:18 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Start of doWork freeMemory: 790122152; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:18	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759519848; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:18	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337637248; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Before output close freeMemory: 815533136; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	After output close freeMemory: 790115840; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:19 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:19 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4980017438557494432.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4980017438557494432.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4980017438557494432.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:19 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Start of doWork freeMemory: 813715008; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765174640; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340146072; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Before output close freeMemory: 789843648; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	After output close freeMemory: 814233256; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:19 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:19 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2800644853170404397.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2800644853170404397.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2800644853170404397.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:19 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Start of doWork freeMemory: 790120896; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	After buildSortedReadEndLists freeMemory: 760033136; totalMemory: 836239360; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:19	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337626008; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Before output close freeMemory: 815532608; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	After output close freeMemory: 790114856; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:20 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:20 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8586835991403013016.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8586835991403013016.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8586835991403013016.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:20 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Start of doWork freeMemory: 813567576; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 764983008; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340479136; totalMemory: 844627968; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Before output close freeMemory: 789607384; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	After output close freeMemory: 814042136; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:20 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:20 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1897626746791712454.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1897626746791712454.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1897626746791712454.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:20 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Start of doWork freeMemory: 790108776; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:20	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Read 18 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759504232; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:20	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337623552; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Marking 12 records as duplicates.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Before output close freeMemory: 815519440; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	After output close freeMemory: 790101912; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:21 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:21 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2609401283054252540.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2609401283054252540.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2609401283054252540.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:21 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Start of doWork freeMemory: 813708184; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:21	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765166824; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340138976; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Before output close freeMemory: 789836096; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	After output close freeMemory: 814226160; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:21 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:21 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6186327714064593210.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6186327714064593210.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6186327714064593210.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:21 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Start of doWork freeMemory: 790114560; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:21	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759511776; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:21	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337629656; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Before output close freeMemory: 815525504; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	After output close freeMemory: 790108248; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:22 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:22 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6932248845123251942.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6932248845123251942.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6932248845123251942.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:22 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Start of doWork freeMemory: 813701120; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:22	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Read 12 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765158880; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340131752; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Marking 8 records as duplicates.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Before output close freeMemory: 789828872; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	After output close freeMemory: 814218936; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:22 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:22 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6121245471037616429.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6121245471037616429.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6121245471037616429.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:22 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Start of doWork freeMemory: 790112560; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:22	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759510336; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:22	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337627816; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Before output close freeMemory: 815523912; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	After output close freeMemory: 790106408; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1425820499847238645.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1425820499847238645.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1425820499847238645.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:23 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Start of doWork freeMemory: 813701888; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:23	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Read 8 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765160128; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340132520; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Before output close freeMemory: 789829640; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	After output close freeMemory: 814219704; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3833942729541993608.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3833942729541993608.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3833942729541993608.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:23 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Start of doWork freeMemory: 790111872; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:23	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759509160; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:23	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337626480; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Before output close freeMemory: 815522576; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	After output close freeMemory: 790105072; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1987389373293884562.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1987389373293884562.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1987389373293884562.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:24 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Start of doWork freeMemory: 813702440; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:24	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765161320; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340133232; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Before output close freeMemory: 789830312; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	After output close freeMemory: 814220416; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4766963027076637001.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4766963027076637001.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4766963027076637001.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:24 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Start of doWork freeMemory: 790108360; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:24	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759505816; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:24	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337623456; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Before output close freeMemory: 815519344; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	After output close freeMemory: 790102048; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4618177673077570448.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4618177673077570448.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4618177673077570448.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:25 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Start of doWork freeMemory: 813700440; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:25	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765159320; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340131096; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Before output close freeMemory: 789828216; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	After output close freeMemory: 814218280; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5846343352543694711.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5846343352543694711.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5846343352543694711.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:25 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Start of doWork freeMemory: 790106272; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:25	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759503728; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:25	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337621368; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Before output close freeMemory: 815517256; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	After output close freeMemory: 790099960; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3368554334334754184.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3368554334334754184.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3368554334334754184.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:26 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Start of doWork freeMemory: 813697816; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:26	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765156696; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340128608; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Before output close freeMemory: 789825840; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	After output close freeMemory: 814215792; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6581597285098714905.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6581597285098714905.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6581597285098714905.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:26 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Start of doWork freeMemory: 790104024; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:26	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759501480; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:26	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337619120; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Before output close freeMemory: 815515368; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	After output close freeMemory: 790097712; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3415968093451336158.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3415968093451336158.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3415968093451336158.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:27 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Start of doWork freeMemory: 813695656; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:27	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765154536; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340126448; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Before output close freeMemory: 789823928; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	After output close freeMemory: 814213632; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6988325629075432313.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6988325629075432313.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6988325629075432313.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:27 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Start of doWork freeMemory: 790102880; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:27	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759500336; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:27	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337617976; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Before output close freeMemory: 815513832; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	After output close freeMemory: 790096568; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6103593914361520582.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6103593914361520582.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6103593914361520582.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:28 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Start of doWork freeMemory: 813694960; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:28	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765153840; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340125752; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Before output close freeMemory: 789822832; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	After output close freeMemory: 814212936; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8791461932732624462.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8791461932732624462.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8791461932732624462.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:28 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Start of doWork freeMemory: 790100952; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:28	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759498408; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:28	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337616048; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Before output close freeMemory: 815511896; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	After output close freeMemory: 790094640; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8194645183546459025.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8194645183546459025.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8194645183546459025.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:29 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Start of doWork freeMemory: 813693032; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:29	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765151912; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340123824; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Before output close freeMemory: 789820904; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	After output close freeMemory: 814211008; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7179939001777935083.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7179939001777935083.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7179939001777935083.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:29 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Start of doWork freeMemory: 790099192; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:29	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759496648; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:29	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337614288; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Before output close freeMemory: 815510136; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	After output close freeMemory: 790092880; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4061737665189129329.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4061737665189129329.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4061737665189129329.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:30 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Start of doWork freeMemory: 813691960; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:30	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Read 2 records. 2 pairs never matched.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	After buildSortedReadEndLists freeMemory: 765151160; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	After generateDuplicateIndexes freeMemory: 340122752; totalMemory: 844103680; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Before output close freeMemory: 789819936; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	After output close freeMemory: 814209936; totalMemory: 840957952; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=840957952
   [testng] [Wed Apr 27 04:30:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.27396492979496044.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.27396492979496044.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.27396492979496044.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:30 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Start of doWork freeMemory: 790098488; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	After buildSortedReadEndLists freeMemory: 759496696; totalMemory: 835715072; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:30	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	After generateDuplicateIndexes freeMemory: 337613856; totalMemory: 841482240; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Before output close freeMemory: 815510200; totalMemory: 842530816; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	After output close freeMemory: 790092216; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.8461811527460254838.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.8461811527460254838.tmp/MarkDuplicates.duplicate_metrics    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:31 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Start of doWork freeMemory: 813695480; totalMemory: 840433664; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:31	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 731357656; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	After generateDuplicateIndexes freeMemory: 333833992; totalMemory: 837812224; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Before output close freeMemory: 789819800; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	After output close freeMemory: 808444872; totalMemory: 835190784; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=835190784
   [testng] [Wed Apr 27 04:30:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.5256484996932216809.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.5256484996932216809.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:31 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Start of doWork freeMemory: 790101840; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:31	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 747085432; totalMemory: 832569344; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:31	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 312861496; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Before output close freeMemory: 803451512; totalMemory: 830472192; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	After output close freeMemory: 790094528; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:32 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Start of doWork freeMemory: 801649888; totalMemory: 828375040; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	After buildSortedReadEndLists freeMemory: 731373064; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 323362888; totalMemory: 827326464; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Before output close freeMemory: 789839224; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	After output close freeMemory: 799023056; totalMemory: 825753600; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Start of doWork freeMemory: 790114920; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	After buildSortedReadEndLists freeMemory: 738711864; totalMemory: 824180736; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:32	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	After generateDuplicateIndexes freeMemory: 312875896; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Before output close freeMemory: 796129424; totalMemory: 823132160; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	After output close freeMemory: 790108928; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1083952908039855080.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1083952908039855080.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1083952908039855080.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:33 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Start of doWork freeMemory: 795335480; totalMemory: 822083584; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:33	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Read 2 records. 2 pairs never matched.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	After buildSortedReadEndLists freeMemory: 740502272; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	After generateDuplicateIndexes freeMemory: 317046728; totalMemory: 821035008; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Before output close freeMemory: 789812456; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	After output close freeMemory: 794279408; totalMemory: 821035008; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=821035008
   [testng] [Wed Apr 27 04:30:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1684893593821843797.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1684893593821843797.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1684893593821843797.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:33 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Start of doWork freeMemory: 790087800; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	After buildSortedReadEndLists freeMemory: 744167880; totalMemory: 820510720; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:33	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 312848576; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Before output close freeMemory: 791905624; totalMemory: 818937856; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	After output close freeMemory: 792702928; totalMemory: 819462144; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=819462144
   [testng] [Wed Apr 27 04:30:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.757303421763184569.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.757303421763184569.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.757303421763184569.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:34 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Start of doWork freeMemory: 792709704; totalMemory: 819462144; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 740498568; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 314946192; totalMemory: 818937856; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Before output close freeMemory: 791906088; totalMemory: 818937856; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	After output close freeMemory: 791130296; totalMemory: 817889280; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=817889280
   [testng] [Wed Apr 27 04:30:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3986955989884539577.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3986955989884539577.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3986955989884539577.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:34 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Start of doWork freeMemory: 791662000; totalMemory: 818413568; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:34	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 742072784; totalMemory: 818413568; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:34	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 312850072; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Before output close freeMemory: 790858824; totalMemory: 817889280; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	After output close freeMemory: 791131560; totalMemory: 817889280; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=817889280
   [testng] [Wed Apr 27 04:30:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.670775670863961782.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.670775670863961782.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.670775670863961782.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:35 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Start of doWork freeMemory: 791133688; totalMemory: 817889280; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 741543760; totalMemory: 817889280; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 313894472; totalMemory: 817889280; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Before output close freeMemory: 790854240; totalMemory: 817889280; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	After output close freeMemory: 790078808; totalMemory: 816840704; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=816840704
   [testng] [Wed Apr 27 04:30:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.744460459750687505.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.744460459750687505.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.744460459750687505.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:35 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Start of doWork freeMemory: 785587864; totalMemory: 817364992; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:35	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:35	MarkDuplicates	Read 10000 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	After buildSortedReadEndLists freeMemory: 737295960; totalMemory: 819462144; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	After generateDuplicateIndexes freeMemory: 307824512; totalMemory: 816840704; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Before output close freeMemory: 786881968; totalMemory: 818937856; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	After output close freeMemory: 787154576; totalMemory: 818937856; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:36 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=818937856
   [testng] [Wed Apr 27 04:30:36 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9103241541042769171.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9103241541042769171.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9103241541042769171.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:36 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Start of doWork freeMemory: 757819888; totalMemory: 810024960; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:36	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:36	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	Read 50000 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 766038288; totalMemory: 872939520; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	After generateDuplicateIndexes freeMemory: 331902288; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	Marking 40000 records as duplicates.
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:37	MarkDuplicates	Before output close freeMemory: 808834752; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	After output close freeMemory: 818796456; totalMemory: 872415232; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
   [testng] Runtime.totalMemory()=872415232
   [testng] [Wed Apr 27 04:30:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1166585875777435262.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1166585875777435262.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1166585875777435262.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:38 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Start of doWork freeMemory: 834822528; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 793620896; totalMemory: 870842368; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 366495944; totalMemory: 871366656; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Before output close freeMemory: 842407392; totalMemory: 870318080; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	After output close freeMemory: 834815960; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.203562016828181274.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.203562016828181274.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.203562016828181274.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:38 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Start of doWork freeMemory: 841638184; totalMemory: 869269504; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:38	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 792573176; totalMemory: 869793792; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:38	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 363874672; totalMemory: 868745216; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Before output close freeMemory: 834543488; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	After output close freeMemory: 840059008; totalMemory: 867696640; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=867696640
   [testng] [Wed Apr 27 04:30:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8284455884654841736.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8284455884654841736.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8284455884654841736.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Start of doWork freeMemory: 840588384; totalMemory: 868220928; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:39	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 789950200; totalMemory: 867172352; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357581760; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Before output close freeMemory: 839260608; totalMemory: 867172352; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	After output close freeMemory: 834814672; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.315734246936466338.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.315734246936466338.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.315734246936466338.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Start of doWork freeMemory: 839014416; totalMemory: 866648064; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:39	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785229976; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:39	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	After generateDuplicateIndexes freeMemory: 360201568; totalMemory: 865075200; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Before output close freeMemory: 837686112; totalMemory: 865599488; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	After output close freeMemory: 837958768; totalMemory: 865599488; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:40 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=865599488
   [testng] [Wed Apr 27 04:30:40 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7732068585830647842.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7732068585830647842.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7732068585830647842.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:40 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Start of doWork freeMemory: 834815168; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:40	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 787846992; totalMemory: 865075200; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357575944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Before output close freeMemory: 836633152; totalMemory: 864550912; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	After output close freeMemory: 836906008; totalMemory: 864550912; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:40 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=864550912
   [testng] [Wed Apr 27 04:30:40 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1838823879674400354.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1838823879674400354.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1838823879674400354.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:40 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Start of doWork freeMemory: 835862864; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:40	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 786797536; totalMemory: 864026624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:40	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	After generateDuplicateIndexes freeMemory: 359147928; totalMemory: 864026624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Before output close freeMemory: 836107984; totalMemory: 864026624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	After output close freeMemory: 835332264; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:41 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:30:41 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7460982278176549358.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7460982278176549358.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7460982278176549358.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Start of doWork freeMemory: 835862520; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	After buildSortedReadEndLists freeMemory: 786272984; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358623296; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Before output close freeMemory: 835583352; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	After output close freeMemory: 835856208; totalMemory: 863502336; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:41 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=863502336
   [testng] [Wed Apr 27 04:30:41 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2900836752052332197.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2900836752052332197.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2900836752052332197.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Start of doWork freeMemory: 835861640; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785223536; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:41	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358098136; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Before output close freeMemory: 835058192; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	After output close freeMemory: 835331048; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:42 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:30:42 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2327474934689750852.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2327474934689750852.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2327474934689750852.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:42 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Start of doWork freeMemory: 835336480; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:42	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785746944; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358097256; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Before output close freeMemory: 835057312; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	After output close freeMemory: 835330168; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:42 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:30:42 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7268572114094327716.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7268572114094327716.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7268572114094327716.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:42 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Start of doWork freeMemory: 835335640; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:42	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:42	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785745944; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358096416; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Before output close freeMemory: 835056472; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	After output close freeMemory: 835329328; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:43 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:30:43 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8872243491982311857.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8872243491982311857.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8872243491982311857.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:43 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Start of doWork freeMemory: 835335808; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:43	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785222064; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357572296; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Before output close freeMemory: 834532352; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	After output close freeMemory: 835329496; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:43 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:30:43 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8602085690194944314.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8602085690194944314.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8602085690194944314.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:43 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Start of doWork freeMemory: 834810000; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:43	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785220544; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:43	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357570776; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Before output close freeMemory: 834530832; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	After output close freeMemory: 834803688; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:44 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:44 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7336974803557188813.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7336974803557188813.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7336974803557188813.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Start of doWork freeMemory: 834809224; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785220088; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357570160; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Before output close freeMemory: 834530384; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	After output close freeMemory: 834803072; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:44 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:44 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7293907341286399214.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7293907341286399214.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7293907341286399214.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Start of doWork freeMemory: 834808504; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785219368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:44	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357569440; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Before output close freeMemory: 834529864; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	After output close freeMemory: 834802352; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:45 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:45 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4752175115680852847.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4752175115680852847.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4752175115680852847.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Start of doWork freeMemory: 834806136; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785216440; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357566840; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Before output close freeMemory: 834526864; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	After output close freeMemory: 834799752; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:45 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:45 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5388028642790649003.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5388028642790649003.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5388028642790649003.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Start of doWork freeMemory: 834805184; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785215488; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357565960; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:45	MarkDuplicates	Before output close freeMemory: 834525112; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	After output close freeMemory: 834797768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5645963152561426899.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5645963152561426899.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5645963152561426899.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:46 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Start of doWork freeMemory: 834803432; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785213736; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357564208; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Before output close freeMemory: 834524232; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	After output close freeMemory: 834797120; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7749378438613419696.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7749378438613419696.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7749378438613419696.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:46 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Start of doWork freeMemory: 834802600; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785212904; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357563304; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Before output close freeMemory: 834523368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	After output close freeMemory: 834796216; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:46 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6289514469406812839.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6289514469406812839.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6289514469406812839.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:46 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Start of doWork freeMemory: 834801248; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:46	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785211560; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357561960; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Before output close freeMemory: 834521984; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	After output close freeMemory: 834794872; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:47 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:47 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8059899306659659229.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8059899306659659229.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8059899306659659229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:47 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Start of doWork freeMemory: 834799632; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785209696; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357560336; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Before output close freeMemory: 834520416; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	After output close freeMemory: 834793248; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:47 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:47 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8194356205642220128.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8194356205642220128.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8194356205642220128.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:47 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Start of doWork freeMemory: 834799984; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:47	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785210288; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357560128; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Before output close freeMemory: 834520192; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	After output close freeMemory: 834793040; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:48 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:48 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5722973536372504541.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5722973536372504541.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5722973536372504541.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Start of doWork freeMemory: 834792888; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:48	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785203432; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357553664; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Before output close freeMemory: 834513720; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	After output close freeMemory: 834786576; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:48 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:48 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1489999049865325244.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1489999049865325244.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1489999049865325244.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Start of doWork freeMemory: 834792808; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:48	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:48	MarkDuplicates	Read 1 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785203672; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357553744; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Before output close freeMemory: 834514048; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	After output close freeMemory: 834786656; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:49 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:49 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3703647387943016674.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3703647387943016674.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3703647387943016674.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Start of doWork freeMemory: 834790824; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:49	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785201288; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357551600; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Before output close freeMemory: 834511696; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	After output close freeMemory: 834784512; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:49 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:49 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1817576163783194562.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1817576163783194562.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1817576163783194562.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Start of doWork freeMemory: 834788680; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:49	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:50	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785198904; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357549456; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Marking 3 records as duplicates.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Before output close freeMemory: 834509552; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	After output close freeMemory: 834782368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:50 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:50 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.686820182306473148.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.686820182306473148.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.686820182306473148.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:50 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Start of doWork freeMemory: 834787368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:50	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785197912; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357548144; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	Before output close freeMemory: 834508240; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:50	MarkDuplicates	After output close freeMemory: 834781056; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:50 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:50 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1127932821394290026.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1127932821394290026.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1127932821394290026.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:50 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Start of doWork freeMemory: 834787256; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785198312; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357548304; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Before output close freeMemory: 834508856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	After output close freeMemory: 834781216; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:51 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:51 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8478990092384593917.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8478990092384593917.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8478990092384593917.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:51 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Start of doWork freeMemory: 834786104; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785197160; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357547152; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Before output close freeMemory: 834507704; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	After output close freeMemory: 834780064; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:51 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:51 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3019356189685785137.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3019356189685785137.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3019356189685785137.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:51 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Start of doWork freeMemory: 834639824; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:30:51	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785006680; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357357080; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Before output close freeMemory: 834272592; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	After output close freeMemory: 834590096; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:52 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:52 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1098946051360895999.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1098946051360895999.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1098946051360895999.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:52 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Start of doWork freeMemory: 834773984; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:52	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Read 18 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785182296; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:52	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357534448; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Marking 12 records as duplicates.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Before output close freeMemory: 834494544; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	After output close freeMemory: 834767360; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:53 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:53 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7789196873860797085.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7789196873860797085.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7789196873860797085.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:53 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Start of doWork freeMemory: 834780440; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:53	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785190504; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357541216; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Before output close freeMemory: 834501312; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	After output close freeMemory: 834774128; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:53 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:53 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8503854255054139728.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8503854255054139728.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8503854255054139728.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:53 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Start of doWork freeMemory: 834779776; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:53	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785189840; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:53	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357540552; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Before output close freeMemory: 834500608; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	After output close freeMemory: 834773464; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:54 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:54 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7109620362398343636.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7109620362398343636.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7109620362398343636.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:54 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Start of doWork freeMemory: 834774888; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:54	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Read 12 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785184072; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357535504; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Marking 8 records as duplicates.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Before output close freeMemory: 834495600; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	After output close freeMemory: 834768416; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:54 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:54 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1795919861897691817.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1795919861897691817.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1795919861897691817.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:54 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Start of doWork freeMemory: 834779288; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:54	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785189912; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:54	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357540224; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Before output close freeMemory: 834500528; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	After output close freeMemory: 834773136; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:55 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:55 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3333023609595306096.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3333023609595306096.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3333023609595306096.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Start of doWork freeMemory: 834775656; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:55	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Read 8 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785185320; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357536272; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Before output close freeMemory: 834496368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	After output close freeMemory: 834769184; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:55 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:55 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6458414416719086131.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6458414416719086131.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6458414416719086131.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Start of doWork freeMemory: 834778600; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:55	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785189384; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357539536; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:55	MarkDuplicates	Before output close freeMemory: 834499840; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	After output close freeMemory: 834772448; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:56 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:56 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6254285960040715207.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6254285960040715207.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6254285960040715207.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:56 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Start of doWork freeMemory: 834776856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:56	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785187160; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357537632; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Before output close freeMemory: 834497688; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	After output close freeMemory: 834770544; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:56 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:56 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6765278922029491204.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6765278922029491204.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6765278922029491204.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:56 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Start of doWork freeMemory: 834775736; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:56	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785186040; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357536512; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	Before output close freeMemory: 834496608; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:56	MarkDuplicates	After output close freeMemory: 834769424; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:56 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:56 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8958004927338596385.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8958004927338596385.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8958004927338596385.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:56 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Start of doWork freeMemory: 834774856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:57	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785185160; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357535632; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Before output close freeMemory: 834495728; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	After output close freeMemory: 834768544; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:57 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:57 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4498053288817958629.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4498053288817958629.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4498053288817958629.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:57 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Start of doWork freeMemory: 834773784; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:57	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785184096; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357534568; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Before output close freeMemory: 834494664; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	After output close freeMemory: 834767480; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:57 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:57 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8161869006335250350.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8161869006335250350.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8161869006335250350.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:57 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Start of doWork freeMemory: 834772256; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:57	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:57	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785182560; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357533032; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Before output close freeMemory: 834493240; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	After output close freeMemory: 834765944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:58 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:58 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8705772850643748788.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8705772850643748788.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8705772850643748788.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:58 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Start of doWork freeMemory: 834771424; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:58	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785181728; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357532120; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Before output close freeMemory: 834492576; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	After output close freeMemory: 834764800; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:58 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:58 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2149296338054635345.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2149296338054635345.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2149296338054635345.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:58 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Start of doWork freeMemory: 834770032; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:58	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:58	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785180336; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357530808; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Before output close freeMemory: 834491016; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	After output close freeMemory: 834763472; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:59 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:59 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4346404995495461767.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4346404995495461767.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4346404995495461767.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:59 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Start of doWork freeMemory: 834769968; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:59	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785180280; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357530752; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Before output close freeMemory: 834490816; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	After output close freeMemory: 834763664; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:30:59 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:30:59 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1166059608945480975.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1166059608945480975.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1166059608945480975.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:30:59 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Start of doWork freeMemory: 834769096; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:30:59	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785179400; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:30:59	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357529872; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Before output close freeMemory: 834489928; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	After output close freeMemory: 834762784; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:00 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:00 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1527144114644620830.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1527144114644620830.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1527144114644620830.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:00 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Start of doWork freeMemory: 834768216; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:00	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785178520; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357528992; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Before output close freeMemory: 834489048; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	After output close freeMemory: 834761904; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:00 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:00 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1619564004433421577.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1619564004433421577.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1619564004433421577.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:00 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Start of doWork freeMemory: 834767336; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:00	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785177640; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357528112; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:00	MarkDuplicates	Before output close freeMemory: 834488168; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	After output close freeMemory: 834761024; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.477564889867316522.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.477564889867316522.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.477564889867316522.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:01 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Start of doWork freeMemory: 834766464; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:01	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785176768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357527240; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Before output close freeMemory: 834487296; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	After output close freeMemory: 834760152; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6463992272805110841.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6463992272805110841.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6463992272805110841.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:01 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Start of doWork freeMemory: 834766664; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:01	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Read 2 records. 2 pairs never matched.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785177288; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357527440; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Before output close freeMemory: 834487600; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	After output close freeMemory: 834760352; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:01 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8390047363068916396.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8390047363068916396.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8390047363068916396.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:01 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Start of doWork freeMemory: 834766104; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:01	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785177160; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357527152; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Before output close freeMemory: 834487704; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	After output close freeMemory: 834760064; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:02 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:02 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.3816574483792492372.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.3816574483792492372.tmp/MarkDuplicates.duplicate_metrics    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Start of doWork freeMemory: 834770144; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:02	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776025280; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357530096; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Before output close freeMemory: 834487424; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	After output close freeMemory: 834763112; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:02 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:02 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.7315301399561756009.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.7315301399561756009.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Start of doWork freeMemory: 834769744; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:02	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
   [testng] INFO	2016-04-27 04:31:02	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776024616; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357529432; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Before output close freeMemory: 834487960; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	After output close freeMemory: 834761768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:03 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Start of doWork freeMemory: 834783488; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776040992; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357545056; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Before output close freeMemory: 834507152; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	After output close freeMemory: 834778088; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Start of doWork freeMemory: 834781456; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776038368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:03	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357542432; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Before output close freeMemory: 834504504; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	After output close freeMemory: 834775464; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:04 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1106372274980148045.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1106372274980148045.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1106372274980148045.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:04 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Start of doWork freeMemory: 834759176; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:04	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Read 2 records. 2 pairs never matched.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785168848; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357519000; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Before output close freeMemory: 834479032; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	After output close freeMemory: 834751912; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:04 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:04 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2920131973246192195.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2920131973246192195.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2920131973246192195.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:04 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Start of doWork freeMemory: 834754528; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785164592; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:04	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357515304; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Before output close freeMemory: 834475200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	After output close freeMemory: 834748216; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.39104280028850129.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.39104280028850129.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.39104280028850129.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:05 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Start of doWork freeMemory: 834755080; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785165384; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357515856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Before output close freeMemory: 834475752; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	After output close freeMemory: 834748768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9063872153974112012.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9063872153974112012.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9063872153974112012.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:05 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Start of doWork freeMemory: 834755920; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:05	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785166704; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357516856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	Before output close freeMemory: 834477032; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:05	MarkDuplicates	After output close freeMemory: 834749768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:05 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:06 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6336569094988592406.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6336569094988592406.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6336569094988592406.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:06 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Start of doWork freeMemory: 834751696; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785161760; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357512472; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Before output close freeMemory: 834472136; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	After output close freeMemory: 834745048; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:06 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:06 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3669499889425954155.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3669499889425954155.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3669499889425954155.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:06 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Start of doWork freeMemory: 828188384; totalMemory: 860880896; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:06	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Read 10000 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	After buildSortedReadEndLists freeMemory: 770822768; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	After generateDuplicateIndexes freeMemory: 353540120; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:06	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Before output close freeMemory: 831024712; totalMemory: 864026624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	After output close freeMemory: 831297320; totalMemory: 864026624; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:07 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=864026624
   [testng] [Wed Apr 27 04:31:07 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4363705929836130904.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4363705929836130904.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4363705929836130904.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Start of doWork freeMemory: 810684136; totalMemory: 864026624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:07	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Read 50000 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	After buildSortedReadEndLists freeMemory: 756720000; totalMemory: 872415232; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:07	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	After generateDuplicateIndexes freeMemory: 331862232; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Marking 40000 records as duplicates.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Before output close freeMemory: 808833304; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	After output close freeMemory: 819067392; totalMemory: 872415232; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:08 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
   [testng] Runtime.totalMemory()=872415232
   [testng] [Wed Apr 27 04:31:08 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1850488475385080353.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1850488475385080353.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1850488475385080353.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:08 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Start of doWork freeMemory: 834763168; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	After buildSortedReadEndLists freeMemory: 784407792; totalMemory: 870842368; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	After generateDuplicateIndexes freeMemory: 366436504; totalMemory: 871366656; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:08	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Before output close freeMemory: 842347952; totalMemory: 870318080; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	After output close freeMemory: 834756520; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7981832521475281658.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7981832521475281658.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7981832521475281658.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Start of doWork freeMemory: 841578872; totalMemory: 869269504; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:09	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776020184; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	After generateDuplicateIndexes freeMemory: 364339704; totalMemory: 869269504; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Before output close freeMemory: 834484232; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	After output close freeMemory: 839999752; totalMemory: 867696640; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=867696640
   [testng] [Wed Apr 27 04:31:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7466632533073738065.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7466632533073738065.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7466632533073738065.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Start of doWork freeMemory: 834762104; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:09	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	After buildSortedReadEndLists freeMemory: 781261968; totalMemory: 867696640; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357522936; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Before output close freeMemory: 838153208; totalMemory: 866123776; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	After output close freeMemory: 838950152; totalMemory: 866648064; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=866648064
   [testng] [Wed Apr 27 04:31:09 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5860117674731861245.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5860117674731861245.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5860117674731861245.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Start of doWork freeMemory: 837907144; totalMemory: 865599488; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:09	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:10	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	After buildSortedReadEndLists freeMemory: 779688416; totalMemory: 866123776; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	After generateDuplicateIndexes freeMemory: 360143688; totalMemory: 865075200; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Before output close freeMemory: 837628232; totalMemory: 865599488; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	After output close freeMemory: 836852312; totalMemory: 864550912; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:10 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=864550912
   [testng] [Wed Apr 27 04:31:10 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.801891433421458054.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.801891433421458054.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.801891433421458054.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Start of doWork freeMemory: 837381008; totalMemory: 865075200; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:10	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	After buildSortedReadEndLists freeMemory: 778637616; totalMemory: 865075200; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357520240; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	Before output close freeMemory: 836577448; totalMemory: 864550912; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:10	MarkDuplicates	After output close freeMemory: 836850304; totalMemory: 864550912; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:10 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=864550912
   [testng] [Wed Apr 27 04:31:10 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4212983608405007112.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4212983608405007112.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4212983608405007112.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Start of doWork freeMemory: 835807288; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:11	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	After buildSortedReadEndLists freeMemory: 777588168; totalMemory: 864026624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	After generateDuplicateIndexes freeMemory: 359092232; totalMemory: 864026624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Before output close freeMemory: 836052288; totalMemory: 864026624; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	After output close freeMemory: 835276568; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:11 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:11 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6188506861675211026.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6188506861675211026.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6188506861675211026.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Start of doWork freeMemory: 835806792; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:11	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	After buildSortedReadEndLists freeMemory: 777063472; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358567464; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:11	MarkDuplicates	Before output close freeMemory: 835527520; totalMemory: 863502336; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	After output close freeMemory: 835800376; totalMemory: 863502336; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:12 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=863502336
   [testng] [Wed Apr 27 04:31:12 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8950008256362698542.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8950008256362698542.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8950008256362698542.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Start of doWork freeMemory: 834757368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:12	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776538336; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358042328; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Before output close freeMemory: 835002384; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	After output close freeMemory: 835275240; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:12 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:12 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1689822718395452301.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1689822718395452301.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1689822718395452301.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Start of doWork freeMemory: 835280808; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:12	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776537488; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358041480; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:12	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Before output close freeMemory: 835001536; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	After output close freeMemory: 835274392; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:13 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:13 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6802508672887183433.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6802508672887183433.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6802508672887183433.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:13 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Start of doWork freeMemory: 835280000; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:13	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776536536; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358040624; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Before output close freeMemory: 835000680; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	After output close freeMemory: 835273304; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:13 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:13 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5772546475179050365.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5772546475179050365.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5772546475179050365.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:13 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Start of doWork freeMemory: 835280152; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:13	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776536904; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:13	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	After generateDuplicateIndexes freeMemory: 358040824; totalMemory: 862978048; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Before output close freeMemory: 834476592; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	After output close freeMemory: 835273736; totalMemory: 862978048; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:14 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:14 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4089999808315922076.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4089999808315922076.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4089999808315922076.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:14 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Start of doWork freeMemory: 834755016; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:14	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776011768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357515688; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Before output close freeMemory: 834475744; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	After output close freeMemory: 834748368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:14 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:14 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7159524721290914077.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7159524721290914077.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7159524721290914077.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:14 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Start of doWork freeMemory: 834754144; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:14	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776011200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:14	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357514976; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Before output close freeMemory: 834475200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	After output close freeMemory: 834747888; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:15 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:15 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4915209723593769833.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4915209723593769833.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4915209723593769833.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Start of doWork freeMemory: 834753456; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:15	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776010512; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357514288; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Before output close freeMemory: 834474712; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	After output close freeMemory: 834747200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:15 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:15 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4542376995997878232.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4542376995997878232.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4542376995997878232.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Start of doWork freeMemory: 834751312; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:15	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776007856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357511920; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Before output close freeMemory: 834471944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	After output close freeMemory: 834744832; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:16 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:16 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.519880281507982436.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.519880281507982436.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.519880281507982436.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:16 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Start of doWork freeMemory: 834750504; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776007040; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357511176; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Before output close freeMemory: 834471200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	After output close freeMemory: 834744088; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:16 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:16 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6708891692776911490.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6708891692776911490.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6708891692776911490.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:16 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Start of doWork freeMemory: 834749648; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:16	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776006168; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357510304; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Before output close freeMemory: 834470328; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	After output close freeMemory: 834743216; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:17 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:17 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4430218963018779180.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4430218963018779180.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4430218963018779180.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:17 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Start of doWork freeMemory: 834748832; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776005368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357509432; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	Before output close freeMemory: 834469496; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:17	MarkDuplicates	After output close freeMemory: 834742344; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:17 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:17 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8749446211788779723.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8749446211788779723.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8749446211788779723.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:17 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Start of doWork freeMemory: 834747648; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776004184; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357508248; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Before output close freeMemory: 834468272; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	After output close freeMemory: 834741160; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:18 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:18 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2912919491502116593.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2912919491502116593.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2912919491502116593.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:18 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Start of doWork freeMemory: 834746056; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776002376; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357506656; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	Before output close freeMemory: 834466736; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:18	MarkDuplicates	After output close freeMemory: 834739568; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:18 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:19 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.980728140845238548.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.980728140845238548.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.980728140845238548.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:19 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Start of doWork freeMemory: 834746472; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776003008; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357507072; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Before output close freeMemory: 834467136; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	After output close freeMemory: 834739984; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:19 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:19 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2766884486180952284.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2766884486180952284.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2766884486180952284.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:19 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Start of doWork freeMemory: 834746480; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:19	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776003216; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357507136; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:19	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Before output close freeMemory: 834467192; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	After output close freeMemory: 834740048; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:20 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:20 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8781212446665220668.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8781212446665220668.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8781212446665220668.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:20 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Start of doWork freeMemory: 834746416; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:20	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Read 1 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776003472; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357507248; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Before output close freeMemory: 834467552; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	After output close freeMemory: 834740160; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:20 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:20 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.9205275713439322846.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9205275713439322846.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9205275713439322846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:20 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Start of doWork freeMemory: 834744464; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:20	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Read 3 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776001152; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:20	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357505144; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Before output close freeMemory: 834465240; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	After output close freeMemory: 834738056; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:21 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:21 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.9217422238416717736.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9217422238416717736.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9217422238416717736.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:21 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Start of doWork freeMemory: 834742240; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:21	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775998704; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357502912; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Marking 3 records as duplicates.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Before output close freeMemory: 834463008; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	After output close freeMemory: 834735824; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:21 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:21 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3453786587682810087.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3453786587682810087.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3453786587682810087.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:21 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Start of doWork freeMemory: 834743192; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:21	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775999944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:21	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357503864; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Before output close freeMemory: 834463960; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	After output close freeMemory: 834736776; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:22 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:22 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8008315251240263044.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8008315251240263044.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8008315251240263044.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:22 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Start of doWork freeMemory: 834743120; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	After buildSortedReadEndLists freeMemory: 776000360; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357504064; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Before output close freeMemory: 834464616; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	After output close freeMemory: 834736976; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:22 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:22 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.9101653547757029496.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9101653547757029496.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9101653547757029496.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:22 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Start of doWork freeMemory: 834742000; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775999240; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:22	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357502944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Before output close freeMemory: 834463496; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	After output close freeMemory: 834735856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3183508508483225510.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3183508508483225510.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3183508508483225510.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:23 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Start of doWork freeMemory: 834595752; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775808840; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357312904; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Before output close freeMemory: 834228416; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	After output close freeMemory: 834545920; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:23 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6601322539377704907.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6601322539377704907.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6601322539377704907.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:23 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Start of doWork freeMemory: 834729944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:23	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Read 18 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775984648; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:23	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357490296; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Marking 12 records as duplicates.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Before output close freeMemory: 834450392; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	After output close freeMemory: 834723208; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5416151868328570962.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5416151868328570962.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5416151868328570962.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:24 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Start of doWork freeMemory: 834735448; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:24	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775991768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357496120; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Before output close freeMemory: 834456216; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	After output close freeMemory: 834729032; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:24 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.455343856044716560.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.455343856044716560.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.455343856044716560.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:24 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Start of doWork freeMemory: 834734848; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:24	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775991016; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:24	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357495368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Before output close freeMemory: 834455424; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	After output close freeMemory: 834728280; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4822665237859531897.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4822665237859531897.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4822665237859531897.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:25 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Start of doWork freeMemory: 834729832; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:25	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Read 12 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775985336; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357490336; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Marking 8 records as duplicates.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Before output close freeMemory: 834450432; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	After output close freeMemory: 834723248; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:25 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7614736919536773741.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7614736919536773741.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7614736919536773741.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:25 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Start of doWork freeMemory: 834733592; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:25	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:25	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775990432; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357494424; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Before output close freeMemory: 834454728; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	After output close freeMemory: 834727336; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.391787931111001111.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.391787931111001111.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.391787931111001111.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:26 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Start of doWork freeMemory: 834730024; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:26	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Read 8 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775985968; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357490536; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Before output close freeMemory: 834450632; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	After output close freeMemory: 834723448; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:26 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.4867012407918902651.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4867012407918902651.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4867012407918902651.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:26 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Start of doWork freeMemory: 834732992; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:26	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:26	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775989960; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357493808; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Before output close freeMemory: 834454112; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	After output close freeMemory: 834726720; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.90873240937606194.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.90873240937606194.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.90873240937606194.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:27 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Start of doWork freeMemory: 834731312; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:27	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775987848; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357491984; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Before output close freeMemory: 834452040; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	After output close freeMemory: 834724896; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:27 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6982943003297061279.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6982943003297061279.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6982943003297061279.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:27 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Start of doWork freeMemory: 834730200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:27	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:27	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775986720; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357490856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Before output close freeMemory: 834450952; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	After output close freeMemory: 834723768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3919368676993392588.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3919368676993392588.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3919368676993392588.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:28 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Start of doWork freeMemory: 834729336; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:28	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775985872; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357490008; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Before output close freeMemory: 834450104; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	After output close freeMemory: 834722688; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:28 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1933420182789736455.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1933420182789736455.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1933420182789736455.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:28 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Start of doWork freeMemory: 834728296; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:28	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:28	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775984832; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357488968; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Before output close freeMemory: 834449064; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	After output close freeMemory: 834721880; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.2892701389354240625.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2892701389354240625.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2892701389354240625.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:29 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Start of doWork freeMemory: 834726912; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:29	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Read 5 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775983448; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357487584; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	Before output close freeMemory: 834447792; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:29	MarkDuplicates	After output close freeMemory: 834720496; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:29 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8134107451605774724.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8134107451605774724.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8134107451605774724.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:29 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Start of doWork freeMemory: 834726112; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:30	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775982656; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357486792; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Before output close freeMemory: 834447248; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	After output close freeMemory: 834719704; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:30 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.6312782937167272988.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6312782937167272988.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6312782937167272988.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:30 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Start of doWork freeMemory: 834724840; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:30	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775981376; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357485512; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:30	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Before output close freeMemory: 834445968; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	After output close freeMemory: 834718424; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3187565044895145708.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3187565044895145708.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3187565044895145708.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:31 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Start of doWork freeMemory: 834725056; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:31	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775981592; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357485728; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Before output close freeMemory: 834445792; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	After output close freeMemory: 834718640; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:31 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.3471723579834342035.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3471723579834342035.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3471723579834342035.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:31 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Start of doWork freeMemory: 834724208; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:31	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775980744; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:31	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357484880; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Before output close freeMemory: 834444936; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	After output close freeMemory: 834717792; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:32 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:32 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5517192663261988339.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5517192663261988339.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5517192663261988339.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:32 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Start of doWork freeMemory: 834719944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:32	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775976480; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357480616; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Before output close freeMemory: 834440672; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	After output close freeMemory: 834713528; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:32 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:32 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7350288372886633955.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7350288372886633955.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7350288372886633955.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:32 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Start of doWork freeMemory: 834719096; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:32	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775975632; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:32	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357479768; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Before output close freeMemory: 834439824; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	After output close freeMemory: 834712680; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.7063137980887200068.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7063137980887200068.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7063137980887200068.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:33 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Start of doWork freeMemory: 834718248; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:33	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775974784; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357478920; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Before output close freeMemory: 834438976; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	After output close freeMemory: 834711832; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:33 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.8448345978669940411.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8448345978669940411.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8448345978669940411.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:33 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Start of doWork freeMemory: 834718488; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:33	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Read 2 records. 2 pairs never matched.
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775975312; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:33	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357479160; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Before output close freeMemory: 834439320; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	After output close freeMemory: 834711840; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.1202585087558216272.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1202585087558216272.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1202585087558216272.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:34 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Start of doWork freeMemory: 834717960; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Read 0 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775975200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357478904; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Before output close freeMemory: 834439456; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	After output close freeMemory: 834711816; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:34 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.7536272435901481262.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.7536272435901481262.tmp/MarkDuplicates.duplicate_metrics    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:34 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Start of doWork freeMemory: 834721336; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:34	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
   [testng] INFO	2016-04-27 04:31:34	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775976368; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357481184; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Before output close freeMemory: 834438512; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	After output close freeMemory: 834714200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.8552930350464270349.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.8552930350464270349.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:35 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Start of doWork freeMemory: 834720832; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:35	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name '1AAXX.1.1'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775975784; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357480600; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	Before output close freeMemory: 834438064; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:35	MarkDuplicates	After output close freeMemory: 834712568; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:35 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Start of doWork freeMemory: 834733592; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775991040; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357495104; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Before output close freeMemory: 834457200; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	After output close freeMemory: 834728136; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Start of doWork freeMemory: 834732896; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775989808; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357493872; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:36	MarkDuplicates	Before output close freeMemory: 834455944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	After output close freeMemory: 834726904; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:37 UTC 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/MarkDuplicatesTester.5237663308504327005.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5237663308504327005.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5237663308504327005.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:37 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Start of doWork freeMemory: 834711312; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Will retain up to 7342048 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:37	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Read 2 records. 2 pairs never matched.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 775967288; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357471136; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Before output close freeMemory: 834431168; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	After output close freeMemory: 834704048; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:37 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:37 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesTester.1975317732350899842.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1975317732350899842.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1975317732350899842.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:37 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Start of doWork freeMemory: 834706640; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785116600; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:37	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357467312; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Before output close freeMemory: 834427208; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	After output close freeMemory: 834700224; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesTester.4436286806818296.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4436286806818296.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4436286806818296.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:38 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Start of doWork freeMemory: 834707272; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Read 4 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785117472; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357467944; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Before output close freeMemory: 834427840; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	After output close freeMemory: 834700856; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:38 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC INPUT=[/tmp/MarkDuplicatesTester.1817364815332477302.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1817364815332477302.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1817364815332477302.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:38 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Start of doWork freeMemory: 834708120; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] WARNING	2016-04-27 04:31:38	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Read 2 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785118784; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:38	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357468936; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Before output close freeMemory: 834429112; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	After output close freeMemory: 834701848; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX INPUT=[/tmp/MarkDuplicatesTester.3713426038936366431.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3713426038936366431.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3713426038936366431.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Start of doWork freeMemory: 834703912; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Reading input file and constructing read end information.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Will retain up to 6197833 data points before spilling to disk.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Read 6 records. 0 pairs never matched.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 785113880; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Sorting list of duplicate records.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	After generateDuplicateIndexes freeMemory: 357464592; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	Before output close freeMemory: 834424360; totalMemory: 862453760; maxMemory: 1908932608
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicates	After output close freeMemory: 834697504; totalMemory: 862453760; maxMemory: 1908932608
   [testng] [Wed Apr 27 04:31:39 UTC 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:39 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4690583887850787308.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4690583887850787308.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4690583887850787308.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:39	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:39	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicatesWithMateCigar	Processed 10000 records
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:39	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:39 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862453760
   [testng] [Wed Apr 27 04:31:40 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8657178026812632534.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8657178026812632534.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8657178026812632534.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:40 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:40	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:40	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 50000 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 40000 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=853016576
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4931655880560837438.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4931655880560837438.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4931655880560837438.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: RUNID:6:101:17616:6888 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6704018060608694090.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6704018060608694090.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6704018060608694090.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7203773243594190416.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7203773243594190416.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7203773243594190416.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 3 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3725872078195843659.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3725872078195843659.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3725872078195843659.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 3 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6416736608081137346.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6416736608081137346.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6416736608081137346.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8861405937824417263.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8861405937824417263.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8861405937824417263.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2553829883235430286.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2553829883235430286.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2553829883235430286.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b unmapped read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3224934008991477525.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3224934008991477525.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3224934008991477525.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.879640536038493172.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.879640536038493172.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.879640536038493172.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4060982309195845358.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4060982309195845358.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4060982309195845358.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3912875949473516790.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3912875949473516790.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3912875949473516790.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6354535062928553048.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6354535062928553048.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6354535062928553048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9159310877002230321.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9159310877002230321.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9159310877002230321.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.80600961127135625.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.80600961127135625.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.80600961127135625.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1967871119155075359.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1967871119155075359.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1967871119155075359.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6280548734659395334.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6280548734659395334.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6280548734659395334.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16834 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5034237275221970406.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5034237275221970406.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5034237275221970406.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8039861781217619301.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8039861781217619301.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8039861781217619301.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.495939920043130644.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.495939920043130644.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.495939920043130644.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2229990508800814658.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2229990508800814658.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2229990508800814658.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0:1:1:1:1 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 6 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8678625993953143267.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8678625993953143267.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8678625993953143267.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: RUNID:3:1:15013:113051 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8981687345873008043.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8981687345873008043.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8981687345873008043.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.344292566750765726.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.344292566750765726.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.344292566750765726.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 1 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2025784986468594422.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2025784986468594422.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2025784986468594422.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 3 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1034980667642173402.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1034980667642173402.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1034980667642173402.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 3 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4163548992259070227.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4163548992259070227.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4163548992259070227.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6452877136159621039.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6452877136159621039.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6452877136159621039.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 1 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3214207537428363003.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3214207537428363003.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3214207537428363003.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4157014043353221583.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4157014043353221583.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4157014043353221583.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4384207349204087301.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4384207349204087301.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4384207349204087301.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 18 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 12 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5732158611273178184.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5732158611273178184.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5732158611273178184.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 6 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2739820056510523631.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2739820056510523631.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2739820056510523631.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 6 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6826314151322455333.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6826314151322455333.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6826314151322455333.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 12 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 8 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7938964379726689754.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7938964379726689754.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7938964379726689754.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7924821334264947961.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7924821334264947961.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7924821334264947961.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 8 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 4 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8397774254184165838.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8397774254184165838.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8397774254184165838.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3866020345650812522.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3866020345650812522.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3866020345650812522.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3506341593975545193.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3506341593975545193.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3506341593975545193.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.436390875362917501.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.436390875362917501.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.436390875362917501.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6323275131515818714.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6323275131515818714.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6323275131515818714.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8515379891444282405.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8515379891444282405.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8515379891444282405.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8437119571544503214.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8437119571544503214.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8437119571544503214.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3556609540095829167.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3556609540095829167.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3556609540095829167.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 6 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4008010087171971802.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4008010087171971802.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4008010087171971802.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8490392459707609750.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8490392459707609750.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8490392459707609750.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2367102292866949536.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2367102292866949536.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2367102292866949536.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3973524817693800146.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3973524817693800146.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3973524817693800146.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2092325306206969731.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2092325306206969731.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2092325306206969731.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=862978048
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1950869518232118988.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1950869518232118988.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1950869518232118988.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 2 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3279108681222365808.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3279108681222365808.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3279108681222365808.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2993803612412863351.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2993803612412863351.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2993803612412863351.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READX. Cause: String 'READX' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READX 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5129766370087722400.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5129766370087722400.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5129766370087722400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2254054295701988846.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2254054295701988846.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2254054295701988846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] record #1: READ1	0	chr1	2000	255	10S100M	*	0	0	GACAGGCTAGTTGCAGGAGACGGCGTACTTGCTCAGATGTTTACCGGACT	++++++++++++++++++++++++++++++++++++++++++++++++++	RG:Z:1
   [testng] record #2: READ2	0	chr1	3000	255	2000S100M	*	0	0	TTCTAAGGTTATCCAAGATGTTCAAGCCGCGGCATGAGGTCATAGAGATT	++++++++++++++++++++++++++++++++++++++++++++++++++	RG:Z:1
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=989 BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.991501226576020430.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.991501226576020430.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.991501226576020430.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] record #1: READ1	0	chr1	2000	255	10S100M	*	0	0	GATTGACAACCAATGGTTCCTTGTTTAAGGGAGAAGCCGCAATAGTTCAC	++++++++++++++++++++++++++++++++++++++++++++++++++	RG:Z:1
   [testng] record #2: READ2	0	chr1	3000	255	2000S100M	*	0	0	ATAAAAGCTACACAAGGCACTTGACAGCTGAGCGCCGCGATGAATGGGGT	++++++++++++++++++++++++++++++++++++++++++++++++++	RG:Z:1
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=990 BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6468554466404161815.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6468554466404161815.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6468554466404161815.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 3 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1720515153756251202.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1720515153756251202.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1720515153756251202.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:41	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] WARNING	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 records with no mate cigar optional tag.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] INFO	2016-04-27 04:31:41	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] [Wed Apr 27 04:31:41 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8377873002839523245.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8377873002839523245.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8377873002839523245.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:41 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:42	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:42	MarkDuplicatesWithMateCigar	Processed 10000 records
   [testng] INFO	2016-04-27 04:31:42	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:42 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=902299648
   [testng] [Wed Apr 27 04:31:42 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6570156157592115170.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6570156157592115170.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6570156157592115170.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:42 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 50000 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 40000 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5589635480294834113.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5589635480294834113.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5589635480294834113.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2765505724903118713.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2765505724903118713.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2765505724903118713.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.471142391647634113.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.471142391647634113.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.471142391647634113.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 3 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8830050386250607689.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8830050386250607689.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8830050386250607689.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 3 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5390984851280339865.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5390984851280339865.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5390984851280339865.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7322626536314480533.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7322626536314480533.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7322626536314480533.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4720041471863213983.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4720041471863213983.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4720041471863213983.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5502547335155355004.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5502547335155355004.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5502547335155355004.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6908109458314875396.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6908109458314875396.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6908109458314875396.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1374936458087096749.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1374936458087096749.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1374936458087096749.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6559061879447614346.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6559061879447614346.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6559061879447614346.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2889974087035962345.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2889974087035962345.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2889974087035962345.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7673293193962296332.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7673293193962296332.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7673293193962296332.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3860084405876332061.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3860084405876332061.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3860084405876332061.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4935157472181776329.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4935157472181776329.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4935157472181776329.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.771229220530805129.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.771229220530805129.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.771229220530805129.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.773279434419950630.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.773279434419950630.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.773279434419950630.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4304508747788955260.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4304508747788955260.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4304508747788955260.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4619141190260836687.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4619141190260836687.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4619141190260836687.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5910658074979064309.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5910658074979064309.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5910658074979064309.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 6 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 4 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7647552591978139978.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7647552591978139978.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7647552591978139978.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5452039551784387790.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5452039551784387790.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5452039551784387790.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1621097493958338041.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1621097493958338041.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1621097493958338041.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 1 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4464975701801946673.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4464975701801946673.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4464975701801946673.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 3 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2887012838213043241.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2887012838213043241.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2887012838213043241.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 3 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3083409711298483612.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3083409711298483612.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3083409711298483612.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4438862215658826593.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4438862215658826593.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4438862215658826593.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 1 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1510002769713356735.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1510002769713356735.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1510002769713356735.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7264958929281706856.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7264958929281706856.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7264958929281706856.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 1 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5500064427593564098.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5500064427593564098.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5500064427593564098.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 18 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 12 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.591717346366779488.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.591717346366779488.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.591717346366779488.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 6 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 4 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1902259135515884397.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1902259135515884397.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1902259135515884397.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 6 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5007202118679792657.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5007202118679792657.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5007202118679792657.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 12 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 8 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.837898237054434140.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.837898237054434140.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.837898237054434140.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944766976
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.945902635720463394.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.945902635720463394.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.945902635720463394.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 8 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 4 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1809961566757488721.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1809961566757488721.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1809961566757488721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 1 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6795783980596534370.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6795783980596534370.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6795783980596534370.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2772345475058326537.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2772345475058326537.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2772345475058326537.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1246167240738455978.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1246167240738455978.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1246167240738455978.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3833666513604844134.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3833666513604844134.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3833666513604844134.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3267106108089765317.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3267106108089765317.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3267106108089765317.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1380463641697755329.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1380463641697755329.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1380463641697755329.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 5 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3189733143768306141.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3189733143768306141.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3189733143768306141.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 6 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2412646580685030444.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2412646580685030444.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2412646580685030444.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7642988181733836618.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7642988181733836618.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7642988181733836618.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6011464660560865358.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6011464660560865358.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6011464660560865358.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9085871414666519581.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9085871414666519581.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9085871414666519581.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8755055030761476277.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8755055030761476277.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8755055030761476277.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:31:44	AbstractOpticalDuplicateFinderCommandLineProgram	A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 4 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 2 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8057413471224892027.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8057413471224892027.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8057413471224892027.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Found 0 optical duplicate clusters.
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Processed 2 records
   [testng] INFO	2016-04-27 04:31:44	MarkDuplicatesWithMateCigar	Marking 0 records as duplicates.
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1397312767516380506.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1397312767516380506.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1397312767516380506.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.vcf.MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null/blah CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:44 UTC 2016] picard.vcf.MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:44 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.600411136565145634.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-random-scatter-0.vcf, testdata/picard/vcf/CEUTrio-random-scatter-1.vcf, testdata/picard/vcf/CEUTrio-random-scatter-2.vcf, testdata/picard/vcf/CEUTrio-random-scatter-3.vcf, testdata/picard/vcf/CEUTrio-random-scatter-4.vcf, testdata/picard/vcf/CEUTrio-random-scatter-5.vcf] OUTPUT=/tmp/random-scatter-test-output.6911368186166546057.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null/blah CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.4912834977126652195.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 1
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 2
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-random-scatter-0.vcf, testdata/picard/vcf/CEUTrio-random-scatter-1.vcf, testdata/picard/vcf/CEUTrio-random-scatter-2.vcf, testdata/picard/vcf/CEUTrio-random-scatter-3.vcf, testdata/picard/vcf/CEUTrio-random-scatter-4.vcf, testdata/picard/vcf/CEUTrio-random-scatter-5.vcf] OUTPUT=/tmp/random-scatter-test-output.3959663839695013671.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 1
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 2
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 3
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 4
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 5
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 6
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/sort-presorted-test-output.4743598096226971859.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 1
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/sort-scrambled-indels-snps-test-output.5428892222778924313.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 1
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 2
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-scrambled.1.vcf, testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.1137651332670413277.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 1
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 2
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=965214208
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/sort-single-scrambled-test-output.7194338032217869271.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 1
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=983040000
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf, testdata/picard/vcf/vcfFormatTest.scrambled.vcf] OUTPUT=/tmp/sort-multiple-scrambled-test-output.8060492772740153717.vcf CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:45 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 1
   [testng] INFO	2016-04-27 04:31:45	SortVcf	Reading entries from input file 2
   [testng] [Wed Apr 27 04:31:45 UTC 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=983040000
   [testng] [Wed Apr 27 04:31:47 UTC 2016] picard.sam.AddCommentsToBam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam OUTPUT=/tmp/addCommentsToBamTest.7698655527781814721.bam COMMENT=[test1, test2, test3]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:47 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:47 UTC 2016] picard.sam.AddCommentsToBam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1015021568
   [testng] [Wed Apr 27 04:31:47 UTC 2016] picard.sam.AddCommentsToBam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test2.sam OUTPUT=/tmp/addCommentsToBamTest.samFile2867698437670002582.bam COMMENT=[test1, test2, test3]    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:47 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:47 UTC 2016] picard.sam.AddCommentsToBam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1015021568
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5146369504732585453IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test5146369504732585453IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1, 2, 3, 4
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	File type .bcl has cycles files of different length.  Current cycle (9) Length of first non-empty file (14) length of current cycle (56581) File(/tmp/ift_test5146369504732585453IlluminaDir/Data/Intensities/BaseCalls/L005/C9.1/s_5_3.bcl)
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 5 FAILED  Total Errors: 1
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	FAILED! There were 1 in the following lanes: 5
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test1707624954041262425IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF, Barcodes] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=true LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test1707624954041262425IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 2
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Could not find a format with available files for the following data types: Barcodes, Position
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 2 FAILED  Total Errors: 2
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	FAILED! There were 2 in the following lanes: 2
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test1707624954041262425IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF, Barcodes] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=true LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test1707624954041262425IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 2
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 2 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test1983683886957482458IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=13T LANES=[2] FAKE_FILES=true LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test1983683886957482458IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 2
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	File type .bcl is missing a file for cycle 13 and tile 1201
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	File type .bcl is missing a file for cycle 13 and tile 2101
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing tile [2101] for file type .filter.
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 2 FAILED  Total Errors: 3
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	FAILED! There were 3 in the following lanes: 2
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test1983683886957482458IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=13T LANES=[2] FAKE_FILES=true LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test1983683886957482458IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 2
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 2 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] FAKE_FILES=true LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 153 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 154 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 155 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 156 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 157 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 158 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 159 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 160 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 161 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 162 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 163 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 164 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 165 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 166 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 167 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 168 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 169 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 170 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 171 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 172 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 173 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 174 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 175 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 176 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 177 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 178 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 179 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 180 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 181 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 182 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 183 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 184 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 185 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 186 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 187 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 188 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 189 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 190 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 191 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 192 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 193 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 194 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 195 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 196 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 197 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 198 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 199 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 200 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 201 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 202 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 203 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 204 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 205 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 206 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 207 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 208 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 209 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 210 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 211 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 212 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 213 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 214 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 215 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 216 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 217 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 218 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 219 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 220 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 221 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 222 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 223 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 224 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 225 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 226 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 227 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 228 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 229 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 230 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 231 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 232 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 233 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 234 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 235 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 236 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 237 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 238 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 239 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 240 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 241 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 242 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 243 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 244 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 245 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 246 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 247 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 248 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 249 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 250 in directory /tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 5 FAILED  Total Errors: 98
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	FAILED! There were 98 in the following lanes: 5
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] FAKE_FILES=true LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test8038731549883226677IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] TILE_NUMBERS=[1301, 2201] FAKE_FILES=true LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1301, 2201
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 153 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 154 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 155 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 156 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 157 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 158 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 159 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 160 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 161 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 162 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 163 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 164 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 165 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 166 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 167 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 168 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 169 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 170 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 171 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 172 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 173 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 174 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 175 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 176 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 177 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 178 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 179 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 180 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 181 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 182 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 183 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 184 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 185 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 186 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 187 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 188 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 189 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 190 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 191 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 192 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 193 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 194 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 195 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 196 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 197 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 198 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 199 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 200 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 201 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 202 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 203 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 204 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 205 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 206 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 207 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 208 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 209 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 210 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 211 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 212 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 213 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 214 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 215 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 216 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 217 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 218 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 219 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 220 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 221 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 222 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 223 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 224 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 225 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 226 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 227 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 228 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 229 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 230 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 231 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 232 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 233 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 234 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 235 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 236 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 237 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 238 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 239 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 240 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 241 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 242 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 243 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 244 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 245 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 246 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 247 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 248 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 249 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Missing file for cycle 250 in directory /tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 5 FAILED  Total Errors: 98
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	FAILED! There were 98 in the following lanes: 5
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] TILE_NUMBERS=[1301, 2201] FAKE_FILES=true LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test5904216131769384710IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1301, 2201
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test4533832191994780871IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[3] FAKE_FILES=false LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:48 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lanes(3 in basecalls directory (/tmp/ift_test4533832191994780871IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Checking lane 3
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	Lane 3 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:48	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:48 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test6990839098860595574IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=8S15T8S LANES=[2] FAKE_FILES=false LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test6990839098860595574IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected cycles: 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lane 2
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Lane 2 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test4967968831017937788IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=false LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test4967968831017937788IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lane 2
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Lane 2 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test6669361382063139134IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[5] FAKE_FILES=false LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test6669361382063139134IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test3407899746221722872IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[5] TILE_NUMBERS=[1301, 2101] FAKE_FILES=false LINK_LOCS=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test3407899746221722872IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected tiles: 1301, 2101
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test2760610599494157742IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test2760610599494157742IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test2760610599494157742IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test2760610599494157742IlluminaDir/Data/Intensities/BaseCalls)
   [testng] 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Checking lane 5
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
   [testng] INFO	2016-04-27 04:31:49	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/simple_fits.sam OUTPUT=/tmp/simple_fits.sam.1691267596978191153.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/simple_overhang.sam OUTPUT=/tmp/simple_overhang.sam.3937177779051019673.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] Ignoring SAM validation error: ERROR: Read name simple_overhang, Read CIGAR M operator maps off end of reference
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/fits_with_deletion.sam OUTPUT=/tmp/fits_with_deletion.sam.197736065121877651.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/overhang_with_deletion.sam OUTPUT=/tmp/overhang_with_deletion.sam.6744676881240629951.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] Ignoring SAM validation error: ERROR: Read name overhang_with_deletion, Read CIGAR M operator maps off end of reference
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/trailing_insertion.sam OUTPUT=/tmp/trailing_insertion.sam.8448292644573715321.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/long_trailing_insertion.sam OUTPUT=/tmp/long_trailing_insertion.sam.7038907530783531484.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.3327051235451591206.tmp/input.sam OUTPUT=/tmp/CleanSamTester.3327051235451591206.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.1580742602310202395.tmp/input.sam OUTPUT=/tmp/CleanSamTester.1580742602310202395.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
   [testng] Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.9193200481589110703.tmp/input.sam OUTPUT=/tmp/CleanSamTester.9193200481589110703.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.600189041171673222.tmp/input.sam OUTPUT=/tmp/CleanSamTester.600189041171673222.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
   [testng] Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.3995070506499221169.tmp/input.sam OUTPUT=/tmp/CleanSamTester.3995070506499221169.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.3353645096726727343.tmp/input.sam OUTPUT=/tmp/CleanSamTester.3353645096726727343.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics133680301416836286.txt    MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics IS_BISULFITE_SEQUENCED=true REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_bisulfite_test.sam OUTPUT=/tmp/alignmentMetrics3097151855360761676.txt    MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=20 REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test_chimeras.sam OUTPUT=/tmp/alignmentMetrics4817597346451759096.txt    EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, LIBRARY, ALL_READS] INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test_multiple.sam OUTPUT=/tmp/alignmentMetrics1836295098722350564.txt    MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics8278268605064040393.txt    MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test2.sam OUTPUT=/tmp/alignmentMetrics5303708066938332341.txt    MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test2304664189644823378.pdf SUMMARY_OUTPUT=/tmp/test8296284300260337754.gc_bias.summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias6341430291923854.bam OUTPUT=/tmp/test4284510330155123102.gc_bias.detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta    STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:49	RExecutor	Executing R script via command: Rscript /tmp/script5890883352121278379.R /tmp/test4284510330155123102.gc_bias.detail_metrics /tmp/test8296284300260337754.gc_bias.summary_metrics /tmp/test2304664189644823378.pdf 100
   [testng] INFO	2016-04-27 04:31:49	ProcessExecutor	Total clusters:  300 , Aligned reads:  600Total clusters:  200 , Aligned reads:  400Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:49 UTC 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test1871409552189210904.pdf SUMMARY_OUTPUT=/tmp/test7287639754701949079.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias6341430291923854.bam OUTPUT=/tmp/test8146537865911916966.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta    STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:49 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:49	RExecutor	Executing R script via command: Rscript /tmp/script8880044460441529759.R /tmp/test8146537865911916966.gc_bias_detail_metrics /tmp/test7287639754701949079.gc_bias_summary_metrics /tmp/test1871409552189210904.pdf 100
   [testng] INFO	2016-04-27 04:31:50	ProcessExecutor	Total clusters:  300 , Aligned reads:  600Total clusters:  200 , Aligned reads:  400Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
   [testng] [Wed Apr 27 04:31:50 UTC 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:50 UTC 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test4734628646618822321.pdf SUMMARY_OUTPUT=/tmp/testAllChr5445820491292689426.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias5302657445652836493.bam OUTPUT=/tmp/testAllChrDetails28782905498826505.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta    STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:50 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:50	RExecutor	Executing R script via command: Rscript /tmp/script4416602265944730957.R /tmp/testAllChrDetails28782905498826505.gc_bias_detail_metrics /tmp/testAllChr5445820491292689426.gc_bias_summary_metrics /tmp/test4734628646618822321.pdf 100
   [testng] INFO	2016-04-27 04:31:50	ProcessExecutor	Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
   [testng] [Wed Apr 27 04:31:50 UTC 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:50 UTC 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=1 CLIP_OVERLAPPING_READS=true TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics148353018171839505.hs_metrics SAMPLE_SIZE=1000    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:50 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:50	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:31:50	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:31:50	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:31:52	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] [Wed Apr 27 04:31:52 UTC 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.03 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:52 UTC 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=2 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=true TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics7421803140365902368.hs_metrics SAMPLE_SIZE=1000    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:52 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:52	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:31:52	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:31:52	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:31:52	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] [Wed Apr 27 04:31:52 UTC 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:52 UTC 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=0 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=true TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics2461333161364033107.hs_metrics SAMPLE_SIZE=1000    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:52 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:52	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:31:52	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:31:52	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:31:53	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] [Wed Apr 27 04:31:53 UTC 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:53 UTC 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=0 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics1924090302879604988.hs_metrics SAMPLE_SIZE=1000    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:53 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:53	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:31:53	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:31:53	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:31:53	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] [Wed Apr 27 04:31:53 UTC 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:53 UTC 2016] picard.illumina.CollectIlluminaBasecallingMetrics BASECALLS_DIR=/tmp/cibm.1681312916880577125.tmp/25T8B25T/Data/Intensities/BaseCalls LANE=1 INPUT=/tmp/cibm.1681312916880577125.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 READ_STRUCTURE=25T8B25T OUTPUT=/tmp/cibm.7783189331162008458.metrics    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:53 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:53 UTC 2016] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:53 UTC 2016] picard.illumina.CollectIlluminaBasecallingMetrics BASECALLS_DIR=/tmp/cibm.1681312916880577125.tmp/125T125T/Data/Intensities/BaseCalls LANE=1 READ_STRUCTURE=125T125T OUTPUT=/tmp/cibm.1769273962613266601.metrics    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:53 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:53 UTC 2016] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:53 UTC 2016] picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/test4492902489977582706.pdf INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test5013040393435720020.insert_size_metrics    DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:53 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:53	RExecutor	Executing R script via command: Rscript /tmp/script3231829152376517110.R /tmp/test5013040393435720020.insert_size_metrics /tmp/test4492902489977582706.pdf insert_size_metrics_test.sam
   [testng] INFO	2016-04-27 04:31:54	ProcessExecutor	null device 
   [testng] INFO	2016-04-27 04:31:54	ProcessExecutor	          1 
   [testng] [Wed Apr 27 04:31:54 UTC 2016] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1082654720
   [testng] [Wed Apr 27 04:31:54 UTC 2016] picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/test2665206069630226622.pdf METRIC_ACCUMULATION_LEVEL=[READ_GROUP] INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test2653406831386708430.insert_size_metrics    DEVIATIONS=10.0 MINIMUM_PCT=0.05 INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:54 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:54	RExecutor	Executing R script via command: Rscript /tmp/script6935135499047157444.R /tmp/test2653406831386708430.insert_size_metrics /tmp/test2665206069630226622.pdf insert_size_metrics_test.sam
   [testng] INFO	2016-04-27 04:31:54	ProcessExecutor	null device 
   [testng] INFO	2016-04-27 04:31:54	ProcessExecutor	          1 
   [testng] [Wed Apr 27 04:31:54 UTC 2016] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] INFO	2016-04-27 04:31:54	RExecutor	Executing R script via command: Rscript /tmp/script7165770303130026827.R /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/directed/CollectInsertSizeMetrics/multiple_orientation.sam.insert_size_metrics /tmp/test5888631213900334408.pdf Flags of Chad and Romania
   [testng] INFO	2016-04-27 04:31:54	ProcessExecutor	null device 
   [testng] INFO	2016-04-27 04:31:54	ProcessExecutor	          1 
   [testng] [Wed Apr 27 04:31:54 UTC 2016] picard.analysis.CollectMultipleMetrics INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics5684143369116960946 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta    ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:54 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:54	RExecutor	Executing R script via command: Rscript /tmp/script139341592113710088.R /tmp/alignmentMetrics5684143369116960946.insert_size_metrics /tmp/alignmentMetrics5684143369116960946.insert_size_histogram.pdf summary_alignment_stats_test.sam
   [testng] INFO	2016-04-27 04:31:54	ProcessExecutor	null device 
   [testng] INFO	2016-04-27 04:31:54	ProcessExecutor	          1 
   [testng] [Wed Apr 27 04:31:54 UTC 2016] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:54 UTC 2016] picard.analysis.CollectMultipleMetrics INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias3118674105087030414.bam OUTPUT=/tmp/test379626875576770048 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, CollectGcBiasMetrics] REFERENCE_SEQUENCE=testdata/picard/quality/chrM.reference.fasta    ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:54 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:54	RExecutor	Executing R script via command: Rscript /tmp/script2296087855775840323.R /tmp/test379626875576770048.gc_bias.detail_metrics /tmp/test379626875576770048.gc_bias.summary_metrics /tmp/test379626875576770048.gc_bias.pdf 100
   [testng] INFO	2016-04-27 04:31:55	ProcessExecutor	Total clusters:  300 , Aligned reads:  600
   [testng] INFO	2016-04-27 04:31:55	RExecutor	Executing R script via command: Rscript /tmp/script4376922132349961920.R /tmp/test379626875576770048.insert_size_metrics /tmp/test379626875576770048.insert_size_histogram.pdf CollectGcBias3118674105087030414.bam
   [testng] INFO	2016-04-27 04:31:55	ProcessExecutor	null device 
   [testng] INFO	2016-04-27 04:31:55	ProcessExecutor	          1 
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectMultipleMetrics INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test4198472026015693957 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta    ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:55	RExecutor	Executing R script via command: Rscript /tmp/script1278724387407274534.R /tmp/test4198472026015693957.insert_size_metrics /tmp/test4198472026015693957.insert_size_histogram.pdf insert_size_metrics_test.sam
   [testng] INFO	2016-04-27 04:31:55	ProcessExecutor	null device 
   [testng] INFO	2016-04-27 04:31:55	ProcessExecutor	          1 
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectQualityYieldMetrics INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test4988451972932542808.quality_yield_metrics    USE_ORIGINAL_QUALITIES=true INCLUDE_SECONDARY_ALIGNMENTS=false INCLUDE_SUPPLEMENTAL_ALIGNMENTS=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectQualityYieldMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.1992846225556651916.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.7930750381883057948.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] INPUT=/tmp/tmp.collectRnaSeqMetrics.3335513552092830868.sam OUTPUT=/tmp/tmp.7630773587880710108.rna_metrics    MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:55	CollectRnaSeqMetrics	Loaded 1 genes.
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.7728960597743537112.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.4576571423092096797.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] METRIC_ACCUMULATION_LEVEL=[SAMPLE, LIBRARY] INPUT=/tmp/tmp.collectRnaSeqMetrics.1138311647137275337.sam OUTPUT=/tmp/tmp.3282985303721298934.rna_metrics    MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:55	CollectRnaSeqMetrics	Loaded 1 genes.
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectRrbsMetrics INPUT=testdata/picard/metrics/chrMReads.sam METRICS_FILE_PREFIX=/tmp/crmt.2160988671668723922.tmp/READ_TEST REFERENCE=testdata/picard/metrics/chrM.reference.fasta    MINIMUM_READ_LENGTH=5 C_QUALITY_THRESHOLD=20 NEXT_BASE_QUALITY_THRESHOLD=10 MAX_MISMATCH_RATE=0.1 ASSUME_SORTED=false METRIC_ACCUMULATION_LEVEL=[ALL_READS] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:55	RExecutor	Executing R script via command: Rscript /tmp/script2771012946393487249.R /tmp/crmt.2160988671668723922.tmp/READ_TEST.rrbs_detail_metrics /tmp/crmt.2160988671668723922.tmp/READ_TEST.rrbs_summary_metrics /tmp/crmt.2160988671668723922.tmp/READ_TEST.rrbs_qc.pdf
   [testng] INFO	2016-04-27 04:31:55	ProcessExecutor	null device 
   [testng] INFO	2016-04-27 04:31:55	ProcessExecutor	          1 
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.CollectRrbsMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=1 INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.6506408399643986621.tmp/with_context REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta    MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics DB_SNP=testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.dbsnp.vcf MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.6506408399643986621.tmp/with_dbsnp REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta    MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics INTERVALS=testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.interval_list MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.6506408399643986621.tmp/with_intervals REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta    MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=0 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.6506408399643986621.tmp/no_bq_cutoff REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta    MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics MINIMUM_MAPPING_QUALITY=0 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.6506408399643986621.tmp/no_mq_cutoff REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta    MINIMUM_QUALITY_SCORE=20 INCLUDE_UNPAIRED=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=0 MAXIMUM_INSERT_SIZE=0 CONTEXT_SIZE=0 INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.6506408399643986621.tmp/unmapped_mate REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta    MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:55 UTC 2016] picard.analysis.directed.CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.single.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.single.interval_list] INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics7542775965639816387.bam OUTPUT=/tmp/test2914453680418370395.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget8061096955868697126.perTargetCoverage SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=testdata/picard/quality/chrM.reference.fasta    NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:55 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:56	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:31:56	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:31:56	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:31:56	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:31:56	TargetMetricsCollector	Calculating GC metrics
   [testng] [Wed Apr 27 04:31:56 UTC 2016] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=1095237632
   [testng] [Wed Apr 27 04:31:56 UTC 2016] picard.analysis.directed.CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.empty.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.empty.interval_list] INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics7542775965639816387.bam OUTPUT=/tmp/test2914453680418370395.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget8061096955868697126.perTargetCoverage SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=testdata/picard/quality/chrM.reference.fasta    NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:56 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:56	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:31:56	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:31:56	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:31:56	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:31:56	TargetMetricsCollector	Calculating GC metrics
   [testng] WARNING	2016-04-27 04:31:56	TargetMetricsCollector	interval of length zero found: chrM:2-1	+	interval-1 skipped.
   [testng] [Wed Apr 27 04:31:56 UTC 2016] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=1120927744
   [testng] INFO	2016-04-27 04:31:56	CollectVariantCallingMetrics	Loading dbSNP file ...
   [testng] INFO	2016-04-27 04:31:56	CollectVariantCallingMetrics	Starting iteration of variants.
   [testng] INFO	2016-04-27 04:31:57	CollectVariantCallingMetrics	Loading dbSNP file ...
   [testng] INFO	2016-04-27 04:31:57	CollectVariantCallingMetrics	Starting iteration of variants.
   [testng] [Wed Apr 27 04:31:57 UTC 2016] picard.analysis.CollectWgsMetricsFromQuerySorted INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/namesorted.test.sam OUTPUT=/tmp/metrics3010252048498049437.txt    MINIMUM_USABLE_MAPPING_QUALITY=20 MINIMUM_USABLE_BASE_QUALITY=20 MINIMUM_RAW_MAPPING_QUALITY=0 MINIMUM_RAW_BASE_QUALITY=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:57 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:57 UTC 2016] picard.analysis.CollectWgsMetricsFromQuerySorted done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1120927744
   [testng] [Wed Apr 27 04:31:57 UTC 2016] picard.analysis.CollectWgsMetricsFromQuerySorted INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/namesorted.test.sam OUTPUT=/tmp/metrics564096993681356266.txt GENOME_TERRITORY=1000    MINIMUM_USABLE_MAPPING_QUALITY=20 MINIMUM_USABLE_BASE_QUALITY=20 MINIMUM_RAW_MAPPING_QUALITY=0 MINIMUM_RAW_BASE_QUALITY=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:57 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:31:57 UTC 2016] picard.analysis.CollectWgsMetricsFromQuerySorted done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1120927744
   [testng] [Wed Apr 27 04:31:57 UTC 2016] picard.analysis.CollectWgsMetricsFromSampledSites INTERVALS=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/contiguous.interval_list INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test9169240678806323281.wgs_metrics REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta SAMPLE_SIZE=1000    MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:57 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:57	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:31:57	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:31:57	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:31:59	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] [Wed Apr 27 04:31:59 UTC 2016] picard.analysis.CollectWgsMetricsFromSampledSites done. Elapsed time: 0.04 minutes.
   [testng] Runtime.totalMemory()=1120927744
   [testng] [Wed Apr 27 04:31:59 UTC 2016] picard.analysis.CollectWgsMetricsFromSampledSites INTERVALS=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/onePos.interval_list INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test372339384943672162.wgs_metrics REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta SAMPLE_SIZE=1000    MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:31:59 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:31:59	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:31:59	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:31:59	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:00	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] [Wed Apr 27 04:32:00 UTC 2016] picard.analysis.CollectWgsMetricsFromSampledSites done. Elapsed time: 0.03 minutes.
   [testng] Runtime.totalMemory()=1120927744
   [testng] [Wed Apr 27 04:32:00 UTC 2016] picard.analysis.CollectWgsMetrics INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectWgsMetrics9132011334233881654.bam OUTPUT=/tmp/testWgsMetrics828100590739198087.txt REFERENCE_SEQUENCE=testdata/picard/quality/chrM.reference.fasta SAMPLE_SIZE=1000    MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:00 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:01	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:01	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:01	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:02	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.02 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] ERROR: 'HiMom' is not a valid value for FrobnicationFlavor.
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] picard.cmdline.CommandLineParserTest$ClpOptionsWithNested AN_INT=123 A_STRING=aString    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json     CLP_NESTED.VERBOSITY=INFO CLP_NESTED.QUIET=false CLP_NESTED.VALIDATION_STRINGENCY=STRICT CLP_NESTED.COMPRESSION_LEVEL=5 CLP_NESTED.MAX_RECORDS_IN_RAM=1000 CLP_NESTED.CREATE_INDEX=false CLP_NESTED.CREATE_MD5_FILE=false CLP_NESTED.GA4GH_CLIENT_SECRETS=client_secrets.json  CLP_NESTED.FROB_NESTED.FROBNICATION_THRESHOLD=-1000 CLP_NESTED.FROB_NESTED.FROBNICATION_FLAVOR=BAZ CLP_NESTED.FROB_NESTED.SHMIGGLE_TYPE=[innershmiggle1, skeezwitz] CLP_NESTED.FROB_NESTED.TRUTHINESS=false     FRAB.FROBNICATION_THRESHOLD=456 FRAB.FROBNICATION_FLAVOR=FOO FRAB.SHMIGGLE_TYPE=[shmiggle1] FRAB.TRUTHINESS=true   
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] ERROR: Problem constructing Integer from the string 'ABC'.
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] USAGE: ClpOptionsWithNested [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#ClpOptionsWithNested
   [testng] 
   [testng] Class with nested options.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] AN_INT=Integer                Required. 
   [testng] 
   [testng] A_STRING=String               Required. 
   [testng] 
   [testng] CLP_NESTED.FROB_NESTED.FROBNICATION_THRESHOLD=Integer
   [testng] CLP_NESTED.FROB_NESTED.T=Integer
   [testng]                               Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] CLP_NESTED.FROB_NESTED.FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] CLP_NESTED.FROB_NESTED.SHMIGGLE_TYPE=String
   [testng]                               Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] CLP_NESTED.FROB_NESTED.TRUTHINESS=Boolean
   [testng]                               Required. Possible values: {true, false} 
   [testng] 
   [testng] <h3 id="ClpOptionsWithNested">ClpOptionsWithNested</h3>
   [testng] <section>
   [testng] <p>Class with nested options.</p>
   [testng] <table>
   [testng] <tr><th>Option</th><th>Description</th></tr>
   [testng] <tr><td>AN_INT (Integer)</td><td>Default value: 123. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>A_STRING (String)</td><td>Default value: aString. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CLP_NESTED.FROB_NESTED.FROBNICATION_THRESHOLD (Integer)</td><td>Frobnication threshold setting.  Default value: -1000. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CLP_NESTED.FROB_NESTED.FROBNICATION_FLAVOR (FrobnicationFlavor)</td><td>Default value: BAZ. This option can be set to 'null' to clear the default value. Possible values: {FOO, BAR, BAZ} </td></tr>
   [testng] <tr><td>CLP_NESTED.FROB_NESTED.SHMIGGLE_TYPE (String)</td><td>Allowed shmiggle types.  Default value: [innershmiggle1, skeezwitz]. This option can be set to 'null' to clear the default value. This option may be specified between 1 and 3 times. This option can be set to 'null' to clear the default list. </td></tr>
   [testng] <tr><td>CLP_NESTED.FROB_NESTED.TRUTHINESS (Boolean)</td><td>Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} </td></tr>
   [testng] </table>
   [testng] </section>
   [testng] USAGE: DynamicPropagationParent [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#DynamicPropagationParent
   [testng] 
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] STRING1=String                Default value: String1ParentDefault. This option can be set to 'null' to clear the 
   [testng]                               default value. 
   [testng] 
   [testng] STRING2=String                Default value: String2ParentDefault. This option can be set to 'null' to clear the 
   [testng]                               default value. 
   [testng] 
   [testng] STRING3=String                Default value: String3ParentDefault. This option can be set to 'null' to clear the 
   [testng]                               default value. 
   [testng] 
   [testng] STRING4=String                Default value: String4ParentDefault. This option can be set to 'null' to clear the 
   [testng]                               default value. 
   [testng] 
   [testng] STRING5=String                Required. 
   [testng] 
   [testng] COLLECTION=String             Default value: null. This option may be specified 0 or more times. 
   [testng] 
   [testng] CHILD.STRING1=String          Required. 
   [testng] 
   [testng] CHILD.STRING2=String          Default value: String2ChildDefault. This option can be set to 'null' to clear the default 
   [testng]                               value. 
   [testng] 
   [testng] CHILD.STRING3=String          Default value: String3ChildDefault. This option can be set to 'null' to clear the default 
   [testng]                               value. 
   [testng] 
   [testng] CHILD.STRING4=String          Required. 
   [testng] 
   [testng] CHILD.STRING5=String          Required. 
   [testng] 
   [testng] CHILD.COLLECTION=String       Default value: null. This option may be specified 0 or more times. 
   [testng] 
   [testng] <h3 id="DynamicPropagationParent">DynamicPropagationParent</h3>
   [testng] <section>
   [testng] <p></p>
   [testng] <table>
   [testng] <tr><th>Option</th><th>Description</th></tr>
   [testng] <tr><td>STRING1 (String)</td><td>Default value: String1ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>STRING2 (String)</td><td>Default value: String2ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>STRING3 (String)</td><td>Default value: String3Parent. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>STRING4 (String)</td><td>Default value: String4ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>STRING5 (String)</td><td>Default value: String5Parent. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>COLLECTION (String)</td><td>Default value: [CollectionParent]. This option can be set to 'null' to clear the default value. This option may be specified 0 or more times. This option can be set to 'null' to clear the default list. </td></tr>
   [testng] <tr><td>CHILD.STRING1 (String)</td><td>Default value: String1ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CHILD.STRING2 (String)</td><td>Default value: String2ChildDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CHILD.STRING3 (String)</td><td>Default value: String3Parent. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CHILD.STRING4 (String)</td><td>Default value: String4Child. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CHILD.STRING5 (String)</td><td>Default value: String5Child. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CHILD.COLLECTION (String)</td><td>Default value: null. This option may be specified 0 or more times. </td></tr>
   [testng] </table>
   [testng] </section>
   [testng] ERROR: Option 'FROBNICATION_FLAVOR' is required.
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] ERROR: Option 'A' is required unless any of [Y, Z, M, N] are specified.
   [testng] 
   [testng] USAGE: MutexOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#MutexOptions
   [testng] 
   [testng] Usage: program [options...]
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] A=String                      Required.  Cannot be used in conjuction with option(s) Y Z M N
   [testng] 
   [testng] B=String                      Required.  Cannot be used in conjuction with option(s) Y Z M N
   [testng] 
   [testng] M=String                      Required.  Cannot be used in conjuction with option(s) A B Y Z
   [testng] 
   [testng] N=String                      Required.  Cannot be used in conjuction with option(s) A B Y Z
   [testng] 
   [testng] Y=String                      Required.  Cannot be used in conjuction with option(s) A B M N
   [testng] 
   [testng] Z=String                      Required.  Cannot be used in conjuction with option(s) A B M N
   [testng] 
   [testng] ERROR: Option 'B' is required unless any of [Y, Z, M, N] are specified.
   [testng] 
   [testng] USAGE: MutexOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#MutexOptions
   [testng] 
   [testng] Usage: program [options...]
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] A=String                      Required.  Cannot be used in conjuction with option(s) Y Z M N
   [testng] 
   [testng] B=String                      Required.  Cannot be used in conjuction with option(s) Y Z M N
   [testng] 
   [testng] M=String                      Required.  Cannot be used in conjuction with option(s) A B Y Z
   [testng] 
   [testng] N=String                      Required.  Cannot be used in conjuction with option(s) A B Y Z
   [testng] 
   [testng] Y=String                      Required.  Cannot be used in conjuction with option(s) A B M N
   [testng] 
   [testng] Z=String                      Required.  Cannot be used in conjuction with option(s) A B M N
   [testng] 
   [testng] ERROR: Option 'A' cannot be used in conjunction with option(s) Y
   [testng] 
   [testng] USAGE: MutexOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#MutexOptions
   [testng] 
   [testng] Usage: program [options...]
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] A=String                      Required.  Cannot be used in conjuction with option(s) Y Z M N
   [testng] 
   [testng] B=String                      Required.  Cannot be used in conjuction with option(s) Y Z M N
   [testng] 
   [testng] M=String                      Required.  Cannot be used in conjuction with option(s) A B Y Z
   [testng] 
   [testng] N=String                      Required.  Cannot be used in conjuction with option(s) A B Y Z
   [testng] 
   [testng] Y=String                      Required.  Cannot be used in conjuction with option(s) A B M N
   [testng] 
   [testng] Z=String                      Required.  Cannot be used in conjuction with option(s) A B M N
   [testng] 
   [testng] ERROR: Option 'A' cannot be used in conjunction with option(s) Y Z M N
   [testng] 
   [testng] USAGE: MutexOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#MutexOptions
   [testng] 
   [testng] Usage: program [options...]
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] A=String                      Required.  Cannot be used in conjuction with option(s) Y Z M N
   [testng] 
   [testng] B=String                      Required.  Cannot be used in conjuction with option(s) Y Z M N
   [testng] 
   [testng] M=String                      Required.  Cannot be used in conjuction with option(s) A B Y Z
   [testng] 
   [testng] N=String                      Required.  Cannot be used in conjuction with option(s) A B Y Z
   [testng] 
   [testng] Y=String                      Required.  Cannot be used in conjuction with option(s) A B M N
   [testng] 
   [testng] Z=String                      Required.  Cannot be used in conjuction with option(s) A B M N
   [testng] 
   [testng] ERROR: Option 'SHMIGGLE_TYPE' must be specified at least 1 times.
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] ERROR: At least 2 positional arguments must be specified.
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'.
   [testng] 
   [testng] USAGE: FrobnicateOptionsWithNullList [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptionsWithNullList
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Required. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Default value: BAR. This option can be set to 'null' to clear the default value. Possible 
   [testng]                               values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option must be specified no more than 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'.
   [testng] 
   [testng] USAGE: FrobnicateOptionsWithNullList [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptionsWithNullList
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Required. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Default value: BAR. This option can be set to 'null' to clear the default value. Possible 
   [testng]                               values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option must be specified no more than 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] ERROR: Option 'FROBNICATION_FLAVOR' cannot be specified more than once.
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] ERROR: Option 'T' cannot be specified more than once.
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] ERROR: Option 'FROB.FROBNICATION_FLAVOR' is required.
   [testng] ERROR: Option 'NESTED.FROB.FROBNICATION_FLAVOR' is required.
   [testng] 
   [testng] USAGE: OptionsWithNested [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithNested
   [testng] 
   [testng] Class with nested option
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] AN_INT=Integer                Required. 
   [testng] 
   [testng] A_STRING=String               Required. 
   [testng] 
   [testng] FROB.FROBNICATION_THRESHOLD=Integer
   [testng] FROB.T=Integer                Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROB.FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] FROB.SHMIGGLE_TYPE=String     Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] FROB.TRUTHINESS=Boolean       Required. Possible values: {true, false} 
   [testng] 
   [testng] NESTED.FROB.FROBNICATION_THRESHOLD=Integer
   [testng] NESTED.FROB.T=Integer         Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] NESTED.FROB.FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] NESTED.FROB.SHMIGGLE_TYPE=String
   [testng]                               Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] NESTED.FROB.TRUTHINESS=BooleanRequired. Possible values: {true, false} 
   [testng] 
   [testng] ERROR: Option 'SHMIGGLE_TYPE' cannot be used more than 3 times.
   [testng] 
   [testng] picard.cmdline.CommandLineParserTest$DynamicPropagationParent STRING3=String3Parent STRING5=String5Parent COLLECTION=[CollectionParent]    STRING1=String1ParentDefault STRING2=String2ParentDefault STRING4=String4ParentDefault VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json  CHILD.STRING4=String4Child CHILD.STRING5=String5Child    CHILD.STRING2=String2ChildDefault CHILD.STRING3=String3ChildDefault
   [testng] picard.cmdline.CommandLineParserTest$OptionsWithNested AN_INT=123 A_STRING=outerString         
   [testng] USAGE: OptionsWithNested [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithNested
   [testng] 
   [testng] Class with nested option
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] AN_INT=Integer                Required. 
   [testng] 
   [testng] A_STRING=String               Required. 
   [testng] 
   [testng] FROB.FROBNICATION_THRESHOLD=Integer
   [testng] FROB.T=Integer                Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROB.FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] FROB.SHMIGGLE_TYPE=String     Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] FROB.TRUTHINESS=Boolean       Required. Possible values: {true, false} 
   [testng] 
   [testng] NESTED.FROB.FROBNICATION_THRESHOLD=Integer
   [testng] NESTED.FROB.T=Integer         Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] NESTED.FROB.FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] NESTED.FROB.SHMIGGLE_TYPE=String
   [testng]                               Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] NESTED.FROB.TRUTHINESS=BooleanRequired. Possible values: {true, false} 
   [testng] 
   [testng] <h3 id="testStaticNestedOptions">testStaticNestedOptions</h3>
   [testng] <section>
   [testng] <p>Class with nested option</p>
   [testng] <table>
   [testng] <tr><th>Option</th><th>Description</th></tr>
   [testng] <tr><td>AN_INT (Integer)</td><td>Required. </td></tr>
   [testng] <tr><td>A_STRING (String)</td><td>Required. </td></tr>
   [testng] <tr><td>FROB.FROBNICATION_THRESHOLD (Integer)</td><td>Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>FROB.FROBNICATION_FLAVOR (FrobnicationFlavor)</td><td>Required. Possible values: {FOO, BAR, BAZ} </td></tr>
   [testng] <tr><td>FROB.SHMIGGLE_TYPE (String)</td><td>Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 3 times. </td></tr>
   [testng] <tr><td>FROB.TRUTHINESS (Boolean)</td><td>Required. Possible values: {true, false} </td></tr>
   [testng] <tr><td>NESTED.FROB.FROBNICATION_THRESHOLD (Integer)</td><td>Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>NESTED.FROB.FROBNICATION_FLAVOR (FrobnicationFlavor)</td><td>Required. Possible values: {FOO, BAR, BAZ} </td></tr>
   [testng] <tr><td>NESTED.FROB.SHMIGGLE_TYPE (String)</td><td>Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 3 times. </td></tr>
   [testng] <tr><td>NESTED.FROB.TRUTHINESS (Boolean)</td><td>Required. Possible values: {true, false} </td></tr>
   [testng] </table>
   [testng] </section>
   [testng] picard.cmdline.CommandLineParserTest$OptionsWithNested AN_INT=123 A_STRING=outerString     FROB.FROBNICATION_FLAVOR=BAR FROB.SHMIGGLE_TYPE=[shmiggle1, shmiggle2] FROB.TRUTHINESS=true    FROB.FROBNICATION_THRESHOLD=20      NESTED.FROB.FROBNICATION_THRESHOLD=10 NESTED.FROB.FROBNICATION_FLAVOR=BAZ NESTED.FROB.SHMIGGLE_TYPE=[inner1, inner2, inner3] NESTED.FROB.TRUTHINESS=false   
   [testng] USAGE: StaticPropagationParent [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#StaticPropagationParent
   [testng] 
   [testng] Usage: program [options...]
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] STRING1=String                Default value: String1ParentDefault. This option can be set to 'null' to clear the 
   [testng]                               default value. 
   [testng] 
   [testng] STRING2=String                Default value: String2ParentDefault. This option can be set to 'null' to clear the 
   [testng]                               default value. 
   [testng] 
   [testng] STRING3=String                Default value: String3ParentDefault. This option can be set to 'null' to clear the 
   [testng]                               default value. 
   [testng] 
   [testng] STRING4=String                Default value: String4ParentDefault. This option can be set to 'null' to clear the 
   [testng]                               default value. 
   [testng] 
   [testng] STRING5=String                Required. 
   [testng] 
   [testng] COLLECTION=String             Default value: null. This option may be specified 0 or more times. 
   [testng] 
   [testng] CHILD.STRING1=String          Required. 
   [testng] 
   [testng] CHILD.STRING2=String          Default value: String2ChildDefault. This option can be set to 'null' to clear the default 
   [testng]                               value. 
   [testng] 
   [testng] CHILD.STRING3=String          Default value: String3ChildDefault. This option can be set to 'null' to clear the default 
   [testng]                               value. 
   [testng] 
   [testng] CHILD.STRING4=String          Required. 
   [testng] 
   [testng] CHILD.STRING5=String          Required. 
   [testng] 
   [testng] CHILD.COLLECTION=String       Default value: null. This option may be specified 0 or more times. 
   [testng] 
   [testng] <h3 id="testStaticPropagation">testStaticPropagation</h3>
   [testng] <section>
   [testng] <p>Usage: program [options...]
   [testng] </p>
   [testng] <table>
   [testng] <tr><th>Option</th><th>Description</th></tr>
   [testng] <tr><td>STRING1 (String)</td><td>Default value: String1ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>STRING2 (String)</td><td>Default value: String2ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>STRING3 (String)</td><td>Default value: String3ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>STRING4 (String)</td><td>Default value: String4ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>STRING5 (String)</td><td>Required. </td></tr>
   [testng] <tr><td>COLLECTION (String)</td><td>Default value: null. This option may be specified 0 or more times. </td></tr>
   [testng] <tr><td>CHILD.STRING1 (String)</td><td>Required. </td></tr>
   [testng] <tr><td>CHILD.STRING2 (String)</td><td>Default value: String2ChildDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CHILD.STRING3 (String)</td><td>Default value: String3ChildDefault. This option can be set to 'null' to clear the default value. </td></tr>
   [testng] <tr><td>CHILD.STRING4 (String)</td><td>Required. </td></tr>
   [testng] <tr><td>CHILD.STRING5 (String)</td><td>Required. </td></tr>
   [testng] <tr><td>CHILD.COLLECTION (String)</td><td>Default value: null. This option may be specified 0 or more times. </td></tr>
   [testng] </table>
   [testng] </section>
   [testng] picard.cmdline.CommandLineParserTest$StaticPropagationParent STRING3=String3Parent STRING5=String5Parent COLLECTION=[CollectionParent]    STRING1=String1ParentDefault STRING2=String2ParentDefault STRING4=String4ParentDefault  CHILD.STRING4=String4Child CHILD.STRING5=String5Child    CHILD.STRING2=String2ChildDefault CHILD.STRING3=String3ChildDefault
   [testng] USAGE: NegativePropagationParent [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#NegativePropagationParent
   [testng] 
   [testng] Usage: program [options...]
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] STRING1=Integer               Default value: 1. This option can be set to 'null' to clear the default value. 
   [testng] 
   [testng] COLLECTION=String             Default value: null. This option may be specified 0 or more times. 
   [testng] 
   [testng] CHILD.STRING1=String          Required. 
   [testng] 
   [testng] CHILD.STRING2=String          Default value: String2ChildDefault. This option can be set to 'null' to clear the default 
   [testng]                               value. 
   [testng] 
   [testng] CHILD.STRING3=String          Default value: String3ChildDefault. This option can be set to 'null' to clear the default 
   [testng]                               value. 
   [testng] 
   [testng] CHILD.STRING4=String          Required. 
   [testng] 
   [testng] CHILD.STRING5=String          Required. 
   [testng] 
   [testng] CHILD.COLLECTION=String       Default value: null. This option may be specified 0 or more times. 
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] USAGE: OptionsWithoutPositional [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithoutPositional
   [testng] 
   [testng] Usage: framistat [options]
   [testng] 
   [testng] Compute the plebnick of the freebozzle.
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] USAGE: OptionsWithoutPositional [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithoutPositional
   [testng] 
   [testng] Usage: framistat [options]
   [testng] 
   [testng] Compute the plebnick of the freebozzle.
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] Match	2
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] Match	2
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line 
   [testng]                               options, unrecognized options are ignored.  A single-valued option set in an options file 
   [testng]                               may be overridden by a subsequent command-line option.  A line starting with '#' is 
   [testng]                               considered a comment.  Required. 
   [testng] 
   [testng] ERROR: No more than 2 positional arguments may be specified on the command line.
   [testng] 
   [testng] USAGE: FrobnicateOptions [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
   [testng] 
   [testng] Usage: frobnicate [options] input-file output-file
   [testng] 
   [testng] Read input-file, frobnicate it, and write frobnicated results to output-file
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] ERROR: Invalid argument 'positional'.
   [testng] 
   [testng] USAGE: OptionsWithoutPositional [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithoutPositional
   [testng] 
   [testng] Usage: framistat [options]
   [testng] 
   [testng] Compute the plebnick of the freebozzle.
   [testng] 
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] FROBNICATION_THRESHOLD=Integer
   [testng] T=Integer                     Frobnication threshold setting.  Default value: 20. This option can be set to 'null' to 
   [testng]                               clear the default value. 
   [testng] 
   [testng] FROBNICATION_FLAVOR=FrobnicationFlavor
   [testng]                               Required. Possible values: {FOO, BAR, BAZ} 
   [testng] 
   [testng] SHMIGGLE_TYPE=String          Allowed shmiggle types.  Default value: null. This option may be specified between 1 and 
   [testng]                               3 times. 
   [testng] 
   [testng] TRUTHINESS=Boolean            Required. Possible values: {true, false} 
   [testng] 
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CreateSequenceDictionary REFERENCE=testdata/picard/sam/basic.fasta OUTPUT=/tmp/CreateSequenceDictionaryTest.636589297229658396.dict TRUNCATE_NAMES_AT_WHITESPACE=false    NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CreateSequenceDictionary REFERENCE=testdata/picard/sam/duplicate_sequence_names.fasta OUTPUT=/tmp/CreateSequenceDictionaryTest.6276882535079977787.dict TRUNCATE_NAMES_AT_WHITESPACE=true    NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity4505773384813188018.els_metrics    MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	EstimateLibraryComplexity	Will store 3098916 read pairs in memory before sorting.
   [testng] INFO	2016-04-27 04:32:02	EstimateLibraryComplexity	Finished reading - read 4 records - moving on to scanning for duplicates.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity793585083042120052.els_metrics MAX_DIFF_RATE=0.0 MIN_GROUP_COUNT=1    MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	EstimateLibraryComplexity	Will store 3098916 read pairs in memory before sorting.
   [testng] INFO	2016-04-27 04:32:02	EstimateLibraryComplexity	Finished reading - read 4 records - moving on to scanning for duplicates.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity377501711352621513.els_metrics MIN_GROUP_COUNT=1    MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	EstimateLibraryComplexity	Will store 3098916 read pairs in memory before sorting.
   [testng] INFO	2016-04-27 04:32:02	EstimateLibraryComplexity	Finished reading - read 4 records - moving on to scanning for duplicates.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity3007068600573465153.els_metrics MAX_DIFF_RATE=0.0 MAX_READ_LENGTH=10 MIN_GROUP_COUNT=1    MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	EstimateLibraryComplexity	Will store 3098916 read pairs in memory before sorting.
   [testng] INFO	2016-04-27 04:32:02	EstimateLibraryComplexity	Finished reading - read 4 records - moving on to scanning for duplicates.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] Match	3
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	1
   [testng] Missing_right	2
   [testng] SAM files differ.
   [testng] Match	3
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	2
   [testng] Missing_right	1
   [testng] SAM files differ.
   [testng] Match	0
   [testng] Differ	5
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	0
   [testng] Differ	5
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	2
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] Match	2
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] Match	2
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] Match	2
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] Match	3
   [testng] Differ	2
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	3
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	3
   [testng] Differ	2
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	3
   [testng] SAM files differ.
   [testng] Name of sequence record 1 differs.
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: chr20
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam: chr21
   [testng] Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Name of sequence record 1 differs.
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam: chr21
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: chr20
   [testng] Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Length of sequence dictionaries differs.
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: 1
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam: 2
   [testng] Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Length of sequence dictionaries differs.
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam: 2
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: 1
   [testng] Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Sort order differs.
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: coordinate
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam: null
   [testng] Sort Order differs.
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: coordinate
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam: unsorted
   [testng] Cannot compare alignments if sort orders differ.
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Sort order differs.
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam: null
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: coordinate
   [testng] Sort Order differs.
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam: unsorted
   [testng] /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: coordinate
   [testng] Cannot compare alignments if sort orders differ.
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	1
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	1
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	1
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	1
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	1
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	0
   [testng] Unmapped_right	1
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	1
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	1
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	1
   [testng] Unmapped_right	1
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	0
   [testng] Unmapped_left	1
   [testng] Unmapped_right	1
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files differ.
   [testng] Match	1
   [testng] Differ	0
   [testng] Unmapped_both	1
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] Match	1
   [testng] Differ	0
   [testng] Unmapped_both	1
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.9160297821854500506.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_dual6981678836051363681.tmp LANE=1 READ_STRUCTURE=25T8B8B25T BARCODE=[CAATAGTCCGACTCTC] METRICS_FILE=/tmp/dual.442547401933358425.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 1 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.8622059371878535341.metrics COMPRESS_OUTPUTS=true    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] ERROR	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Error processing tile 1101
   [testng] htsjdk.samtools.SAMException: Error opening file for writing: s_1_1101_barcode.txt.gz
   [testng] 	at htsjdk.samtools.util.IOUtil.openGzipFileForWriting(IOUtil.java:638)
   [testng] 	at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:576)
   [testng] 	at htsjdk.samtools.util.IOUtil.openFileForBufferedWriting(IOUtil.java:591)
   [testng] 	at htsjdk.samtools.util.IOUtil.openFileForBufferedWriting(IOUtil.java:598)
   [testng] 	at picard.illumina.ExtractIlluminaBarcodes$PerTileBarcodeExtractor.run(ExtractIlluminaBarcodes.java:586)
   [testng] 	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
   [testng] 	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
   [testng] 	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
   [testng] 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
   [testng] 	at java.lang.Thread.run(Thread.java:745)
   [testng] Caused by: java.io.FileNotFoundException: /tmp/eib.6372182154036961472.tmp/s_1_1101_barcode.txt.gz (Permission denied)
   [testng] 	at java.io.FileOutputStream.open0(Native Method)
   [testng] 	at java.io.FileOutputStream.open(FileOutputStream.java:270)
   [testng] 	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
   [testng] 	at htsjdk.samtools.util.IOUtil.openGzipFileForWriting(IOUtil.java:630)
   [testng] 	... 9 more
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] ERROR	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Abandoning metrics calculation because one or more PerTileBarcodeExtractors failed.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=4M21T8B21T4M BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.3232048362774396811.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.971241920797057808.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=25T25T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.2631603821677172342.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_qual2059183522844969252.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAATAGTC] METRICS_FILE=/tmp/qual.3655806322027187122.metrics MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=16    MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 1 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_qual2059183522844969252.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAATAGTC] METRICS_FILE=/tmp/qual.3154376300058758349.metrics MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=25    MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 1 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=25T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.8495867851970441227.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=4M21T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.4112796290465295114.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.5522854761046397817.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.6372182154036961472.tmp LANE=1 READ_STRUCTURE=8B4M21T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.4323572288971222419.metrics    MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
   [testng] INFO	2016-04-27 04:32:02	ExtractIlluminaBarcodes	Processed 3 tiles.
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-qual-header.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/bad-qual-header.txt1760834434212535409.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-seq-header.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/bad-seq-header.txt1239176622089589721.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/extra-line.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/extra-line.txt128478241493817701.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/too-many-quals.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/too-many-quals.txt4671148807712714912.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/1lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/1lines.txt8161759719076139732.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/2lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/2lines.txt9160257549893247697.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/3lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/3lines.txt5685136095521393146.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/sanger_full_range_as_sanger-63.fastq8636403302899733854.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt1677914580660799905.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:02 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/5k-v1-Rhodobacter_LW1.sam.fastq2273611827321451304.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:02 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:02	FastqToSam	Auto-detected quality format as: Standard.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 5000 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1123549184
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/5k-30BB2AAXX.3.aligned.sam.fastq3082455400026360912.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 4952 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/sanger_full_range_as_sanger-63.fastq5370707609287091315.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 1 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt QUALITY_FORMAT=Solexa OUTPUT=/tmp/s_1_sequence.txt5289429189519240103.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Solexa.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 25 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_solexa.fastq QUALITY_FORMAT=Solexa OUTPUT=/tmp/solexa_full_range_as_solexa.fastq6843353648095084783.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Solexa.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 2 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt400327506562879325.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 10 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt1662628352032811789.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 10 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt3354192503210537097.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 10 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-one-more-record.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt5591314340868225016.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-one-more-record.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-one-more-record.txt6278942625231610317.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-badnum.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt4993122061433752492.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-badnum.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-badnum.txt994442487673994144.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-nonum.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-nonum.txt3314506701239535157.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-onetoken.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-onetoken.txt3416141731554445549.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt1152812203042010989.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 5 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_1_sequence.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt5012312889722724529.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 10 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt1763237444289734039.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt489137024933335653.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt7648948734552590467.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair2.txt5524691356084883183.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt2569069566049475317.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt2715541825890711620.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt5462682006370866981.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt4899848993448328306.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 5 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt1095447231179632055.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 10 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt3849122548221590590.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 5 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair2.txt6164061951171377439.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Standard.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 5 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt233919370179205748.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 10 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt5124906862652761612.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 10 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt761683646570685518.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 10 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/single_end_R1_001.fastq5583943659051592392.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 1 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina OUTPUT=/tmp/single_end_R1_001.fastq6580968620585274686.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 1 fastq reads
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 1 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/paired_end_R1_001.fastq6988197272267546765.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 1 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1142947840
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam FASTQ=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq FASTQ2=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina OUTPUT=/tmp/paired_end_R1_001.fastq3610887103128754328.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true    SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:03 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] WARNING	2016-04-27 04:32:03	FastqToSam	Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Auto-detected quality format as: Illumina.
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 1 fastq reads
   [testng] INFO	2016-04-27 04:32:03	FastqToSam	Processed 1 fastq reads
   [testng] [Wed Apr 27 04:32:03 UTC 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=1146617856
   [testng] INFO	2016-04-27 04:32:06	FilterSamReads	Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.9138465523860837283.sam [sortorder=coordinate]
   [testng] INFO	2016-04-27 04:32:06	FilterSamReads	3 SAMRecords written to FilterSamReads.output.9138465523860837283.sam
   [testng] INFO	2016-04-27 04:32:06	FilterSamReads	Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.6167616958107619923.sam [sortorder=coordinate]
   [testng] INFO	2016-04-27 04:32:06	FilterSamReads	0 SAMRecords written to FilterSamReads.output.6167616958107619923.sam
   [testng] [Wed Apr 27 04:32:06 UTC 2016] picard.sam.FixMateInformation INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam] OUTPUT=/tmp/outMissingMateTest4816235926180855869sam IGNORE_MISSING_MATES=false    ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:06 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Sorting input into queryname order.
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Sorting by queryname complete.
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Output will be sorted by coordinate
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Traversing query name sorted records and fixing up mate pair information.
   [testng] [Wed Apr 27 04:32:06 UTC 2016] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:06 UTC 2016] picard.sam.FixMateInformation INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam] OUTPUT=/tmp/outMissingMateTest3416540032250421135sam IGNORE_MISSING_MATES=true    ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:06 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Sorting input into queryname order.
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Sorting by queryname complete.
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Output will be sorted by coordinate
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Traversing query name sorted records and fixing up mate pair information.
   [testng] INFO	2016-04-27 04:32:06	FixMateInformation	Finished processing reads; re-sorting output file.
   [testng] [Wed Apr 27 04:32:06 UTC 2016] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.sam.GatherBamFiles INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam] OUTPUT=/tmp/gatherBamFilesTest.samFile.3656187782910889660.bam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam ...
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	8
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	10
   [testng] SAM files differ.
   [testng] Match	10
   [testng] Differ	0
   [testng] Unmapped_both	8
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam ...
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.sam.GatherBamFiles done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.sam.GatherBamFiles INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam] OUTPUT=/tmp/gatherBamFilesTest.samFile.7140219071734966279.bam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam ...
   [testng] INFO	2016-04-27 04:32:07	BamFileIoUtils	Block copying /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam ...
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.sam.GatherBamFiles done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERVALS=[testdata/picard/vcf/IntervalListChr1Small.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting to load intervals list(s).
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Finished loading up intervals list(s).
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 1
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalListChr1Small.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting to load intervals list(s).
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Finished loading up intervals list(s).
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/NIST.selected.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalList1PerChrom.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting to load intervals list(s).
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Finished loading up intervals list(s).
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-indels.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-indels.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 3
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_del_line.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=true USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=40 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=40 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance    TRUTH_VCF=testdata/picard/vcf/NIST.selected.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest8274243698751771459.tmp/actualGtConc TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalList1PerChrom.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting to load intervals list(s).
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Finished loading up intervals list(s).
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Starting iteration over variants.
   [testng] INFO	2016-04-27 04:32:07	GenotypeConcordance	Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MULTIPLEX_PARAMS=/tmp/multiplexedBarcode.5945846678538221486.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100    ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	IlluminaBasecallsToFastq	READ STRUCTURE IS 25T8B25T
   [testng] INFO	2016-04-27 04:32:07	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=742391808
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B4M21T MULTIPLEX_PARAMS=/tmp/multiplexedBarcodeWithIndex.6491537262989753706.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100    ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:07 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:07	IlluminaBasecallsToFastq	READ STRUCTURE IS 25T8B4M21T
   [testng] INFO	2016-04-27 04:32:07	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:07 UTC 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=760741888
   [testng] INFO	2016-04-27 04:32:07	IlluminaBasecallsConverter	All work is complete.
   [testng] INFO	2016-04-27 04:32:07	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B4M4M17T MULTIPLEX_PARAMS=/tmp/multiplexedBarcodeWithTwoIndexes.27894293965540326.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100    ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:08 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsToFastq	READ STRUCTURE IS 25T8B4M4M17T
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=762314752
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B8B25T MULTIPLEX_PARAMS=/tmp/dualBarcode.1014607042215001779.dir/barcode_double.params MAX_READS_IN_RAM_PER_TILE=100    ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:08 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsToFastq	READ STRUCTURE IS 25T8B8B25T
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=792199168
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=/tmp/testMultiplexRH.2099410989477614367.dir/testMultiplexRH RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MAX_READS_IN_RAM_PER_TILE=100 READ_NAME_FORMAT=ILLUMINA    ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:08 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsToFastq	READ STRUCTURE IS 25T8B25T
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=792199168
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=/tmp/nonBarcoded.7035851923705556603 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MAX_READS_IN_RAM_PER_TILE=100    ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:08 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsToFastq	READ STRUCTURE IS 25T8B25T
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=792199168
   [testng] [Wed Apr 27 04:32:08 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam2229772271919218918.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias READ_STRUCTURE=125T125T    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:08 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:08	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 125T125T
   [testng] Ouput Sam file is in /tmp/.1.illuminaBasecallsToSam2229772271919218918.sam
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=792199168
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam4323417183366550688.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias READ_STRUCTURE=125T125T    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 125T125T
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=821559296
   [testng] Ouput Sam file is in /tmp/.2.illuminaBasecallsToSam4323417183366550688.sam
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/multiplexedBarcode.4984624805005440662.dir/barcode.params    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 25T8B25T
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=821559296
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom READ_STRUCTURE=25T8B4M4M17T LIBRARY_PARAMS=/tmp/multiplexedBarcode2.5372016613466628747.dir/barcode.params    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 25T8B4M4M17T
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=821559296
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom READ_STRUCTURE=25T8B4M21T LIBRARY_PARAMS=/tmp/multiplexedBarcode.75846623024703114.dir/barcode.params    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 25T8B4M21T
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=821559296
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/singleBarcodeAltName.8685974540310863380.dir/multiplexed_positive_rgtags.params    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 25T8B25T
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=942145536
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/nonBarcoded.3755115211413742176.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World READ_STRUCTURE=25S8S25T    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 25S8S25T
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=942145536
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/nonBarcodedWithDualMI.1434730916707362754.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World READ_STRUCTURE=25S4M4M25T    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:09 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 25S4M4M25T
   [testng] INFO	2016-04-27 04:32:09	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:09 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=942145536
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/nonBarcodedWithMI.5387339279391620105.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World READ_STRUCTURE=25S8M25T    SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:10	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 25S8M25T
   [testng] INFO	2016-04-27 04:32:10	IlluminaBasecallsConverter	All work is complete.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=942145536
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest5552234075153637191.tmp/test.illumina_lane_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest5552234075153637191.tmp/test.illumina_phasing_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest8155090111179797759.tmp/test.illumina_lane_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest8155090111179797759.tmp/test.illumina_phasing_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest7785656334933260843.tmp/test.illumina_lane_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest7785656334933260843.tmp/test.illumina_phasing_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest2340094342684430266.tmp/test.illumina_lane_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest2340094342684430266.tmp/test.illumina_phasing_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest8750606504987652734.tmp/test.illumina_lane_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 0 lane metrics to /tmp/illuminaLaneMetricsCollectorTest8750606504987652734.tmp/test.illumina_phasing_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest8087966105880012051.tmp/test.illumina_lane_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest8087966105880012051.tmp/test.illumina_phasing_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest7269670890070099560.tmp/test.illumina_lane_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest7269670890070099560.tmp/test.illumina_phasing_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest3505665566845575686.tmp/test.illumina_lane_metrics ...
   [testng] INFO	2016-04-27 04:32:10	IlluminaLaneMetricsCollector	Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest3505665566845575686.tmp/test.illumina_phasing_metrics ...
   [testng] idealSplitLength=100
   [testng] idealSplitLength=50
   [testng] idealSplitLength=40
   [testng] idealSplitLength=99
   [testng] idealSplitLength=100
   [testng] idealSplitLength=200
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.util.IntervalListToBed INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/util/interval_list_to_bed_test.interval_list OUTPUT=/tmp/interval_list_to_bed_test_output645563119463385997.bed SCORE=333    SORT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.util.IntervalListToBed done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.vcf.LiftoverVcf INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/testLiftover.vcf OUTPUT=/tmp/LiftoverVcfsTest3324305198305653482.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/test.over.chain REJECT=/tmp/LiftoverVcfsTest3324305198305653482.tmp/reject-delete-me.vcf REFERENCE_SEQUENCE=testdata/picard/vcf/dummy.reference.fasta CREATE_INDEX=false    WARN_ON_MISSING_CONTIG=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] Time taken: 306ms.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Loading up the target reference genome.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Lifting variants over and sorting.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Processed 2 variants.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	2 variants failed to liftover.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	100.0000% of variants were not successfully lifted over and written to the output.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Writing out sorted records to final VCF.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.vcf.LiftoverVcf INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/testLiftoverUsingMissingContig.vcf OUTPUT=/tmp/LiftoverVcfsTest3324305198305653482.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/test.over.badContig.chain REJECT=/tmp/LiftoverVcfsTest3324305198305653482.tmp/reject-delete-me.vcf REFERENCE_SEQUENCE=testdata/picard/vcf/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Loading up the target reference genome.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Lifting variants over and sorting.
   [testng] ERROR	2016-04-27 04:32:10	LiftoverVcf	Encountered a contig, missingContig that is not part of the target reference.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.vcf.LiftoverVcf INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/testLiftoverUsingMissingContig.vcf OUTPUT=/tmp/LiftoverVcfsTest3324305198305653482.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/test.over.badContig.chain REJECT=/tmp/LiftoverVcfsTest3324305198305653482.tmp/reject-delete-me.vcf REFERENCE_SEQUENCE=testdata/picard/vcf/dummy.reference.fasta WARN_ON_MISSING_CONTIG=true CREATE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Loading up the target reference genome.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Lifting variants over and sorting.
   [testng] WARNING	2016-04-27 04:32:10	LiftoverVcf	Encountered a contig, missingContig that is not part of the target reference.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Processed 2 variants.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	2 variants failed to liftover.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	100.0000% of variants were not successfully lifted over and written to the output.
   [testng] INFO	2016-04-27 04:32:10	LiftoverVcf	Writing out sorted records to final VCF.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.7596987274514880561.sam ALIGNED_BAM=[/tmp/aligned.5159504187332576084.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndincludeSecondary2084662698291949497.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:10	SamAlignmentMerger	[/tmp/aligned.5159504187332576084.sam]
   [testng] INFO	2016-04-27 04:32:10	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2376380577866829537.sam ALIGNED_BAM=[/tmp/aligned.869836458655868011.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndexcludeSecondary8020841920895193632.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:10	SamAlignmentMerger	[/tmp/aligned.869836458655868011.sam]
   [testng] INFO	2016-04-27 04:32:10	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.7497964272428269119.sam ALIGNED_BAM=[/tmp/aligned.5541541900430516161.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndincludeSecondary5039926742877062865.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:10	SamAlignmentMerger	[/tmp/aligned.5541541900430516161.sam]
   [testng] INFO	2016-04-27 04:32:10	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.4399604209652840157.sam ALIGNED_BAM=[/tmp/aligned.2582644941559676888.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndexcludeSecondary3945596620813944875.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:10	SamAlignmentMerger	[/tmp/aligned.2582644941559676888.sam]
   [testng] INFO	2016-04-27 04:32:10	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.500845671376591875.sam ALIGNED_BAM=[/tmp/aligned.1340197544016553098.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndincludeSecondary4695020849437942261.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:10 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:10	SamAlignmentMerger	[/tmp/aligned.1340197544016553098.sam]
   [testng] INFO	2016-04-27 04:32:10	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:10 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6480778524429298433.sam ALIGNED_BAM=[/tmp/aligned.6132676661342842158.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndexcludeSecondary3963034326972876492.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.6132676661342842158.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.4693886022282637503.sam ALIGNED_BAM=[/tmp/aligned.2596640979972807018.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds1includeSecondary6923519559598394080.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.2596640979972807018.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 10 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.5882689493871518793.sam ALIGNED_BAM=[/tmp/aligned.1492702834470802006.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds1excludeSecondary6960179561913748927.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.1492702834470802006.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 10 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.603620778728791366.sam ALIGNED_BAM=[/tmp/aligned.7164279745001618187.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds2includeSecondary2559820995074112917.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.7164279745001618187.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 5 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2658724897582910464.sam ALIGNED_BAM=[/tmp/aligned.596862559144774536.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds2excludeSecondary3611162480793515684.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.596862559144774536.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 5 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.7517116203268474691.sam ALIGNED_BAM=[/tmp/aligned.7703813426700777620.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndincludeSecondary868806193865552762.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.7703813426700777620.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.11109570215790287.sam ALIGNED_BAM=[/tmp/aligned.3563986550423961672.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndexcludeSecondary4101640801100238793.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.3563986550423961672.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=933232640
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1636323004749184345.sam ALIGNED_BAM=[/tmp/aligned.4083976341483983028.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleSecondEndincludeSecondary3878379838075054126.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.4083976341483983028.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2123295972667390800.sam ALIGNED_BAM=[/tmp/aligned.8757223323096368054.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleSecondEndexcludeSecondary7296309233533816691.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.8757223323096368054.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.7376974909728834036.sam ALIGNED_BAM=[/tmp/aligned.7296709320021880618.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndincludeSecondary7038720119968151710.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.7296709320021880618.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 6 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.8111967275032391659.sam ALIGNED_BAM=[/tmp/aligned.3644129656704152801.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndexcludeSecondary6048187983004335856.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.3644129656704152801.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 6 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1152965180327097604.sam ALIGNED_BAM=[/tmp/aligned.2329220275432541296.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndincludeSecondary2609647911999384751.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.2329220275432541296.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 6 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.5339767570839537691.sam ALIGNED_BAM=[/tmp/aligned.2749583681045043055.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndexcludeSecondary818702413520612029.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.2749583681045043055.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 6 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged6096396347301506758.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 UNMAP_CONTAMINANT_READS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam]
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_multiple_primary_1 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_multiple_primary_1 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_primary_clipped 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_primary_clipped 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_primary_clipped 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_clipped 1/2 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_clipped 2/2 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_perfect 1/2 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_perfect 2/2 50b aligned read.
   [testng] WARNING	2016-04-27 04:32:11	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_unmapped 1/2 50b aligned read.
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 4 alignment records and 11 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged6096396347301506758.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1684603773125740928.sam ALIGNED_BAM=[/tmp/aligned.6937897410735578241.sam] OUTPUT=/tmp/simpleForward5665984809586266849.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.6937897410735578241.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 1 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] No errors found
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2514653522765907765.sam ALIGNED_BAM=[/tmp/aligned.1007210428146551583.sam] OUTPUT=/tmp/simpleReverse2708999884487474829.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.1007210428146551583.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 1 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.8150952808154811489.sam ALIGNED_BAM=[/tmp/aligned.4107758083414349693.sam] OUTPUT=/tmp/2 forward one earlier1260896958829597215.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.4107758083414349693.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1166029403645873650.sam ALIGNED_BAM=[/tmp/aligned.672864284371912100.sam] OUTPUT=/tmp/forward earlier than reverse2097660099174091372.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.672864284371912100.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6228286426561395357.sam ALIGNED_BAM=[/tmp/aligned.6618388604269270181.sam] OUTPUT=/tmp/reverse earlier than forward8462290950947120396.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.6618388604269270181.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.183093175314297000.sam ALIGNED_BAM=[/tmp/aligned.1811514014646277393.sam] OUTPUT=/tmp/tie resolved via MAPQ6535369794227979802.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.1811514014646277393.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2259894958514159051.sam ALIGNED_BAM=[/tmp/aligned.9000456330352489117.sam] OUTPUT=/tmp/tie with same MAPQ resolved arbitrarily2462102332790871552.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.9000456330352489117.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1165450800344350938.sam ALIGNED_BAM=[/tmp/aligned.3013443430962646125.sam] OUTPUT=/tmp/one cigar with deletion and higher MAPQ7718974694647778039.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.3013443430962646125.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.4572965573101458544.sam ALIGNED_BAM=[/tmp/aligned.6021172757270926573.sam] OUTPUT=/tmp/one cigar with deletion and lower MAPQ8505523385914109257.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.6021172757270926573.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.281660508736488604.sam ALIGNED_BAM=[/tmp/aligned.5463208227925179159.sam] OUTPUT=/tmp/Insertion makes alignment later4670577920781442066.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.5463208227925179159.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.8937134058339501936.sam ALIGNED_BAM=[/tmp/aligned.7698445406225297396.sam] OUTPUT=/tmp/one cigar with deletion and higher MAPQ -- reverse3154374989644435499.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.7698445406225297396.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=940572672
   [testng] No errors found
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6258642526666474507.sam ALIGNED_BAM=[/tmp/aligned.6892774425497310951.sam] OUTPUT=/tmp/one cigar with deletion and lower MAPQ -- reverse3829767183440673322.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.6892774425497310951.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2464144621577439329.sam ALIGNED_BAM=[/tmp/aligned.7053546790675228599.sam] OUTPUT=/tmp/Insertion makes alignment later -- reverse1053292900624540500.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.7053546790675228599.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.8829004315729958542.sam ALIGNED_BAM=[/tmp/aligned.2491048210998740088.sam] OUTPUT=/tmp/mergeTest4234032671766489993.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.2491048210998740088.sam]
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8884265484860057989.sam] OUTPUT=/tmp/merged.2575534670250511921.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.8884265484860057989.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.2575534670250511921.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8359699178236319794.sam] OUTPUT=/tmp/merged.8269462721529353824.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.8359699178236319794.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.8269462721529353824.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.5020550226306248262.sam] OUTPUT=/tmp/merged.1211221768546597796.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.5020550226306248262.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.1211221768546597796.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8618556000836902051.sam] OUTPUT=/tmp/merged.7266881257327339435.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.8618556000836902051.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 1 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.7266881257327339435.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.2798931178513488225.sam] OUTPUT=/tmp/merged.8821007326799883548.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.2798931178513488225.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 0 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.8821007326799883548.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/aligned.sam] OUTPUT=/tmp/mergeTest6880165885811657339.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/aligned.sam]
   [testng] WARNING	2016-04-27 04:32:11	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned read. > both_reads_align_clip_adapter 2/2 101b aligned read.
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	Finished reading 8 total records from alignment SAM/BAM.
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/aligned.sam] OUTPUT=/tmp/mergeTest6880165885811657339.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/aligned.sam]
   [testng] WARNING	2016-04-27 04:32:11	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned read. > both_reads_align_clip_adapter 2/2 101b aligned read.
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	Finished reading 8 total records from alignment SAM/BAM.
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/onehalfaligned.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/otherhalfaligned.sam] OUTPUT=/tmp/mergeTest551045672920584312.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/onehalfaligned.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/otherhalfaligned.sam]
   [testng] WARNING	2016-04-27 04:32:11	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: both_reads_present_only_first_aligns 1/2 101b aligned read. > both_reads_align_clip_adapter 2/2 101b aligned read.
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	Finished reading 8 total records from alignment SAM/BAM.
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam] OUTPUT=/tmp/mergeWithSupplementalTest4961757540124857596.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 8 alignment records and 4 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam READ1_ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam] READ2_ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam] OUTPUT=/tmp/mergeMultipleAlignmentsTest3595223794515166962.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 READ1_TRIM=17 READ2_TRIM=20 EXPECTED_ORIENTATIONS=[FR]    ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 8 alignment records and 4 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam READ1_ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam] READ2_ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam] OUTPUT=/tmp/mergeMultipleAlignmentsTest3382489092078927081.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 READ1_TRIM=17 READ2_TRIM=20 EXPECTED_ORIENTATIONS=[FR]    ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[]
   [testng] WARNING	2016-04-27 04:32:11	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: test:6 1/2 36b aligned read. > test:2 1/2 36b aligned read.
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	Finished reading 12 total records from alignment SAM/BAM.
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 8 alignment records and 4 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6359067242215913384.sam ALIGNED_BAM=[/tmp/aligned.4794009838650726547.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.includeSecondary1364951509365598601.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.4794009838650726547.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 14 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.7356540938223395575.sam ALIGNED_BAM=[/tmp/aligned.3034755993029010362.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.excludeSecondary8530221878731514916.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.3034755993029010362.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 14 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.9122854767774074029.sam ALIGNED_BAM=[/tmp/aligned.4857923992183307400.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.includeSecondary8504973916837946057.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.4857923992183307400.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 14 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6223895383397283666.sam ALIGNED_BAM=[/tmp/aligned.3643638472109537366.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.excludeSecondary2804413573086281258.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.3643638472109537366.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 14 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.8989922794412283475.sam ALIGNED_BAM=[/tmp/aligned.2006547852481875760.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.includeSecondary1622239859239935558.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.2006547852481875760.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 8 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.5684320481723276917.sam ALIGNED_BAM=[/tmp/aligned.5097754368345038225.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.excludeSecondary4516583273051383338.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.5097754368345038225.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 8 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.4418404434756526122.sam ALIGNED_BAM=[/tmp/aligned.1134974183870274651.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.includeSecondary7019425838109750896.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.1134974183870274651.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 8 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.750576325576322447.sam ALIGNED_BAM=[/tmp/aligned.586257847805422246.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.excludeSecondary7942215785240242226.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.586257847805422246.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 8 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.unmapped.sam ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam] OUTPUT=/tmp/merged960209704903319464.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 20 alignment records and 7 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged960209704903319464.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.badorder.sam ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam] OUTPUT=/tmp/merged1501127899840028675.bam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam]
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7622304044119401417.sam] OUTPUT=/tmp/merged.2045906986507758457.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.7622304044119401417.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.2045906986507758457.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.4632442953244586569.sam] OUTPUT=/tmp/merged.291977966042992873.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.4632442953244586569.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.291977966042992873.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8928904322411589868.sam] OUTPUT=/tmp/merged.2172268592223567738.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:11 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:11	SamAlignmentMerger	[/tmp/aligned.8928904322411589868.sam]
   [testng] INFO	2016-04-27 04:32:11	AbstractAlignmentMerger	Wrote 0 alignment records and 2 unmapped reads.
   [testng] [Wed Apr 27 04:32:11 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.2172268592223567738.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.6103953066241613380.sam] OUTPUT=/tmp/merged.8089051978660848130.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.6103953066241613380.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 0 alignment records and 2 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.8089051978660848130.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=932184064
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.2115179662178126345.sam] OUTPUT=/tmp/merged.6562492285404748516.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.2115179662178126345.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.6562492285404748516.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.457664221309657119.sam] OUTPUT=/tmp/merged.6393783958190055444.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.457664221309657119.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 4 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.6393783958190055444.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8700172453968536485.sam] OUTPUT=/tmp/merged.4195362315398702403.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.8700172453968536485.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.4195362315398702403.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.5612829628997730432.sam] OUTPUT=/tmp/merged.5638799090554628513.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.5612829628997730432.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.5638799090554628513.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7854504021462441573.sam] OUTPUT=/tmp/merged.7914958315472463641.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.7854504021462441573.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 3 alignment records and 1 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.7914958315472463641.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.4463352172559336614.sam] OUTPUT=/tmp/merged.4015691229147824016.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.4463352172559336614.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.4015691229147824016.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8746528662240505565.sam] OUTPUT=/tmp/merged.3578573426008710008.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.8746528662240505565.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 5 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.3578573426008710008.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7000389203788422624.sam] OUTPUT=/tmp/merged.8815580392708525348.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.7000389203788422624.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 5 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.8815580392708525348.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7446985393740340412.sam] OUTPUT=/tmp/merged.6646299791795354217.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/tmp/aligned.7446985393740340412.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 0 alignment records and 2 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.6646299791795354217.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.sam ALIGNED_BAM=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam] OUTPUT=/tmp/testShortFragmentClipping573825003017805487.sam REFERENCE_SEQUENCE=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 10 alignment records and 0 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[testdata/picard/sam/aligned_queryname_sorted.sam]
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
   [testng] No errors found
   [testng] No errors found
   [testng] No errors found
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	[testdata/picard/sam/aligned.sam]
   [testng] WARNING	2016-04-27 04:32:12	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned read. > both_reads_align_clip_adapter 2/2 101b aligned read.
   [testng] INFO	2016-04-27 04:32:12	SamAlignmentMerger	Finished reading 8 total records from alignment SAM/BAM.
   [testng] INFO	2016-04-27 04:32:12	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeSamFiles INPUT=[/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/1.sam, /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/2.sam] OUTPUT=/tmp/unsortedInputSortedOutputTest.1506846836919836662.bam SORT_ORDER=coordinate    ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	MergeSamFiles	Sorting input files using temp directory [/tmp/buildd]
   [testng] INFO	2016-04-27 04:32:12	MergeSamFiles	Finished reading inputs.
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile INPUT=/tmp/unsortedInputSortedOutputTest.1506846836919836662.bam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.reference.NonNFastaSize INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/reference/test.fasta OUTPUT=/tmp/nonNcount1718564147337207896.txt    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.reference.NonNFastaSize done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.reference.NonNFastaSize INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/reference/test.fasta OUTPUT=/tmp/nonNcount1060408623406766238.txt INTERVALS=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/reference/test.intervals    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.reference.NonNFastaSize done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [1m[31mUSAGE: PicardCommandLine [32m<program name>[1m[31m [-h]
   [testng] 
   [testng] [0m[1m[31mAvailable Programs:
   [testng] [0m[37m--------------------------------------------------------------------------------------
   [testng] [0m[31mAlpha Tools:                                     Tools that are currently UNSUPPORTED until further testing and maturation.[0m
   [testng] [32m    CheckFingerprint                             [36mComputes a fingerprint from the supplied SAM/BAM file and compares it to the provided genotypes[0m
   [testng] [32m    CrosscheckReadGroupFingerprints              [36mChecks if all read groups appear to come from the same individual[0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] [0m[31mFasta:                                           Tools for manipulating FASTA, or related data.[0m
   [testng] [32m    CreateSequenceDictionary                     [36mCreates a sequence dictionary for a reference sequence.  [0m
   [testng] [32m    ExtractSequences                             [36mSubsets intervals from a reference sequence to a new FASTA file.[0m
   [testng] [32m    NonNFastaSize                                [36mCounts the number of non-N bases in a fasta file.[0m
   [testng] [32m    NormalizeFasta                               [36mNormalizes lines of sequence in a FASTA file to be of the same length.[0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] [0m[31mIllumina Tools:                                  Tools for manipulating data specific to Illumina sequencers.[0m
   [testng] [32m    CheckIlluminaDirectory                       [36mAsserts the validity of the data in the specified Illumina basecalling data[0m
   [testng] [32m    CollectIlluminaBasecallingMetrics            [36mGiven an Illumina basecalling and a lane, produces per-lane-barcode basecalling metrics[0m
   [testng] [32m    CollectIlluminaLaneMetrics                   [36mCollects Illumina lane metrics for the given basecalling analysis directory[0m
   [testng] [32m    ExtractIlluminaBarcodes                      [36mTool to determine the barcode for each read in an Illumina lane[0m
   [testng] [32m    IlluminaBasecallsToFastq                     [36mGenerate fastq file(s) from data in an Illumina basecalls output directory[0m
   [testng] [32m    IlluminaBasecallsToSam                       [36mGenerate a SAM or BAM file from data in an Illumina basecalls output directory[0m
   [testng] [32m    MarkIlluminaAdapters                         [36mReads a SAM or BAM file and rewrites it with new adapter-trimming tags[0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] [0m[31mInterval Tools:                                  Tools for manipulating Picard interval lists.[0m
   [testng] [32m    BedToIntervalList                            [36mConverts a BED file to a Picard Interval List.  [0m
   [testng] [32m    IntervalListToBed                            [36mConverts an Picard IntervalList file to a BED file.[0m
   [testng] [32m    IntervalListTools                            [36mManipulates interval lists.  [0m
   [testng] [32m    LiftOverIntervalList                         [36mLifts over an interval list from one reference build to another.  [0m
   [testng] [32m    ScatterIntervalsByNs                         [36mWrites an interval list based on splitting the reference by Ns.  [0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] [0m[31mMetrics:                                         Tools for reporting metrics on various data types.[0m
   [testng] [32m    CalculateHsMetrics                           [36mDEPRECATED: Use CollectHsMetrics instead.[0m
   [testng] [32m    CollectAlignmentSummaryMetrics               [36mProduce a summary of alignment metrics from a SAM or BAM file[0m
   [testng] [32m    CollectBaseDistributionByCycle               [36mChart the nucleotide distribution per cycle in a SAM or BAM file[0m
   [testng] [32m    CollectGcBiasMetrics                         [36mCollect metrics regarding GC bias. [0m
   [testng] [32m    CollectHiSeqXPfFailMetrics                   [36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.[0m
   [testng] [32m    CollectHsMetrics                             [36mCollects Hybrid Selection-specific metrics for a SAM or BAM file[0m
   [testng] [32m    CollectInsertSizeMetrics                     [36mCollect metrics about the insert size distribution of a paired-end library.[0m
   [testng] [32m    CollectJumpingLibraryMetrics                 [36mCollect jumping library metrics. [0m
   [testng] [32m    CollectMultipleMetrics                       [36mCollect multiple classes of metrics.  [0m
   [testng] [32m    CollectOxoGMetrics                           [36mCollect metrics to assess oxidative artifacts.[0m
   [testng] [32m    CollectQualityYieldMetrics                   [36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters.  [0m
   [testng] [32m    CollectRawWgsMetrics                         [36mCollect whole genome sequencing-related metrics.  [0m
   [testng] [32m    CollectRnaSeqMetrics                         [36mProduces RNA alignment metrics for a SAM or BAM file[0m
   [testng] [32m    CollectRrbsMetrics                           [36mCollect metrics from reduced representation bisulfite sequencing (RRBS) data.  [0m
   [testng] [32m    CollectSequencingArtifactMetrics             [36mCollect metrics to quantify single-base sequencing artifacts.[0m
   [testng] [32m    CollectTargetedPcrMetrics                    [36mCalculate PCR-related metrics from targeted sequencing data. [0m
   [testng] [32m    CollectVariantCallingMetrics                 [36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file[0m
   [testng] [32m    CollectWgsMetrics                            [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.[0m
   [testng] [32m    CollectWgsMetricsFromQuerySorted             [36mWrites sequencing-related metrics for a SAM or BAM file[0m
   [testng] [32m    CollectWgsMetricsFromSampledSites            [36mWrites whole genome sequencing-related metrics for a SAM or BAM file[0m
   [testng] [32m    CompareMetrics                               [36mCompare two metrics files.[0m
   [testng] [32m    ConvertSequencingArtifactToOxoG              [36mExtract OxoG metrics from generalized artifacts metrics[0m
   [testng] [32m    EstimateLibraryComplexity                    [36mEstimates library complexity.   [0m
   [testng] [32m    MeanQualityByCycle                           [36mCollect mean quality by cycle.[0m
   [testng] [32m    QualityScoreDistribution                     [36mChart the distribution of quality scores.  [0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] [0m[31mMiscellaneous Tools:                             A set of miscellaneous tools.                [0m
   [testng] [32m    BaitDesigner                                 [36mDesigns baits or oligos for hybrid selection reactions.[0m
   [testng] [32m    FifoBuffer                                   [36mFIFO buffer used to buffer input and output streams with a customizable buffer size [0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] [0m[31mSAM/BAM:                                         Tools for manipulating SAM, BAM, or related data.[0m
   [testng] [32m    AddCommentsToBam                             [36mAdds comments to the header of a BAM file.[0m
   [testng] [32m    AddOrReplaceReadGroups                       [36mReplace read groups in a BAM file.[0m
   [testng] [32m    BamIndexStats                                [36mGenerate index statistics from a BAM file[0m
   [testng] [32m    BamToBfq                                     [36mCreate BFQ files from a BAM file for use by the maq aligner.  [0m
   [testng] [32m    BuildBamIndex                                [36mGenerates a BAM index ".bai" file.  [0m
   [testng] [32m    CalculateReadGroupChecksum                   [36mCreates a hash code based on the read groups (RG).  [0m
   [testng] [32m    CheckTerminatorBlock                         [36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise[0m
   [testng] [32m    CleanSam                                     [36mCleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads[0m
   [testng] [32m    CompareSAMs                                  [36mCompare two input ".sam" or ".bam" files.  [0m
   [testng] [32m    DownsampleSam                                [36mDownsample a SAM or BAM file.  [0m
   [testng] [32m    FastqToSam                                   [36mConverts a FASTQ file to an unaligned BAM or SAM file.  [0m
   [testng] [32m    FilterSamReads                               [36mSubset read data from a SAM or BAM file[0m
   [testng] [32m    FixMateInformation                           [36mVerify mate-pair information between mates and fix if needed.[0m
   [testng] [32m    GatherBamFiles                               [36mConcatenate one or more BAM files as efficiently as possible[0m
   [testng] [32m    MarkDuplicates                               [36mIdentifies duplicate reads.  [0m
   [testng] [32m    MarkDuplicatesWithMateCigar                  [36mIdentifies duplicate reads, accounting for mate CIGAR.  [0m
   [testng] [32m    MergeBamAlignment                            [36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file.  [0m
   [testng] [32m    MergeSamFiles                                [36mMerges multiple SAM and/or BAM files into a single file.  [0m
   [testng] [32m    PositionBasedDownsampleSam                   [36mDownsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.[0m
   [testng] [32m    ReorderSam                                   [36mReorders reads in a SAM or BAM file to match ordering in reference[0m
   [testng] [32m    ReplaceSamHeader                             [36mReplaces the SAMFileHeader in a SAM or BAM file.  [0m
   [testng] [32m    RevertOriginalBaseQualitiesAndAddMateCigar   [36mReverts the original base qualities and adds the mate cigar tag to read-group BAMs[0m
   [testng] [32m    RevertSam                                    [36mReverts SAM or BAM files to a previous state.  [0m
   [testng] [32m    SamFormatConverter                           [36mConvert a BAM file to a SAM file, or a SAM to a BAM[0m
   [testng] [32m    SamToFastq                                   [36mConverts a SAM or BAM file to FASTQ.  [0m
   [testng] [32m    SortSam                                      [36mSorts a SAM or BAM file.  [0m
   [testng] [32m    SplitSamByLibrary                            [36mSplits a SAM or BAM file into individual files by library[0m
   [testng] [32m    ValidateSamFile                              [36mValidates a SAM or BAM file.  [0m
   [testng] [32m    ViewSam                                      [36mPrints a SAM or BAM file to the screen[0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] [0m[31mUnit Testing:                                    Unit testing                                 [0m
   [testng] [32m    SimpleMarkDuplicatesWithMateCigar            [36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.[0m
   [testng] [32m    TestParserFail                               [36mThis tool offers.....[0m
   [testng] [32m    TestParserSucceed                            [36m X &lt; Y [0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] [0m[31mVCF/BCF:                                         Tools for manipulating VCF, BCF, or related data.[0m
   [testng] [32m    FilterVcf                                    [36mHard filters a VCF.[0m
   [testng] [32m    GatherVcfs                                   [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
   [testng] [32m    GenotypeConcordance                          [36mEvaluate genotype concordance between callsets.[0m
   [testng] [32m    LiftoverVcf                                  [36mLifts over a VCF file from one reference build to another.  [0m
   [testng] [32m    MakeSitesOnlyVcf                             [36mCreates a VCF bereft of genotype information from an input VCF or BCF[0m
   [testng] [32m    MergeVcfs                                    [36mMerges multiple VCF or BCF files into one VCF file or BCF[0m
   [testng] [32m    RenameSampleInVcf                            [36mRenames a sample within a VCF or BCF.  [0m
   [testng] [32m    SortVcf                                      [36mSorts one or more VCF files.  [0m
   [testng] [32m    SplitVcfs                                    [36mSplits SNPs and INDELs into separate files.  [0m
   [testng] [32m    UpdateVcfSequenceDictionary                  [36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.[0m
   [testng] [32m    VcfFormatConverter                           [36mConverts VCF to BCF or BCF to VCF.  [0m
   [testng] [32m    VcfToIntervalList                            [36mConverts a VCF or BCF file to a Picard Interval List.[0m
   [testng] 
   [testng] [37m--------------------------------------------------------------------------------------
   [testng] 
   [testng] [0m'' is not a valid command. See PicardCommandLine --help for more information.
   [testng] FRACTION must be a value between 0 and 1, found: -1.0
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] FRACTION must be a value between 0 and 1, found: -1.0E-5
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] FRACTION must be a value between 0 and 1, found: -5.0
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] No errors found
   [testng] FRACTION must be a value between 0 and 1, found: 1.00001
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] FRACTION must be a value between 0 and 1, found: 5.0
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] FRACTION must be a value between 0 and 1, found: 50.0
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] FRACTION must be a value between 0 and 1, found: 1.7976931348623157E308
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] FRACTION must be a value between 0 and 1, found: Infinity
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] FRACTION must be a value between 0 and 1, found: -Infinity
   [testng] USAGE: PositionBasedDownsampleSam [options]
   [testng] 
   [testng] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
   [testng] 
   [testng] Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither 
   [testng] end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence 
   [testng] the read came from. The downsampling is based on this position. Results with the exact same input will produce the 
   [testng] same results.
   [testng] 
   [testng] Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
   [testng] BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. 
   [testng] This has been designed with Illumina MiSeq/HiSeq in mind.
   [testng] Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
   [testng] Note 3: Downsampling twice with this program is not supported.
   [testng] Note 4: You should call MarkDuplicates after downsampling.
   [testng] 
   [testng] Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample 
   [testng] fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling 
   [testng] percentage will not be accurately determined by the input argument FRACTION.
   [testng] Version: null
   [testng] 
   [testng] 
   [testng] Options:
   [testng] 
   [testng] --help
   [testng] -h                            Displays options specific to this tool.
   [testng] 
   [testng] --stdhelp
   [testng] -H                            Displays options specific to this tool AND options common to all Picard command line 
   [testng]                               tools.
   [testng] 
   [testng] --version                     Displays program version.
   [testng] 
   [testng] INPUT=File
   [testng] I=File                        The input SAM or BAM file to downsample.  Required. 
   [testng] 
   [testng] OUTPUT=File
   [testng] O=File                        The output, downsampled, SAM or BAM file to write.  Required. 
   [testng] 
   [testng] FRACTION=Double
   [testng] F=Double                      The (approximate) fraction of reads to be kept, between 0 and 1.  Required. 
   [testng] 
   [testng] STOP_AFTER=Long               Stop after processing N reads, mainly for debugging.  Default value: null. 
   [testng] 
   [testng] ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
   [testng]                               Allow Downsampling again despite this being a bad idea with possibly unexpected results.  
   [testng]                               Default value: false. This option can be set to 'null' to clear the default value. 
   [testng]                               Possible values: {true, false} 
   [testng] 
   [testng] REMOVE_DUPLICATE_INFORMATION=Boolean
   [testng]                               Determines whether the duplicate tag should be reset since the downsampling requires 
   [testng]                               re-marking duplicates.  Default value: true. This option can be set to 'null' to clear 
   [testng]                               the default value. Possible values: {true, false} 
   [testng] 
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam7006439003206799986.bam FRACTION=0.1    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Second pass done.
   [testng] WARNING	2016-04-27 04:32:12	PositionBasedDownsampleSam	You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.069400.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Finished! Kept 1388 out of 20000 reads (P=0.0694000).
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam7006439003206799986.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam2225548055143513144.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=true    REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] WARNING	2016-04-27 04:32:12	PositionBasedDownsampleSam	Found previous Program Record that indicates that this BAM has been downsampled already with this program. Operation not supported! Previous PG: SAMProgramRecord{PN=PositionBasedDownsampleSam, CL=picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam7006439003206799986.bam FRACTION=0.1    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json}
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Second pass done.
   [testng] WARNING	2016-04-27 04:32:12	PositionBasedDownsampleSam	You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.998559.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Finished! Kept 1386 out of 1388 reads (P=0.998559).
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam5683296134219665331.bam FRACTION=0.1    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Second pass done.
   [testng] WARNING	2016-04-27 04:32:12	PositionBasedDownsampleSam	You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.069400.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Finished! Kept 1388 out of 20000 reads (P=0.0694000).
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam5683296134219665331.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4829867238039001676.bam FRACTION=0.1    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] ERROR	2016-04-27 04:32:12	PositionBasedDownsampleSam	Found previous Program Record that indicates that this BAM has been downsampled already with this program. Operation not supported! Previous PG: SAMProgramRecord{PN=PositionBasedDownsampleSam, CL=picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam5683296134219665331.bam FRACTION=0.1    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json}
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:12 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam2290217720796713160.bam FRACTION=0.3 CREATE_INDEX=true    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:12 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:12	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Second pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Finished! Kept 5544 out of 20000 reads (P=0.277200).
   [testng] [Wed Apr 27 04:32:13 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:13 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam3312736440120710374.bam FRACTION=0.4 CREATE_INDEX=true    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:13 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] No errors found
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Second pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Finished! Kept 7652 out of 20000 reads (P=0.382600).
   [testng] [Wed Apr 27 04:32:13 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] [Wed Apr 27 04:32:13 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam2261142406579868033.bam FRACTION=0.5 CREATE_INDEX=true    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:13 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] No errors found
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Second pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Finished! Kept 9688 out of 20000 reads (P=0.484400).
   [testng] [Wed Apr 27 04:32:13 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=937951232
   [testng] No errors found
   [testng] [Wed Apr 27 04:32:13 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam3842659004705905777.bam FRACTION=0.6 CREATE_INDEX=true    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:13 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Second pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Finished! Kept 12348 out of 20000 reads (P=0.617400).
   [testng] [Wed Apr 27 04:32:13 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] [Wed Apr 27 04:32:13 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam5965447466572668902.bam FRACTION=0.7 CREATE_INDEX=true    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:13 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] No errors found
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:13	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Second pass done.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Finished! Kept 14456 out of 20000 reads (P=0.722800).
   [testng] [Wed Apr 27 04:32:14 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] No errors found
   [testng] [Wed Apr 27 04:32:14 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam1762990107454288219.bam FRACTION=0.7999999999999999 CREATE_INDEX=true    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:14 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Second pass done.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Finished! Kept 16642 out of 20000 reads (P=0.832100).
   [testng] [Wed Apr 27 04:32:14 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] [Wed Apr 27 04:32:14 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4163729916529243896.bam FRACTION=0.8999999999999999 CREATE_INDEX=true    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:14 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] No errors found
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Second pass done.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Finished! Kept 18612 out of 20000 reads (P=0.930600).
   [testng] [Wed Apr 27 04:32:14 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] [Wed Apr 27 04:32:14 UTC 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam4925383805034064888.bam OUTPUT=/tmp/pds_test4710923370137973445PositionalDownsampling/PositionalDownsampleSam5129995234503836135.bam FRACTION=0.9999999999999999 CREATE_INDEX=true    ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:14 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Checking to see if input file has been downsampled with this program before.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Starting first pass. Examining read distribution in tiles.
   [testng] No errors found
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	First pass done.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Starting second pass. Outputting reads.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Second pass done.
   [testng] INFO	2016-04-27 04:32:14	PositionBasedDownsampleSam	Finished! Kept 20000 out of 20000 reads (P=1.00000).
   [testng] [Wed Apr 27 04:32:14 UTC 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] INFO	2016-04-27 04:32:14	RExecutor	Executing R script via command: Rscript /tmp/script4044123829125205067.R
   [testng] No errors found
   [testng] ERROR	2016-04-27 04:32:15	ProcessExecutor	Error: object 'alsdfj' not found
   [testng] ERROR	2016-04-27 04:32:15	ProcessExecutor	Execution halted
   [testng] INFO	2016-04-27 04:32:15	RExecutor	Executing R script via command: Rscript /tmp/script4580051092935922814.R
   [testng] INFO	2016-04-27 04:32:15	ProcessExecutor	[1] "Wed Apr 27 04:32:15 2016"
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam INPUT=testdata/picard/sam/revert_sam_negative.sam OUTPUT=/tmp/bad698684090632461208.sam SAMPLE_ALIAS=NewSample    SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam INPUT=testdata/picard/sam/revert_sam_negative.sam OUTPUT=/tmp/bad4516921221342892437.sam LIBRARY_NAME=NewLibrary    SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam INPUT=testdata/picard/sam/revert_sam_negative.sam OUTPUT=/tmp/bad8702409707552626624.sam SAMPLE_ALIAS=NewSample LIBRARY_NAME=NewLibrary    SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted8746846169857312395.sam RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true    SORT_ORDER=queryname ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted6756917625823101147.sam SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, XT] SAMPLE_ALIAS=Hey,Dad!    SANITIZE=false MAX_DISCARD_FRACTION=0.01 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted6023983177360304197.sam RESTORE_ORIGINAL_QUALITIES=false REMOVE_DUPLICATE_INFORMATION=false REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, XT] SAMPLE_ALIAS=Hey,Dad! LIBRARY_NAME=NewLibraryName    SORT_ORDER=queryname SANITIZE=false MAX_DISCARD_FRACTION=0.01 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=941621248
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted9099264312444847299.sam RESTORE_ORIGINAL_QUALITIES=false REMOVE_DUPLICATE_INFORMATION=false REMOVE_ALIGNMENT_INFORMATION=false    SORT_ORDER=queryname ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] No errors found
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	12
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] No errors found
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	12
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] No errors found
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	12
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] No errors found
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	12
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] No errors found
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	12
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam FASTQ=/tmp/tt-pair1.5945863419301162018.fastq SECOND_END_FASTQ=/tmp/tt-pair2.1914001452508050663.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/buildd    RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest11698795261468995800fastq SECOND_END_FASTQ=/tmp/clippingtest25610417105267646393fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest16567905245097374996fastq SECOND_END_FASTQ=/tmp/clippingtest27017157268944383646fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=X    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest12107299866296379793fastq SECOND_END_FASTQ=/tmp/clippingtest21165301553046575560fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=N    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest14664331855635370442fastq SECOND_END_FASTQ=/tmp/clippingtest23489163518514122143fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=2    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] No errors found
   [testng] Match	0
   [testng] Differ	0
   [testng] Unmapped_both	12
   [testng] Unmapped_left	0
   [testng] Unmapped_right	0
   [testng] Missing_left	0
   [testng] Missing_right	0
   [testng] SAM files match.
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair11997551007690526431.fastq SECOND_END_FASTQ=/tmp/pair22075449545952123741.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair12951666052243029533.fastq SECOND_END_FASTQ=/tmp/pair24850962617653366931.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair11977494105805685352.fastq SECOND_END_FASTQ=/tmp/pair2730075104281151165.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair13546232733511573917.fastq SECOND_END_FASTQ=/tmp/pair28642448396737157272.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/buildd    RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair1441215537364281564.fastq INTERLEAVE=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair5897305337637029776.fastq INTERLEAVE=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair4012130410780392334.fastq INTERLEAVE=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair1794374973215923423.fastq INTERLEAVE=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair13539565337602081469.fastq SECOND_END_FASTQ=/tmp/pair21102441566321251549.fastq READ1_TRIM=6 READ1_MAX_BASES_TO_WRITE=7 READ2_TRIM=5 READ2_MAX_BASES_TO_WRITE=8    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair18570556829861915139.fastq SECOND_END_FASTQ=/tmp/pair223765244192688705.fastq READ1_TRIM=7 READ1_MAX_BASES_TO_WRITE=7 READ2_TRIM=3 READ2_MAX_BASES_TO_WRITE=8    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] ERROR	2016-04-27 04:32:15	SplitSamByLibrary	No individual libraries are specified in the header of /«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/sam/invalid_coord_sort_order.sam
   [testng] [Wed Apr 27 04:32:15 UTC 2016] picard.vcf.SplitVcfs INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/CEUTrio-merged-indels-snps.vcf SNP_OUTPUT=/tmp/SplitVcfsTest2270001783343434305.tmp/split-vcfs-test-snps-delete-me.vcf INDEL_OUTPUT=/tmp/SplitVcfsTest2270001783343434305.tmp/split-vcfs-test-indels-delete-me.vcf    STRICT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:15 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:16 UTC 2016] picard.vcf.SplitVcfs done. Elapsed time: 0.01 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:16	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:17	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:17	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:17	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:17	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:29	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:29	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:29	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:29	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:37	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:37	TheoreticalSensitivity	Creating Roulette Wheel
   [testng] INFO	2016-04-27 04:32:37	TheoreticalSensitivity	Calculating quality sums from quality sampler
   [testng] INFO	2016-04-27 04:32:37	TheoreticalSensitivity	0 sampling iterations completed
   [testng] INFO	2016-04-27 04:32:38	TheoreticalSensitivity	Calculating theoretical het sensitivity
   [testng] INFO	2016-04-27 04:32:39	TheoreticalSensitivity	0 sampling iterations completed
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.UpdateVcfSequenceDictionary    INPUT=testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/UpdateVcfSequenceDictionaryTest5801215491408884405.tmp/updateVcfSequenceDictionaryTest-delete-me.vcf SEQUENCE_DICTIONARY=testdata/picard/vcf/vcfFormatTest.bad_dict.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.UpdateVcfSequenceDictionary done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf OUTPUT=/tmp/likeTest2017026832164004655.bcf    REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf OUTPUT=/tmp/backAndForth5545388380886255950.vcf    REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=944242688
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter INPUT=/tmp/backAndForth5545388380886255950.vcf OUTPUT=/tmp/backAndForth6176642612219487737.bcf    REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=946864128
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/backAndForth4882992991777810073.bcf    REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=946864128
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter INPUT=/tmp/backAndForth4882992991777810073.bcf OUTPUT=/tmp/backAndForth6814249233523916553.vcf    REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=946864128
   [testng] [Wed Apr 27 04:32:39 UTC 2016] picard.vcf.VcfFormatConverter INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/likeTest1869399757060971484.vcf    REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:39 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:40 UTC 2016] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=946864128
   [testng] [Wed Apr 27 04:32:40 UTC 2016] picard.vcf.VcfFormatConverter INPUT=/«BUILDDIR»/picard-tools-2.1.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/backAndForth1460254288813600477.vcf.gz CREATE_INDEX=false    REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:40 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:40 UTC 2016] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=946864128
   [testng] [Wed Apr 27 04:32:40 UTC 2016] picard.vcf.VcfFormatConverter INPUT=/tmp/backAndForth1460254288813600477.vcf.gz OUTPUT=/tmp/backAndForth1042361779570778994.vcf REQUIRE_INDEX=false    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [testng] [Wed Apr 27 04:32:40 UTC 2016] Executing as buildd@lgw01-16 on Linux 3.13.0-85-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-2ubuntu1-b14; Picard version: null JdkDeflater
   [testng] [Wed Apr 27 04:32:40 UTC 2016] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes.
   [testng] Runtime.totalMemory()=893386752
   [testng] PASSED: invalidFileNamesTest("whatever.locs")
   [testng] PASSED: invalidFileNamesTest("whatever.clocs")
   [testng] PASSED: invalidFileNamesTest("whatever.pos")
   [testng] PASSED: invalidFileNamesTest("s_1.clocs")
   [testng] PASSED: invalidFileNamesTest("s__2.clocs")
   [testng] PASSED: invalidFileNamesTest("s_1_4.Notclocs")
   [testng] PASSED: invalidFileNamesTest("a_1_4.pos")
   [testng] PASSED: invalidFileNamesTest("a_1_4.pos.txt")
   [testng] PASSED: invalidReaderTest([F@2e4eda17, [F@7b5021d1)
   [testng] PASSED: invalidReaderTest([F@21d9cd04, [F@799f354a)
   [testng] PASSED: invalidReaderTest([F@159ac15f, [F@7ac48f05)
   [testng] PASSED: invalidReaderTest([F@27ffd9f8, [F@642c6461)
   [testng] PASSED: invalidReaderTest([F@4e48462d, [F@17216605)
   [testng] PASSED: iteratorRemoveTest
   [testng] PASSED: validReaderTest
   [testng] PASSED: testBulkFragmentsNoDuplicates
   [testng] PASSED: testBulkFragmentsWithDuplicates
   [testng] PASSED: testDifferentChromosomesInOppositeOrder
   [testng] PASSED: testMappedFragmentAndMappedPairFirstOfPairNonPrimary
   [testng] PASSED: testMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairWithFirstEndSamePositionAndOther
   [testng] PASSED: testMappedPairWithSamePosition
   [testng] PASSED: testMappedPairWithSamePositionSameCigar
   [testng] PASSED: testMatePairFirstUnmapped
   [testng] PASSED: testMatePairSecondUnmapped
   [testng] PASSED: testOpticalDuplicateClusterOneEndSamePositionOneCluster
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicates
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate
   [testng] PASSED: testOpticalDuplicateFinding
   [testng] PASSED: testPathologicalOrderingAtTheSamePosition
   [testng] PASSED: testSecondEndIsBeforeFirstInCoordinate
   [testng] PASSED: testSingleMappedFragment
   [testng] PASSED: testSingleMappedFragmentAndSingleMappedPair
   [testng] PASSED: testSingleMappedFragmentAndTwoMappedPairs
   [testng] PASSED: testSingleMappedPair
   [testng] PASSED: testSingleUnmappedFragment
   [testng] PASSED: testSingleUnmappedPair
   [testng] PASSED: testStackOverFlowPairSetSwap
   [testng] PASSED: testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testThreeMappedPairs
   [testng] PASSED: testThreeMappedPairsWithMatchingSecondMate
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoFragments
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs
   [testng] PASSED: testTwoMappedFragments
   [testng] PASSED: testTwoMappedPairWithSamePosition
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands2
   [testng] PASSED: testTwoMappedPairs
   [testng] PASSED: testTwoMappedPairsAndMappedSecondaryFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedPair
   [testng] PASSED: testTwoMappedPairsMatesSoftClipped
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientations
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientationsNumberTwo
   [testng] PASSED: testTwoMappedPairsWithSoftClipping
   [testng] PASSED: testTwoMappedPairsWithSoftClippingBoth
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar
   [testng] PASSED: testTwoUnmappedFragments
   [testng] PASSED: pgRecordChainingTest(false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@61b838f2, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2a04ab05, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ebbde60], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@a056b26, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2a5abd3c], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@250967f1]})
   [testng] PASSED: pgRecordChainingTest(true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@25c1f5ee, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bce62b], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bf018dd], 1AAXX.3.1=[]})
   [testng] PASSED: testOpticalDuplicateDetection(testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)
   [testng] PASSED: testOpticalDuplicateDetection(testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnly
   [testng] PASSED: testWithBarcodeComplex
   [testng] PASSED: testWithBarcodeDuplicate
   [testng] PASSED: testWithBarcodeFragmentDuplicate
   [testng] PASSED: testWithIndividualReadBarcodes
   [testng] PASSED: testBulkFragmentsNoDuplicates
   [testng] PASSED: testBulkFragmentsWithDuplicates
   [testng] PASSED: testDifferentChromosomesInOppositeOrder
   [testng] PASSED: testMappedFragmentAndMappedPairFirstOfPairNonPrimary
   [testng] PASSED: testMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairWithFirstEndSamePositionAndOther
   [testng] PASSED: testMappedPairWithSamePosition
   [testng] PASSED: testMappedPairWithSamePositionSameCigar
   [testng] PASSED: testMatePairFirstUnmapped
   [testng] PASSED: testMatePairSecondUnmapped
   [testng] PASSED: testOpticalDuplicateClusterOneEndSamePositionOneCluster
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicates
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate
   [testng] PASSED: testOpticalDuplicateFinding
   [testng] PASSED: testPathologicalOrderingAtTheSamePosition
   [testng] PASSED: testSecondEndIsBeforeFirstInCoordinate
   [testng] PASSED: testSingleMappedFragment
   [testng] PASSED: testSingleMappedFragmentAndSingleMappedPair
   [testng] PASSED: testSingleMappedFragmentAndTwoMappedPairs
   [testng] PASSED: testSingleMappedPair
   [testng] PASSED: testSingleUnmappedFragment
   [testng] PASSED: testSingleUnmappedPair
   [testng] PASSED: testStackOverFlowPairSetSwap
   [testng] PASSED: testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testThreeMappedPairs
   [testng] PASSED: testThreeMappedPairsWithMatchingSecondMate
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoFragments
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs
   [testng] PASSED: testTwoMappedFragments
   [testng] PASSED: testTwoMappedPairWithSamePosition
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands2
   [testng] PASSED: testTwoMappedPairs
   [testng] PASSED: testTwoMappedPairsAndMappedSecondaryFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedPair
   [testng] PASSED: testTwoMappedPairsMatesSoftClipped
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientations
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientationsNumberTwo
   [testng] PASSED: testTwoMappedPairsWithSoftClipping
   [testng] PASSED: testTwoMappedPairsWithSoftClippingBoth
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar
   [testng] PASSED: testTwoUnmappedFragments
   [testng] PASSED: pgRecordChainingTest(false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@15a8cebd, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3f6c2763, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5c82031b], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@274fdea6, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@74c121d4], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2a484710]})
   [testng] PASSED: pgRecordChainingTest(true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@661e1399, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ffd4b12], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@424f02b8], 1AAXX.3.1=[]})
   [testng] PASSED: testOpticalDuplicateDetection(testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)
   [testng] PASSED: testOpticalDuplicateDetection(testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnly
   [testng] PASSED: testWithBarcodeComplex
   [testng] PASSED: testWithBarcodeDuplicate
   [testng] PASSED: testWithBarcodeFragmentDuplicate
   [testng] PASSED: testWithIndividualReadBarcodes
   [testng] PASSED: testBulkFragmentsNoDuplicates
   [testng] PASSED: testBulkFragmentsWithDuplicates
   [testng] PASSED: testDifferentChromosomesInOppositeOrder
   [testng] PASSED: testMappedFragmentAndMappedPairFirstOfPairNonPrimary
   [testng] PASSED: testMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairWithFirstEndSamePositionAndOther
   [testng] PASSED: testMappedPairWithSamePosition
   [testng] PASSED: testMappedPairWithSamePositionSameCigar
   [testng] PASSED: testMatePairFirstUnmapped
   [testng] PASSED: testMatePairSecondUnmapped
   [testng] PASSED: testOpticalDuplicateClusterOneEndSamePositionOneCluster
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicates
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate
   [testng] PASSED: testOpticalDuplicateFinding
   [testng] PASSED: testPathologicalOrderingAtTheSamePosition
   [testng] PASSED: testSecondEndIsBeforeFirstInCoordinate
   [testng] PASSED: testSingleMappedFragment
   [testng] PASSED: testSingleMappedFragmentAndSingleMappedPair
   [testng] PASSED: testSingleMappedFragmentAndTwoMappedPairs
   [testng] PASSED: testSingleMappedPair
   [testng] PASSED: testSingleUnmappedFragment
   [testng] PASSED: testSingleUnmappedPair
   [testng] PASSED: testStackOverFlowPairSetSwap
   [testng] PASSED: testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testThreeMappedPairs
   [testng] PASSED: testThreeMappedPairsWithMatchingSecondMate
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoFragments
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs
   [testng] PASSED: testTwoMappedFragments
   [testng] PASSED: testTwoMappedPairWithSamePosition
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands2
   [testng] PASSED: testTwoMappedPairs
   [testng] PASSED: testTwoMappedPairsAndMappedSecondaryFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedPair
   [testng] PASSED: testTwoMappedPairsMatesSoftClipped
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientations
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientationsNumberTwo
   [testng] PASSED: testTwoMappedPairsWithSoftClipping
   [testng] PASSED: testTwoMappedPairsWithSoftClippingBoth
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar
   [testng] PASSED: testTwoUnmappedFragments
   [testng] PASSED: pgRecordChainingTest(false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2ad7bd26, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3cc3f13e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@69b3886f], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@53d30d23, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44faa4f2], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6793f752]})
   [testng] PASSED: pgRecordChainingTest(true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1216eb3f, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@59e7564b], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@482ba4b1], 1AAXX.3.1=[]})
   [testng] PASSED: testOpticalDuplicateDetection(testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)
   [testng] PASSED: testOpticalDuplicateDetection(testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnly
   [testng] PASSED: testWithBarcodeComplex
   [testng] PASSED: testWithBarcodeDuplicate
   [testng] PASSED: testWithBarcodeFragmentDuplicate
   [testng] PASSED: testWithIndividualReadBarcodes
   [testng] PASSED: testBulkFragmentsNoDuplicates
   [testng] PASSED: testBulkFragmentsWithDuplicates
   [testng] PASSED: testDifferentChromosomesInOppositeOrder
   [testng] PASSED: testMappedFragmentAndMappedPairFirstOfPairNonPrimary
   [testng] PASSED: testMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairWithFirstEndSamePositionAndOther
   [testng] PASSED: testMappedPairWithSamePosition
   [testng] PASSED: testMappedPairWithSamePositionSameCigar
   [testng] PASSED: testMatePairFirstUnmapped
   [testng] PASSED: testMatePairSecondUnmapped
   [testng] PASSED: testOpticalDuplicateClusterOneEndSamePositionOneCluster
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicates
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate
   [testng] PASSED: testOpticalDuplicateFinding
   [testng] PASSED: testPathologicalOrderingAtTheSamePosition
   [testng] PASSED: testSecondEndIsBeforeFirstInCoordinate
   [testng] PASSED: testSingleMappedFragment
   [testng] PASSED: testSingleMappedFragmentAndSingleMappedPair
   [testng] PASSED: testSingleMappedFragmentAndTwoMappedPairs
   [testng] PASSED: testSingleMappedPair
   [testng] PASSED: testSingleUnmappedFragment
   [testng] PASSED: testSingleUnmappedPair
   [testng] PASSED: testStackOverFlowPairSetSwap
   [testng] PASSED: testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testThreeMappedPairs
   [testng] PASSED: testThreeMappedPairsWithMatchingSecondMate
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoFragments
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs
   [testng] PASSED: testTwoMappedFragments
   [testng] PASSED: testTwoMappedPairWithSamePosition
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands2
   [testng] PASSED: testTwoMappedPairs
   [testng] PASSED: testTwoMappedPairsAndMappedSecondaryFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedPair
   [testng] PASSED: testTwoMappedPairsMatesSoftClipped
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientations
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientationsNumberTwo
   [testng] PASSED: testTwoMappedPairsWithSoftClipping
   [testng] PASSED: testTwoMappedPairsWithSoftClippingBoth
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar
   [testng] PASSED: testTwoUnmappedFragments
   [testng] PASSED: pgRecordChainingTest(false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307af381, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1510b9a2, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@76a6f045], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@633ddc0c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bcdd11], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1471b98d]})
   [testng] PASSED: pgRecordChainingTest(true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5514579e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@58c42c8c], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3af236d0], 1AAXX.3.1=[]})
   [testng] PASSED: testOpticalDuplicateDetection(testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)
   [testng] PASSED: testOpticalDuplicateDetection(testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnly
   [testng] PASSED: testWithBarcodeComplex
   [testng] PASSED: testWithBarcodeDuplicate
   [testng] PASSED: testWithBarcodeFragmentDuplicate
   [testng] PASSED: testWithIndividualReadBarcodes
   [testng] PASSED: testBulkFragmentsNoDuplicates
   [testng] PASSED: testBulkFragmentsWithDuplicates
   [testng] PASSED: testDifferentChromosomesInOppositeOrder
   [testng] PASSED: testMappedFragmentAndMappedPairFirstOfPairNonPrimary
   [testng] PASSED: testMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairWithFirstEndSamePositionAndOther
   [testng] PASSED: testMappedPairWithSamePosition
   [testng] PASSED: testMappedPairWithSamePositionSameCigar
   [testng] PASSED: testMatePairFirstUnmapped
   [testng] PASSED: testMatePairSecondUnmapped
   [testng] PASSED: testOpticalDuplicateClusterOneEndSamePositionOneCluster
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicates
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate
   [testng] PASSED: testOpticalDuplicateFinding
   [testng] PASSED: testPathologicalOrderingAtTheSamePosition
   [testng] PASSED: testSecondEndIsBeforeFirstInCoordinate
   [testng] PASSED: testSingleMappedFragment
   [testng] PASSED: testSingleMappedFragmentAndSingleMappedPair
   [testng] PASSED: testSingleMappedFragmentAndTwoMappedPairs
   [testng] PASSED: testSingleMappedPair
   [testng] PASSED: testSingleUnmappedFragment
   [testng] PASSED: testSingleUnmappedPair
   [testng] PASSED: testStackOverFlowPairSetSwap
   [testng] PASSED: testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testThreeMappedPairs
   [testng] PASSED: testThreeMappedPairsWithMatchingSecondMate
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoFragments
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs
   [testng] PASSED: testTwoMappedFragments
   [testng] PASSED: testTwoMappedPairWithSamePosition
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands2
   [testng] PASSED: testTwoMappedPairs
   [testng] PASSED: testTwoMappedPairsAndMappedSecondaryFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedPair
   [testng] PASSED: testTwoMappedPairsMatesSoftClipped
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientations
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientationsNumberTwo
   [testng] PASSED: testTwoMappedPairsWithSoftClipping
   [testng] PASSED: testTwoMappedPairsWithSoftClippingBoth
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar
   [testng] PASSED: testTwoUnmappedFragments
   [testng] PASSED: testScoringStrategyForMateReferenceLengthComparison
   [testng] PASSED: testScoringStrategyForReadNameComparison
   [testng] PASSED: testTwoFragmentsLargeSoftClip
   [testng] PASSED: testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure
   [testng] PASSED: testTwoFragmentsLargeSoftClipWithMinimumDistanceOK
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnly
   [testng] PASSED: testBulkFragmentsNoDuplicates
   [testng] PASSED: testBulkFragmentsWithDuplicates
   [testng] PASSED: testDifferentChromosomesInOppositeOrder
   [testng] PASSED: testMappedFragmentAndMappedPairFirstOfPairNonPrimary
   [testng] PASSED: testMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMappedFragmentAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped
   [testng] PASSED: testMappedPairAndMatePairFirstUnmapped
   [testng] PASSED: testMappedPairAndMatePairSecondUnmapped
   [testng] PASSED: testMappedPairWithFirstEndSamePositionAndOther
   [testng] PASSED: testMappedPairWithSamePosition
   [testng] PASSED: testMappedPairWithSamePositionSameCigar
   [testng] PASSED: testMatePairFirstUnmapped
   [testng] PASSED: testMatePairSecondUnmapped
   [testng] PASSED: testOpticalDuplicateClusterOneEndSamePositionOneCluster
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicates
   [testng] PASSED: testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance
   [testng] PASSED: testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate
   [testng] PASSED: testOpticalDuplicateFinding
   [testng] PASSED: testPathologicalOrderingAtTheSamePosition
   [testng] PASSED: testSecondEndIsBeforeFirstInCoordinate
   [testng] PASSED: testSingleMappedFragment
   [testng] PASSED: testSingleMappedFragmentAndSingleMappedPair
   [testng] PASSED: testSingleMappedFragmentAndTwoMappedPairs
   [testng] PASSED: testSingleMappedPair
   [testng] PASSED: testSingleUnmappedFragment
   [testng] PASSED: testSingleUnmappedPair
   [testng] PASSED: testStackOverFlowPairSetSwap
   [testng] PASSED: testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testThreeMappedPairs
   [testng] PASSED: testThreeMappedPairsWithMatchingSecondMate
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoFragments
   [testng] PASSED: testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs
   [testng] PASSED: testTwoMappedFragments
   [testng] PASSED: testTwoMappedPairWithSamePosition
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands
   [testng] PASSED: testTwoMappedPairWithSamePositionDifferentStrands2
   [testng] PASSED: testTwoMappedPairs
   [testng] PASSED: testTwoMappedPairsAndMappedSecondaryFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedFragment
   [testng] PASSED: testTwoMappedPairsAndTerminalUnmappedPair
   [testng] PASSED: testTwoMappedPairsMatesSoftClipped
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientations
   [testng] PASSED: testTwoMappedPairsWithOppositeOrientationsNumberTwo
   [testng] PASSED: testTwoMappedPairsWithSoftClipping
   [testng] PASSED: testTwoMappedPairsWithSoftClippingBoth
   [testng] PASSED: testTwoUnmappedFragments
   [testng] PASSED: testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar
   [testng] PASSED: testFailsOnDissimilarContigLists
   [testng] PASSED: testFailsOnDissimilarSampleLists
   [testng] PASSED: testFailsOnNoContigList
   [testng] PASSED: testMergeIndelsSnps
   [testng] PASSED: testMergeRandomScatter
   [testng] PASSED: testFailsOnDissimilarContigLists
   [testng] PASSED: testFailsOnDissimilarSampleLists
   [testng] PASSED: testFailsOnNoContigList
   [testng] PASSED: testMergeIndelsSnps
   [testng] PASSED: testMergeRandomScatter
   [testng] PASSED: testPresortedFile
   [testng] PASSED: testScrambledSnpsAndOrderedIndels
   [testng] PASSED: testScrambledSnpsAndScrambledIndels
   [testng] PASSED: testSingleScrambledFile
   [testng] PASSED: testTwoScrambledSnpFiles
   [testng] PASSED: test
   [testng] PASSED: testAddCommentsToBam
   [testng] PASSED: testUsingNewlines
   [testng] PASSED: testUsingSam
   [testng] PASSED: testFileLengthMatchesHeaderLength
   [testng] PASSED: testGZFileIsActuallyGZipped
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( G G G G G G G G G , 13,7,35,32,31,33,31,26,29,, 13,7,35,32,31,33,31,26,29,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( G G G G G G G G G , 13,7,35,26,18,19,35,8,33,, 13,7,35,26,18,19,35,8,33,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( A C C C C C C C C C C C T G G C T A A , 7,8,33,7,2,33,16,17,19,7,6,5,35,2,33,22,18,16,25,, 7,8,33,7,2,33,16,17,19,7,6,5,35,2,33,22,18,16,25,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( T G G G G G G G . . G G G G G G G T A A G G G , 7,8,33,7,2,33,16,17,2,2,6,5,35,2,33,22,18,16,25,33,32,16,18,, 7,8,33,7,2,33,16,17,2,2,6,5,35,2,33,22,18,16,25,33,32,16,18,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( T A C , 25,16,16,, 25,16,16,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( T A C G G . . T C C C C T T T G G G A T G C A T A C G G . . T C C C C T T T G G G A T G C A , 25,16,16,33,22,2,2,33,35,3,31,38,22,19,25,16,16,31,30,2,2,33,26,3,31,38,22,19,2,2,30,27,28,16,2,2,30,16,19,21,22,17,19,16,16,16,, 25,16,16,33,22,2,2,33,35,3,31,38,22,19,25,16,16,31,30,2,2,33,26,3,31,38,22,19,2,2,30,27,28,16,2,2,30,16,19,21,22,17,19,16,16,16,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( G G G G G G G G G , 13,7,35,32,2,16,33,14,19,, 13,7,35,32,2,16,33,2,2,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( G G G G G G G G G , 13,7,35,33,18,2,6,8,33,, 13,7,35,33,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( A C C C C C C C C C C C T G G C T A A , 7,8,33,7,2,33,16,17,19,32,33,5,8,2,2,2,33,16,25,, 7,8,33,7,2,33,16,17,19,32,33,2,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( T G G G G G G G . . G G G G G G G T A A G G G , 7,8,33,7,2,33,16,17,2,2,6,5,35,2,33,30,13,16,7,2,2,16,18,, 7,8,33,7,2,33,16,17,2,2,6,5,35,2,33,30,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( T A C , 2,11,13,, 2,2,2,))
   [testng] PASSED: eamssParsingTestNoGSeries(BasesAndQuals( T A C G G . . T C C C C T T T G G G A T G C A T A C G G . . T C C C C T T T G G G A T G C A , 25,16,16,33,22,2,2,33,35,3,31,38,22,19,25,16,16,31,30,2,2,33,26,3,31,38,22,19,2,2,30,27,28,16,2,2,30,16,19,21,22,2,19,16,2,2,, 25,16,16,33,22,2,2,33,35,3,31,38,22,19,25,16,16,31,30,2,2,33,26,3,31,38,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C G G T G G G G G G G G G A C T , 7,8,33,7,12,33,16,17,2,2,32,35,35,35,2,15,9,, 7,8,33,7,12,2,2,2,2,2,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C G G T G G G G G G G G G A C T , 7,8,2,7,2,2,16,17,2,2,32,35,35,35,2,15,9,, 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C G G T G G G G G G G G G A C T , 7,8,2,7,2,2,16,17,2,2,32,35,35,35,33,15,9,, 7,8,2,7,2,2,16,17,2,2,32,35,35,35,33,2,2,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C C G C C G G G G G G G G G G T T A , 33,31,29,32,28,27,30,18,18,18,18,19,19,19,33,18,9,9,19,, 33,31,29,32,28,27,2,2,2,2,2,2,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C C G C C G G G G G G G G G G T T A , 33,31,29,32,28,27,30,18,18,18,18,19,19,19,33,18,33,32,34,, 33,31,29,32,28,27,30,18,18,18,18,19,19,19,33,18,33,32,34,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C C G C C G G G G A G G G G G T T A , 33,31,29,32,28,27,30,18,18,18,18,19,19,19,33,18,9,9,19,, 33,31,29,32,28,27,2,2,2,2,2,2,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C G G G C G G G G G G G G G G T T A , 33,31,29,32,28,16,33,18,18,18,18,19,19,19,33,18,3,9,19,, 33,31,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C G G C C G G G G G G G G G G G G G , 33,31,29,32,28,16,33,18,18,18,18,19,19,19,33,34,33,33,3,, 33,31,29,32,28,16,2,2,2,2,2,2,2,2,2,2,2,2,2,))
   [testng] PASSED: eamssParsingTestWithGSeries(BasesAndQuals( A C G G C C G G G G G G G G G G G G G T A C T T G G G G G G G G G G G G G , 33,31,29,32,28,16,33,18,18,18,18,19,19,19,33,34,33,33,3,33,34,2,4,8,33,7,35,15,16,31,30,38,16,15,22,29,25,, 33,31,29,32,28,16,33,18,18,18,18,19,19,19,33,34,33,33,3,33,34,2,4,8,33,7,35,15,16,31,30,38,16,15,22,29,25,))
   [testng] PASSED: fullBclParserTest([I@20a3e10c, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTest([I@426c0486, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTest([I@5e2a6991, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTest([I@5002fde9, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTest([I@6f96dd64, 60, -1, -1, -1)
   [testng] PASSED: fullBclParserTest([I@4d7cac24, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTest([I@409732fb, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTest([I@73d62b5, 80, 19, 0, 1)
   [testng] PASSED: fullBclParserTest([I@5e99e2cb, 156, 35, 0, 0)
   [testng] PASSED: fullBclParserTest([I@76ac68b0, 66, 5, 0, 0)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@f559c74, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@677349fb, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@2450256f, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@1c74d19, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@2776fd8f, 60, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@49b89425, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@478967eb, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@7a358613, 80, 19, 0, 1)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@401e02b4, 156, 35, 0, 0)
   [testng] PASSED: fullBclParserTestWBadDeletedSkips([I@5ac044ef, 66, 5, 0, 0)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@48567727, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@10e9a5fe, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@259287ac, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@1abcd059, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@61a87366, 60, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@3c33fcf8, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@dada335, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@716f94c1, 80, 19, 0, 1)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@53feeac9, 156, 35, 0, 0)
   [testng] PASSED: fullBclParserTestWDeletedSkips([I@70091872, 66, 5, 0, 0)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@105db94d, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@1d99ee1b, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@3915e7c3, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@167a21b, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@7c0df4ab, 60, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@2e362407, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@388be5fd, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@440ef8d, 80, 19, 0, 1)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@17fbfb02, 156, 35, 0, 0)
   [testng] PASSED: fullBclParserTestWPartiallyDeletedSkips([I@8f2e3e6, 66, 5, 0, 0)
   [testng] PASSED: fullBclParserTestWSkips([I@6f315b08, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWSkips([I@6c8efde4, 180, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWSkips([I@24e5389c, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWSkips([I@3b170235, 120, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWSkips([I@5e9bf744, 60, -1, -1, -1)
   [testng] PASSED: fullBclParserTestWSkips([I@45e140ae, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTestWSkips([I@48cdb156, 206, 25, 0, 0)
   [testng] PASSED: fullBclParserTestWSkips([I@4b4814d0, 80, 19, 0, 1)
   [testng] PASSED: fullBclParserTestWSkips([I@4ae8fb2a, 156, 35, 0, 0)
   [testng] PASSED: fullBclParserTestWSkips([I@54326e9, 66, 5, 0, 0)
   [testng] PASSED: failingFileTest(testdata/picard/illumina/readerTests/bcl_failing.bcl)
   [testng] PASSED: failingFileTest(testdata/picard/illumina/readerTests/bcl_failing2.bcl)
   [testng] PASSED: failingFileTest(testdata/picard/illumina/readerTests/SomeNoneExistentFile.bcl)
   [testng] PASSED: failingFileTest(testdata/picard/illumina/readerTests/bcl_tooLong.bcl)
   [testng] PASSED: failingFileTest(testdata/picard/illumina/readerTests/bcl_tooShort.bcl)
   [testng] PASSED: lowQualityAndFailingTest
   [testng] PASSED: lowQualityButPassingTest
   [testng] PASSED: readValidFile
   [testng] PASSED: testBedToIntervalList("simple.bed")
   [testng] PASSED: testBedToIntervalList("overlapping.bed")
   [testng] PASSED: testBedToIntervalList("extended.bed")
   [testng] PASSED: testBedToIntervalList("one_base_interval.bed")
   [testng] PASSED: testBedToIntervalList("zero_base_interval.bed")
   [testng] PASSED: testBedToIntervalListBadSequenceDictionary("seq_dict_test.dictionary.bad")
   [testng] PASSED: testBedToIntervalListBadSequenceDictionary("seq_dict_test.dictionary.bad.vcf")
   [testng] PASSED: testBedToIntervalListOutOfBounds("end_after_chr.bed")
   [testng] PASSED: testBedToIntervalListOutOfBounds("end_before_chr.bed")
   [testng] PASSED: testBedToIntervalListOutOfBounds("missing_chr.bed")
   [testng] PASSED: testBedToIntervalListOutOfBounds("start_after_chr.bed")
   [testng] PASSED: testBedToIntervalListOutOfBounds("start_before_chr.bed")
   [testng] PASSED: testBedToIntervalListOutOfBounds("off_by_one_interval.bed")
   [testng] PASSED: testBedToIntervalListSequenceDictionary("seq_dict_test.dictionary.interval_list")
   [testng] PASSED: testBedToIntervalListSequenceDictionary("seq_dict_test.dictionary.fasta")
   [testng] PASSED: testBedToIntervalListSequenceDictionary("seq_dict_test.dictionary.dict")
   [testng] PASSED: testBedToIntervalListSequenceDictionary("seq_dict_test.dictionary.sam")
   [testng] PASSED: testBedToIntervalListSequenceDictionary("seq_dict_test.dictionary.vcf")
   [testng] PASSED: test
   [testng] PASSED: testGetSingletonSample([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[het A*/C]], "het")
   [testng] PASSED: testGetSingletonSample([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[het A*/C],[homref A*]], "het")
   [testng] PASSED: testGetSingletonSample([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[het A*/C],[homref A*],[homvar C]], null)
   [testng] PASSED: testGetSingletonSample([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[het A*/C],[het2 A*/G],[homref A*]], null)
   [testng] PASSED: testGetSingletonSample([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[homvar C]], null)
   [testng] PASSED: testGetSingletonSample([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[homref A*],[homvar C]], null)
   [testng] PASSED: testGetSingletonSample([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[homref A*],[homref2 A*]], null)
   [testng] PASSED: basedirDoesntExistTest
   [testng] PASSED: differentSizedBclTest
   [testng] PASSED: negativeTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@1894fa9f, [Lpicard.illumina.parser.IlluminaDataType;@1144a02b, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@26a4f9ed, "68T8B68T", 2, [], true)
   [testng] PASSED: negativeTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7a572ea0, [Lpicard.illumina.parser.IlluminaDataType;@45287377, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7159d601, "13T", 3, [], true)
   [testng] PASSED: negativeTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@70b33256, [Lpicard.illumina.parser.IlluminaDataType;@33d230ce, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@35e74e08, "250T", 98, [], true)
   [testng] PASSED: negativeTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@a316f6b, [Lpicard.illumina.parser.IlluminaDataType;@63f9ddf9, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@410fc508, "250T", 98, [1301, 2201], true)
   [testng] PASSED: positiveTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@23564dd2, [Lpicard.illumina.parser.IlluminaDataType;@54895681, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@2dd0a0d0, "25T25T", [])
   [testng] PASSED: positiveTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@6bf570c, [Lpicard.illumina.parser.IlluminaDataType;@1796b2d4, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@935d3f9, "8S15T8S", [])
   [testng] PASSED: positiveTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@214b342f, [Lpicard.illumina.parser.IlluminaDataType;@5db0003d, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7f12094d, "68T8B68T", [])
   [testng] PASSED: positiveTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@589fb74d, [Lpicard.illumina.parser.IlluminaDataType;@200d1a3d, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@7de147e9, "25T25T", [])
   [testng] PASSED: positiveTests([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@12567179, [Lpicard.illumina.parser.IlluminaDataType;@37d699a1, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@7f42b194, "25T25T", [1301, 2101])
   [testng] PASSED: symlinkLocsTest
   [testng] PASSED: testCleanSam("simple_fits.sam", "100M")
   [testng] PASSED: testCleanSam("simple_overhang.sam", "99M1S")
   [testng] PASSED: testCleanSam("fits_with_deletion.sam", "91M2D9M")
   [testng] PASSED: testCleanSam("overhang_with_deletion.sam", "91M2D8M1S")
   [testng] PASSED: testCleanSam("trailing_insertion.sam", "99M1I")
   [testng] PASSED: testCleanSam("long_trailing_insertion.sam", "90M10I")
   [testng] PASSED: testCleanSamTester("100M", "100M", 101, 2)
   [testng] PASSED: testCleanSamTester("100M", "99M1S", 101, 3)
   [testng] PASSED: testCleanSamTester("91M2D9M", "91M2D9M", 102, 1)
   [testng] PASSED: testCleanSamTester("91M2D9M", "91M2D8M1S", 101, 1)
   [testng] PASSED: testCleanSamTester("99M1I", "99M1I", 101, 3)
   [testng] PASSED: testCleanSamTester("90M10I", "90M10I", 101, 3)
   [testng] PASSED: testAdapterInAllReadPositions(100)
   [testng] PASSED: testAdapterInAllReadPositions(36)
   [testng] PASSED: testAdapterListTruncation(PAIRED_END)
   [testng] PASSED: testAdapterListTruncation(INDEXED)
   [testng] PASSED: testAdapterListTruncation(SINGLE_END)
   [testng] PASSED: testAdapterListTruncation(NEXTERA_V1)
   [testng] PASSED: testAdapterListTruncation(NEXTERA_V2)
   [testng] PASSED: testAdapterListTruncation(DUAL_INDEXED)
   [testng] PASSED: testAdapterListTruncation(FLUIDIGM)
   [testng] PASSED: testAdapterListTruncation(TRUSEQ_SMALLRNA)
   [testng] PASSED: testAdapterListTruncation(ALTERNATIVE_SINGLE_END)
   [testng] PASSED: testAdapterTruncation
   [testng] PASSED: testBasicClip("Simple test 1", "AAAAACCCCCAGATCGGAAGAGCA", "AGATCGGAAGAGCG", 14, 0.15, 10)
   [testng] PASSED: testBasicClip("Simple test 2", "AAAAACCCCCGGGGGAGATCGGAAGAGCA", "AGATCGGAAGAGCG", 14, 0.15, 15)
   [testng] PASSED: testBasicClip("No adapter", "AAAAACCCCCGGGGGTTTTT", "AGATCGGAAGAGCG", 6, 0.15, -1)
   [testng] PASSED: testBasicClip("Partial adapter", "AAAAACCCCCTGATCGGAA", "AGATCGGAAGAGCG", 9, 0.15, 10)
   [testng] PASSED: testBasicClip("No sequence", null, "AGATCGGAAGAGCG", 6, 0.15, -1)
   [testng] PASSED: testBasicClip("Read too short", "AGATCGGAAG", "AGATCGGAAGAGCG", 11, 0.15, -1)
   [testng] PASSED: testBasicClip("All No Calls", "AAACCCNNNNNNNNNNNNNNNNNNNN", "AGATCGGAAGAGCG", 6, 0.15, -1)
   [testng] PASSED: testBasicClip("From Test Data1", "CGGCATTCCTGCTGAACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGGGGGTGGATCTCGGTGGGCGGCGTGTTGT", "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", 57, 0.15, 19)
   [testng] PASSED: testBasicClip("From Test Data2a", "CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCCGAA", "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", 9, 0.14, 27)
   [testng] PASSED: testBasicClip("From Test Data2b", "CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAA", "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", 10, 0.14, -1)
   [testng] PASSED: testBasicClip("From PE Test Data1", "CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT", "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG", 17, 0.14, 19)
   [testng] PASSED: testBasicClip("From PE Test Data2", "CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT", "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", 5, 0.14, -1)
   [testng] PASSED: testBasicClip("From Test 8-clipped", "TGGGGTGGTTATTGTTGATTTTTGTTTGTGTGTTAGGTTGTTTGTGTTAGTTTTTTATTTTATTTTCGAGATCGAA", "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG", 8, 0.14, 68)
   [testng] PASSED: testBasicClip("50% can be bad", "AAAAACCCCCAGGTCGGAAGAGCG", "AGATCGGAAGAGCG", 5, 0.5, 18)
   [testng] PASSED: testBasicClip("From 30E54AAXX.5.a", "ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG", "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG", 34, 0.14, 0)
   [testng] PASSED: testBasicClip("From 30E54AAXX.5.b", "ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG", "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG", 34, 0.14, 0)
   [testng] PASSED: testOneSidedMatchSupersededByTwoSidedMatch
   [testng] PASSED: testPairedEndClip("Basic positive paired test matching", "CTACTGGCGCTGAAACTGAGCAGCCAAGCAGATCGG", "GCTTGGCTGCTCAGTTTCAGCGCCAGTAGAGATCGG", INDEXED)
   [testng] PASSED: testPairedEndClip("Basic positive first end one-sided test matching", "CTACTGGCGCTGAAAAGATCGGAAGAGCGGTTCAGC", "AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT", PAIRED_END)
   [testng] PASSED: testPairedEndClip("Basic positive second end one-sided test matching", "AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT", "AAAAAATTTTTTCCCAGATCGGAAGAGCGTCGTGTA", PAIRED_END)
   [testng] PASSED: testPairedEndClip("Basic negative one-sided test matching", "GGCGCTGAAACTACTGGCGCTGAAAAGATCGGAAGA", "AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT", null)
   [testng] PASSED: testPairedEndClip("Mis-match paired test matching", "CTACTGGCGCTGAAACTGAGCAGCCAAGCAGATCGG", "AGCTTGGCTGCTCAGTTTCAGCGCCAGTAGAGATCG", null)
   [testng] PASSED: testSingleEndSamRecordClip("Simple test 1", "AAAAACCCCCAGATCGGAAGAGCA", "AGATCGGAAGAGCG", 14, 0.15, 10)
   [testng] PASSED: testSingleEndSamRecordClip("Simple test 2", "AAAAACCCCCGGGGGAGATCGGAAGAGCA", "AGATCGGAAGAGCG", 14, 0.15, 15)
   [testng] PASSED: testSingleEndSamRecordClip("No adapter", "AAAAACCCCCGGGGGTTTTT", "AGATCGGAAGAGCG", 6, 0.15, -1)
   [testng] PASSED: testSingleEndSamRecordClip("Partial adapter", "AAAAACCCCCTGATCGGAA", "AGATCGGAAGAGCG", 9, 0.15, 10)
   [testng] PASSED: testSingleEndSamRecordClip("No sequence", null, "AGATCGGAAGAGCG", 6, 0.15, -1)
   [testng] PASSED: testSingleEndSamRecordClip("Read too short", "AGATCGGAAG", "AGATCGGAAGAGCG", 11, 0.15, -1)
   [testng] PASSED: testSingleEndSamRecordClip("All No Calls", "AAACCCNNNNNNNNNNNNNNNNNNNN", "AGATCGGAAGAGCG", 6, 0.15, -1)
   [testng] PASSED: testSingleEndSamRecordClip("From Test Data1", "CGGCATTCCTGCTGAACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGGGGGTGGATCTCGGTGGGCGGCGTGTTGT", "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", 57, 0.15, 19)
   [testng] PASSED: testSingleEndSamRecordClip("From Test Data2a", "CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCCGAA", "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", 9, 0.14, 27)
   [testng] PASSED: testSingleEndSamRecordClip("From Test Data2b", "CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAA", "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", 10, 0.14, -1)
   [testng] PASSED: testSingleEndSamRecordClip("From PE Test Data1", "CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT", "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG", 17, 0.14, 19)
   [testng] PASSED: testSingleEndSamRecordClip("From PE Test Data2", "CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT", "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", 5, 0.14, -1)
   [testng] PASSED: testSingleEndSamRecordClip("From Test 8-clipped", "TGGGGTGGTTATTGTTGATTTTTGTTTGTGTGTTAGGTTGTTTGTGTTAGTTTTTTATTTTATTTTCGAGATCGAA", "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG", 8, 0.14, 68)
   [testng] PASSED: testSingleEndSamRecordClip("50% can be bad", "AAAAACCCCCAGGTCGGAAGAGCG", "AGATCGGAAGAGCG", 5, 0.5, 18)
   [testng] PASSED: testSingleEndSamRecordClip("From 30E54AAXX.5.a", "ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG", "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG", 34, 0.14, 0)
   [testng] PASSED: testSingleEndSamRecordClip("From 30E54AAXX.5.b", "ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG", "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG", 34, 0.14, 0)
   [testng] PASSED: multiBinMixedEmptyBinTest
   [testng] PASSED: multiBinTest(testdata/picard/illumina/readerTests/s_3_2102.clocs, 0, 2102)
   [testng] PASSED: multiBinTest(testdata/picard/illumina/readerTests/s_3_2103.clocs, 2, 2103)
   [testng] PASSED: multiBinTest(testdata/picard/illumina/readerTests/s_3_2104.clocs, 0, 2104)
   [testng] PASSED: multiRowFileTest
   [testng] PASSED: singleBinTest
   [testng] PASSED: test
   [testng] PASSED: testBisulfite
   [testng] PASSED: testChimeras
   [testng] PASSED: testMultipleLevelsOfMetrics
   [testng] PASSED: testNoReference
   [testng] PASSED: testZeroLengthReads
   [testng] PASSED: runGcBiasMultiLevelTest
   [testng] PASSED: runWindowsComparisonTest
   [testng] PASSED: runCollectTargetedMetricsTest("testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam", "testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta", "testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list", "NONE", 1, 1, true, 2, 202, 0.5, 0.0, 0.505, 0.0, 1000)
   [testng] PASSED: runCollectTargetedMetricsTest("testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam", "testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta", "testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list", "NONE", 2, 0, true, 2, 202, 0, 0.0, 0.505, 0.0, 1000)
   [testng] PASSED: runCollectTargetedMetricsTest("testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam", "testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta", "testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list", "NONE", 0, 0, true, 2, 202, 0, 0.5, 0.505, 0.505, 1000)
   [testng] PASSED: runCollectTargetedMetricsTest("testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam", "testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta", "testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list", "NONE", 0, 0, false, 2, 202, 0, 0.0, 0.505, 0.505, 1000)
   [testng] PASSED: testIndexedRunLane1
   [testng] PASSED: testNonIndexedRunLane1
   [testng] PASSED: test
   [testng] PASSED: testHistogramWidthIsSetProperly
   [testng] PASSED: testMultipleOrientationsForHistogram
   [testng] PASSED: testAlignmentSummaryViaMultipleMetrics
   [testng] PASSED: testGcBiasMetrics
   [testng] PASSED: testInsertSize
   [testng] PASSED: test
   [testng] PASSED: basic
   [testng] PASSED: testMultiLevel
   [testng] PASSED: chrMReads
   [testng] PASSED: testContext
   [testng] PASSED: testDbSnp
   [testng] PASSED: testIntervalList
   [testng] PASSED: testNoBqCutoff
   [testng] PASSED: testNoMqCutoff
   [testng] PASSED: testUnmappedMate
   [testng] PASSED: runCollectTargetedMetricsTest(testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics7542775965639816387.bam, /tmp/test2914453680418370395.TargetedMetrics_Coverage, /tmp/perTarget8061096955868697126.perTargetCoverage, "testdata/picard/quality/chrM.reference.fasta", "testdata/picard/quality/chrM.single.interval_list", 1000)
   [testng] PASSED: runCollectTargetedMetricsTest(testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics7542775965639816387.bam, /tmp/test2914453680418370395.TargetedMetrics_Coverage, /tmp/perTarget8061096955868697126.perTargetCoverage, "testdata/picard/quality/chrM.reference.fasta", "testdata/picard/quality/chrM.empty.interval_list", 1000)
   [testng] PASSED: testMetricsTiny
   [testng] PASSED: testMetricsTinyGVCF
   [testng] PASSED: testMetricsFromClippedOverhangs
   [testng] PASSED: testPassingInGenomeTerritory
   [testng] PASSED: testContiguousIntervals
   [testng] PASSED: testOnePos
   [testng] PASSED: testMetricsFromWGS(testdata/picard/sam/CollectWgsMetrics9132011334233881654.bam, /tmp/testWgsMetrics828100590739198087.txt, "testdata/picard/quality/chrM.reference.fasta")
   [testng] PASSED: testAddToDefaultValuesListOption
   [testng] PASSED: testBadEnumValue
   [testng] PASSED: testBadValue
   [testng] PASSED: testClearDefaultValuesFromListOption
   [testng] PASSED: testClearDefaultValuesFromListOptionAndAddNew
   [testng] PASSED: testCollectionThatCannotBeAutoInitialized
   [testng] PASSED: testDefault
   [testng] PASSED: testDynamicNestedOptions
   [testng] PASSED: testDynamicPropagation
   [testng] PASSED: testHTMLConverter("hello", "hello")
   [testng] PASSED: testHTMLConverter("", "")
   [testng] PASSED: testHTMLConverter("hi</th>bye", "hi	bye")
   [testng] PASSED: testHTMLConverter("hi<th>bye", "hibye")
   [testng] PASSED: testHTMLConverter("hi<li>bye", "hi - bye")
   [testng] PASSED: testHTMLConverter("hi<NOT_A_REAL_TAG>bye", "hibye")
   [testng] PASSED: testHTMLConverter("</h4><pre>", "
   [testng] 
   [testng] ")
   [testng] PASSED: testHTMLConverter("<a href="http://go.here.org"> string</ a >", " string (http://go.here.org)")
   [testng] PASSED: testHTMLConverter("<a href="http://go.here.org" > string</ a>", " string (http://go.here.org)")
   [testng] PASSED: testHTMLConverter("< a href="http://go.here.org"> string<a />", " string (http://go.here.org)")
   [testng] PASSED: testHTMLConverter("hi</li>bye", "hi
   [testng] bye")
   [testng] PASSED: testHTMLConverter("Using read outputs from high throughput sequencing (HTS) technologies, this tool provides metrics regarding the quality of read alignments to a reference sequence, as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters (Illumina).<h4>Usage example:</h4><pre>    java -jar picard.jar CollectAlignmentSummaryMetrics \<br />          R=reference_sequence.fasta \<br />          I=input.bam \<br />          O=output.txt</pre>Please see <a href='http://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics'>the AlignmentSummaryMetrics documentation</a> for detailed explanations of each metric. <br /> <br />Additional information about Illumina's quality filters can be found in the following documents on the Illumina website:<ul><li><a href="http://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-percent-pf-technical-note-770-2014-043.pdf">hiseq-x-percent-pf-technical-note</a></li><li><a href="http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseqx/hiseq-x-system-guide-15050091-d.pdf">hiseq-x-system-guide</a></li></ul><hr />", "Using read outputs from high throughput sequencing (HTS) technologies, this tool provides metrics regarding the quality of read alignments to a reference sequence, as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters (Illumina).
   [testng] Usage example:
   [testng] 
   [testng]     java -jar picard.jar CollectAlignmentSummaryMetrics \
   [testng]           R=reference_sequence.fasta \
   [testng]           I=input.bam \
   [testng]           O=output.txt
   [testng] Please see the AlignmentSummaryMetrics documentation (http://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics) for detailed explanations of each metric. 
   [testng]  
   [testng] Additional information about Illumina's quality filters can be found in the following documents on the Illumina website:
   [testng]  - hiseq-x-percent-pf-technical-note (http://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-percent-pf-technical-note-770-2014-043.pdf)
   [testng]  - hiseq-x-system-guide (http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseqx/hiseq-x-system-guide-15050091-d.pdf)
   [testng] 
   [testng] 
   [testng] ")
   [testng] PASSED: testHtmlUnescape("<", "&lt;")
   [testng] PASSED: testHtmlUnescape("x<y", "x&lt;y")
   [testng] PASSED: testHtmlUnescape("x<y<z", "x&lt;y&lt;z")
   [testng] PASSED: testHtmlUnescape("
   [testng] ", "<p>")
   [testng] PASSED: testHtmlUnescape("<html> x<y </html> y< <strong> x </strong>", "<html> x&lt;y </html> y&lt; <strong> x </strong>")
   [testng] PASSED: testMissingRequiredArgument
   [testng] PASSED: testMutex("pass", [Ljava.lang.String;@51424203, true)
   [testng] PASSED: testMutex("no args", [Ljava.lang.String;@7336fd8f, false)
   [testng] PASSED: testMutex("1 of group required", [Ljava.lang.String;@701c223a, false)
   [testng] PASSED: testMutex("mutex", [Ljava.lang.String;@550c973e, false)
   [testng] PASSED: testMutex("mega mutex", [Ljava.lang.String;@161d95c6, false)
   [testng] PASSED: testNonAsciiAssertion
   [testng] PASSED: testNonAsciiConverted
   [testng] PASSED: testNotEnoughOfListOption
   [testng] PASSED: testNotEnoughPositional
   [testng] PASSED: testNullValue
   [testng] PASSED: testOptionDefinitionCaseClash
   [testng] PASSED: testOptionUseCaseClash
   [testng] PASSED: testOptionsFile
   [testng] PASSED: testOptionsFileWithDisallowedOverride
   [testng] PASSED: testOveriddenOptions
   [testng] PASSED: testPositive
   [testng] PASSED: testPositiveTerminalEqualSign
   [testng] PASSED: testPositiveWithSpaces
   [testng] PASSED: testPositiveWithoutPositional
   [testng] PASSED: testStaticNestedNegative
   [testng] PASSED: testStaticNestedOptions
   [testng] PASSED: testStaticPropagation
   [testng] PASSED: testStaticPropagationNegative
   [testng] PASSED: testTooManyListOption
   [testng] PASSED: testTooManyPositional
   [testng] PASSED: testUnexpectedPositional
   [testng] PASSED: testUninitializedCollections
   [testng] PASSED: testUsage
   [testng] PASSED: testUsageWithDefault
   [testng] PASSED: testUsageWithoutPositional
   [testng] PASSED: testUsageWithoutPositionalWithDefault
   [testng] PASSED: testBiggerSequenceDictionaries
   [testng] PASSED: testGroupWithSameCoordinate
   [testng] PASSED: testGroupWithSameCoordinateAndNoMatchInOther
   [testng] PASSED: testHasNonPrimary
   [testng] PASSED: testIdentical
   [testng] PASSED: testMoreOnOneSide
   [testng] PASSED: testSequenceDictionariesDifferent1
   [testng] PASSED: testSequenceDictionariesDifferent2
   [testng] PASSED: testSortsDifferent
   [testng] PASSED: testUnmapped1
   [testng] PASSED: testUnmapped2
   [testng] PASSED: testUnmapped3
   [testng] PASSED: testUnmapped4
   [testng] PASSED: testBasic
   [testng] PASSED: testNonUniqueSequenceName
   [testng] PASSED: basicParsingTest
   [testng] PASSED: parsingWithColumnHeadersTest
   [testng] PASSED: testDefaultMinGroupCount
   [testng] PASSED: testMaxDiffRate
   [testng] PASSED: testSimpleDuplicate
   [testng] PASSED: testSimpleDuplicateWithMaxReadLength
   [testng] PASSED: testBarcodeMatching
   [testng] PASSED: testDualBarcodes
   [testng] PASSED: testNonWritableOutputFile
   [testng] PASSED: testPairedEndWithBarcodeAndMolecularIndicies
   [testng] PASSED: testPairedEndWithBarcodeOnFirstEnd
   [testng] PASSED: testPairedEndWithBarcodeOnSecondEnd
   [testng] PASSED: testQualityBarcodes(16, 0, 1, 0, "Barcode has good quality, 1 match")
   [testng] PASSED: testQualityBarcodes(25, 0, 0, 0, "Barcode has quality failures, no matches")
   [testng] PASSED: testSingleEndWithBarcodeAtEnd
   [testng] PASSED: testSingleEndWithBarcodeAtEndAndMolecularIndicies
   [testng] PASSED: testSingleEndWithBarcodeAtStart
   [testng] PASSED: testSingleEndWithBarcodeAtStartAndMolecularIndicies
   [testng] PASSED: readPairNameBad("", "")
   [testng] PASSED: readPairNameBad("aa/1", "bb/2")
   [testng] PASSED: readPairNameBad("aa", "bb")
   [testng] PASSED: readPairNameBad("aa/1", "aa")
   [testng] PASSED: readPairNameBad("aa", "aa/2")
   [testng] PASSED: readPairNameBad("aa/1", "aa/1")
   [testng] PASSED: readPairNameBad("aa/2", "aa/2")
   [testng] PASSED: readPairNameOk("aa/1", "aa/2")
   [testng] PASSED: readPairNameOk("aa", "aa")
   [testng] PASSED: readPairNameOk("aa/bb", "aa/bb")
   [testng] PASSED: readPairNameOk("aa/bb/", "aa/bb/")
   [testng] PASSED: readPairNameOk("aa/bb/1", "aa/bb/2")
   [testng] PASSED: readPairNameOk("aa/bb/cc/dd/ee/ff/1", "aa/bb/cc/dd/ee/ff/2")
   [testng] PASSED: readPairNameOk("////1", "////2")
   [testng] PASSED: readPairNameOk("/", "/")
   [testng] PASSED: readPairNameOk("////", "////")
   [testng] PASSED: readPairNameOk("/aa", "/aa")
   [testng] PASSED: readPairNameOk("aa/", "aa/")
   [testng] PASSED: readPairNameOk("ab/c", "ab/c")
   [testng] PASSED: testBadFile("bad-format/bad-qual-header.txt")
   [testng] PASSED: testBadFile("bad-format/bad-seq-header.txt")
   [testng] PASSED: testBadFile("bad-format/extra-line.txt")
   [testng] PASSED: testBadFile("bad-format/too-many-quals.txt")
   [testng] PASSED: testBadFile("bad-format/1lines.txt")
   [testng] PASSED: testBadFile("bad-format/2lines.txt")
   [testng] PASSED: testBadFile("bad-format/3lines.txt")
   [testng] PASSED: testFastqVersionBad("fastq-sanger/sanger_full_range_as_sanger-63.fastq", Illumina)
   [testng] PASSED: testFastqVersionBad("fastq-solexa/s_1_sequence.txt", Illumina)
   [testng] PASSED: testFastqVersionOk("fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq", Standard)
   [testng] PASSED: testFastqVersionOk("fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq", Standard)
   [testng] PASSED: testFastqVersionOk("fastq-sanger/sanger_full_range_as_sanger-63.fastq", Standard)
   [testng] PASSED: testFastqVersionOk("fastq-solexa/s_1_sequence.txt", Solexa)
   [testng] PASSED: testFastqVersionOk("fastq-solexa/solexa_full_range_as_solexa.fastq", Solexa)
   [testng] PASSED: testFastqVersionOk("fastq-illumina/s_1_2_sequence.txt", Illumina)
   [testng] PASSED: testFastqVersionOk("fastq-illumina/s_1_2_sequence.txt", Illumina)
   [testng] PASSED: testFastqVersionOk("fastq-illumina/s_1_sequence.txt", Illumina)
   [testng] PASSED: testPairedBad("ok-paired/pair1.txt", "bad-paired/pair2-one-more-record.txt")
   [testng] PASSED: testPairedBad("bad-paired/pair1-one-more-record.txt", "ok-paired/pair2.txt")
   [testng] PASSED: testPairedBad("ok-paired/pair1.txt", "bad-paired/pair2-badnum.txt")
   [testng] PASSED: testPairedBad("bad-paired/pair1-badnum.txt", "ok-paired/pair2.txt")
   [testng] PASSED: testPairedBad("bad-paired/pair1-nonum.txt", "ok-paired/pair2.txt")
   [testng] PASSED: testPairedBad("bad-paired/pair1-onetoken.txt", "ok-paired/pair2.txt")
   [testng] PASSED: testPairedOk("ok-paired/pair1.txt", "ok-paired/pair2.txt", Standard)
   [testng] PASSED: testPairedOk("fastq-illumina/s_1_1_sequence.txt", "fastq-illumina/s_1_2_sequence.txt", Illumina)
   [testng] PASSED: testPermissiveFail("permissive-format/pair1.txt", "permissive-format/pair2.txt", Standard)
   [testng] PASSED: testPermissiveFail("permissive-format/s_1_1_sequence.txt", "permissive-format/s_1_2_sequence.txt", Illumina)
   [testng] PASSED: testPermissiveFail("permissive-format/pair1.txt", null, Standard)
   [testng] PASSED: testPermissiveFail("permissive-format/pair2.txt", null, Standard)
   [testng] PASSED: testPermissiveFail("permissive-format/s_1_1_sequence.txt", null, Illumina)
   [testng] PASSED: testPermissiveFail("permissive-format/s_1_2_sequence.txt", null, Illumina)
   [testng] PASSED: testPermissiveFail("permissive-format/s_1_sequence.txt", null, Illumina)
   [testng] PASSED: testPermissiveOk("permissive-format/pair1.txt", "permissive-format/pair2.txt", Standard)
   [testng] PASSED: testPermissiveOk("permissive-format/s_1_1_sequence.txt", "permissive-format/s_1_2_sequence.txt", Illumina)
   [testng] PASSED: testPermissiveOk("permissive-format/pair1.txt", null, Standard)
   [testng] PASSED: testPermissiveOk("permissive-format/pair2.txt", null, Standard)
   [testng] PASSED: testPermissiveOk("permissive-format/s_1_1_sequence.txt", null, Illumina)
   [testng] PASSED: testPermissiveOk("permissive-format/s_1_2_sequence.txt", null, Illumina)
   [testng] PASSED: testPermissiveOk("permissive-format/s_1_sequence.txt", null, Illumina)
   [testng] PASSED: testSequentialFiles
   [testng] PASSED: testFifoBuffer
   [testng] PASSED: testBasic
   [testng] PASSED: readFakedFile
   [testng] PASSED: readInvalidValuesForPicardException("pf_failing1.filter")
   [testng] PASSED: readInvalidValuesForPicardException("pf_failing2.filter")
   [testng] PASSED: readInvalidValuesForPicardException("pf_tooLarge.filter")
   [testng] PASSED: readInvalidValuesForPicardException("pf_tooShort.filter")
   [testng] PASSED: readInvalidValuesForPicardException("pf_badOpeningBytes.filter")
   [testng] PASSED: readInvalidValuesForPicardException("pf_badVersionBytes.filter")
   [testng] PASSED: readInvalidValuesForSAMException("pf_nonExistentFile.filter")
   [testng] PASSED: readPastEnd
   [testng] PASSED: readValidFile
   [testng] PASSED: passingParserTest([Ljava.lang.Integer;@4e17442f)
   [testng] PASSED: passingParserTest([Ljava.lang.Integer;@4f5c30b1)
   [testng] PASSED: passingParserTest([Ljava.lang.Integer;@62e73ab6)
   [testng] PASSED: passingParserTest([Ljava.lang.Integer;@5d7f8467)
   [testng] PASSED: passingParserTest([Ljava.lang.Integer;@29bd85db)
   [testng] PASSED: passingParserTest([Ljava.lang.Integer;@7caf1e5)
   [testng] PASSED: passingSeekingParserTest(0, 2, [Ljava.lang.Integer;@5c234920, [[Ljava.lang.Boolean;@7ddeb27f)
   [testng] PASSED: passingSeekingParserTest(4, 4, [Ljava.lang.Integer;@38087342, [[Ljava.lang.Boolean;@681de87f)
   [testng] PASSED: passingSeekingParserTest(0, 3, [Ljava.lang.Integer;@2eb1c615, [[Ljava.lang.Boolean;@2674d4f6)
   [testng] PASSED: passingSeekingParserTest(15, 3, [Ljava.lang.Integer;@5d9d2119, [[Ljava.lang.Boolean;@5a4464c5)
   [testng] PASSED: verifyDataTest([Ljava.lang.Integer;@7a55fb81, [Ljava.lang.Integer;@5a3cf878)
   [testng] PASSED: verifyDataTest([Ljava.lang.Integer;@34cd65ac, [Ljava.lang.Integer;@61911947)
   [testng] PASSED: verifyDataTest([Ljava.lang.Integer;@2dcd0e41, [Ljava.lang.Integer;@7272ee51)
   [testng] PASSED: verifyDataTest([Ljava.lang.Integer;@5940b14e, [Ljava.lang.Integer;@1cba0321)
   [testng] PASSED: verifyDataTest([Ljava.lang.Integer;@66d3b881, [Ljava.lang.Integer;@3a45afd4)
   [testng] PASSED: verifyDataTest([Ljava.lang.Integer;@74431b9c, [Ljava.lang.Integer;@f2fb225)
   [testng] PASSED: verifyDataTest([Ljava.lang.Integer;@3e0a9b1d, [Ljava.lang.Integer;@52f9e8bb)
   [testng] PASSED: testJavaScriptFilters("testdata/picard/sam/aligned.sam", "testdata/picard/sam/FilterSamReads/filterOddStarts.js", 3)
   [testng] PASSED: testJavaScriptFilters("testdata/picard/sam/aligned.sam", "testdata/picard/sam/FilterSamReads/filterReadsWithout5primeSoftClip.js", 0)
   [testng] PASSED: testRandomSublist
   [testng] PASSED: ignoreMissingMateExceptionTest
   [testng] PASSED: ignoreMissingMateTest
   [testng] PASSED: sanityCheckTheGathering
   [testng] PASSED: testTheGathering
   [testng] PASSED: testGA4GHScheme
   [testng] PASSED: testGA4GHSchemeDiffSamples
   [testng] PASSED: testGA4GHSchemeDiffSamplesWithIntervals
   [testng] PASSED: testGA4GHSchemeWithIntervals
   [testng] PASSED: testMissingHomRefSchemeWithIntervals
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", null, null, false, false, "CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff")
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/CEUTrio-indels.vcf, "NA12878", testdata/picard/vcf/CEUTrio-indels.vcf, "NA12878", null, null, false, false, "CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff")
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, "NA12878", null, null, false, false, "CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff")
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, "NA12878", null, null, false, false, "CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff")
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", testdata/picard/vcf/CEUTrio-snps_del_line.vcf, "NA12878", null, null, false, false, "CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff")
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", null, null, true, false, "CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows")
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", testdata/picard/vcf/CEUTrio-snps.vcf, "NA12891", 40, null, false, false, "CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq")
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", testdata/picard/vcf/CEUTrio-snps.vcf, "NA12891", null, 40, false, false, "CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp")
   [testng] PASSED: testGenotypeConcordance(testdata/picard/vcf/NIST.selected.vcf, "NA12878", testdata/picard/vcf/CEUTrio-snps.vcf, "NA12878", null, null, false, true, "NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff")
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, A*, C, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, C, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, A*, G, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, G, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, A*, T, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, T, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, C, C, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, G, G, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, T, T, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, A*, C, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, C, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, A*, C, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, C, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, A*, G, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, G, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, A*, G, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, G, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, A*, T, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, T, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, A*, T, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, T, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, A*, C, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, C, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, A*, C, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, C, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, A*, G, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, G, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, A*, G, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, G, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, A*, T, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, T, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, A*, T, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, T, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, A*, C, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, C, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, A*, C, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, C, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, A*, G, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, G, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, A*, G, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, G, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, A*, T, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, T, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, A*, T, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, T, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, G, T, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, T, G, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, G, T, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, T, G, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, C, T, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, T, C, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, C, T, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, T, C, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, C, G, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, G, C, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, C, G, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, G, C, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, C, C, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, C, C, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, G, G, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, G, G, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, C, HET_REF_VAR1, T, T, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, A*, HET_REF_VAR1, T, T, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, C, C, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, C, C, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, G, G, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, G, G, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, G, HET_REF_VAR1, T, T, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, A*, HET_REF_VAR1, T, T, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, C, C, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, C, C, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, G, G, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, G, G, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, T, HET_REF_VAR1, T, T, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, A*, HET_REF_VAR1, T, T, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, A*, C, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, C, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, A*, C, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, C, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, A*, G, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, G, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, A*, G, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, G, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, A*, T, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, T, A*, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, A*, T, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, T, A*, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, A*, C, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, C, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, A*, C, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, C, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, A*, G, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, G, A*, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, A*, G, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, G, A*, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, A*, T, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, T, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, A*, T, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, T, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, A*, C, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, C, A*, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, A*, C, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, C, A*, HET_REF_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, A*, G, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, G, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, A*, G, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, G, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, A*, T, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, T, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, A*, T, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, T, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, C, C, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, C, C, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, G, G, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, G, G, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, T, T, HOM_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, T, T, HOM_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, C, C, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, C, C, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, G, G, HOM_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, G, G, HOM_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, T, T, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, T, T, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, C, C, HOM_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, C, C, HOM_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, G, G, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, G, G, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, T, T, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, T, T, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, C, T, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, T, C, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, C, T, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, T, C, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, G, T, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, G, HET_VAR1_VAR2, T, G, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, G, T, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, C, HET_VAR1_VAR2, T, G, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, C, G, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, G, C, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, C, G, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, G, C, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, G, T, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, T, HET_VAR1_VAR2, T, G, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, G, T, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, C, HET_VAR1_VAR2, T, G, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, C, G, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, G, C, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, C, G, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, G, C, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, C, T, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, T, C, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, C, T, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, T, C, HET_VAR1_VAR3)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, T, HET_VAR1_VAR2, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, G, HET_VAR1_VAR2, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, A*, C, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, C, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, A*, G, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, G, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, A*, T, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, T, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, A*, C, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, C, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, A*, G, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, G, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, A*, T, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, T, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, A*, C, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, C, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, A*, G, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, G, A*, HET_REF_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, A*, T, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, T, A*, HET_REF_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, C, C, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, G, G, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, T, T, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, C, C, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, G, G, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, T, T, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, C, C, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, G, G, HOM_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, T, T, HOM_VAR1)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, G, T, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, C, HOM_VAR1, T, G, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, C, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, G, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, C, T, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, T, C, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(G, G, HOM_VAR1, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, C, G, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, G, C, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, C, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, T, C, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, G, T, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(T, T, HOM_VAR1, T, G, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, AA, HOM_VAR1, AAAA, AAAAA, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, AA, HOM_VAR1, AAAAA, AAAA, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, AAA, HET_VAR1_VAR2, AAAA, AAAAA, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, AAA, HET_VAR1_VAR2, AAAAA, AAAA, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AAA, AA, HET_VAR1_VAR2, AAAA, AAAAA, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AAA, AA, HET_VAR1_VAR2, AAAAA, AAAA, HET_VAR3_VAR4)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, AA, IS_MIXED, AAAA, AAAAA, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, AA, IS_MIXED, AAAAA, AAAA, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, C, IS_MIXED, AAAA, AAAAA, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, C, IS_MIXED, AAAAA, AAAA, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, C, IS_MIXED, AAAA, AAAAA, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, C, IS_MIXED, AAAAA, AAAA, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, AA, IS_MIXED, AAAA, AAAAA, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(C, AA, IS_MIXED, AAAAA, AAAA, HET_VAR1_VAR2)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, AA, HOM_VAR1, C, AAAAA, IS_MIXED)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, AA, HOM_VAR1, AAAAA, C, IS_MIXED)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, AAA, HET_VAR1_VAR2, AAAA, C, IS_MIXED)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AA, AAA, HET_VAR1_VAR2, C, AAAA, IS_MIXED)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AAA, AA, HET_VAR1_VAR2, AAAA, C, IS_MIXED)
   [testng] PASSED: testGenotypeConcordanceDetermineState(AAA, AA, HET_VAR1_VAR2, C, AAAA, IS_MIXED)
   [testng] PASSED: testGenotypeConcordanceDetermineState(., A*, NO_CALL, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, ., NO_CALL, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, ., NO_CALL, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(., A*, NO_CALL, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(., ., NO_CALL, A*, A*, HOM_REF)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, ., A*, NO_CALL)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, A*, ., NO_CALL)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, A*, ., NO_CALL)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, ., A*, NO_CALL)
   [testng] PASSED: testGenotypeConcordanceDetermineState(A*, A*, HOM_REF, ., ., NO_CALL)
   [testng] PASSED: testGenotypeConcordanceDetermineStateDp
   [testng] PASSED: testGenotypeConcordanceDetermineStateFilter
   [testng] PASSED: testGenotypeConcordanceDetermineStateGq
   [testng] PASSED: testGenotypeConcordanceDetermineStateNull
   [testng] PASSED: testHaplotypeMapReader
   [testng] PASSED: testHaplotypeMapWriter
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@4e67cfe1, test:1, 0, 0)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@55bf35e5, test:1, 0, 1)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@25567581, test:1, 0, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@179ee36b, test:1, 3, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@67763ebe, test:1, 7, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@4b4a2fa8, test:1, 35, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@5da6b13d, test:1, 40, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@3dc39459, test:1, 45, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@6b16de91, test:1, 69, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@71bb8b34, test:1, 73, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@197ce367, test:1, 76, 76)
   [testng] PASSED: testHaplotypeProbabilitiesFromSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromSequence@383cdd4d, test:1, [B@65036e8d, 7)
   [testng] PASSED: testHaplotypeProbabilitiesFromSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromSequence@48ccbb32, test:1, [B@36551e97, 7)
   [testng] PASSED: testHaplotypeProbabilitiesFromSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromSequence@685d7ba5, test:1, [B@16d41725, 7)
   [testng] PASSED: testHaplotypeProbabilitiesFromSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromSequence@3b6c2be6, test:1, [B@25533bba, 7)
   [testng] PASSED: testHaplotypeProbabilitiesFromSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromSequence@26d0ece6, test:1, [B@100bba26, 7)
   [testng] PASSED: testHaplotypeProbabilitiesFromSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromSequence@4ae280da, test:1, [B@76d0ecd7, 7)
   [testng] PASSED: testHaplotypeProbabilitiesFromSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromSequence@57c69937, test:1, [B@1ad1c363, 7)
   [testng] PASSED: testHaplotypeProbabilitiesFromSequenceAddToProbs(picard.fingerprint.HaplotypeProbabilitiesFromSequence@446b64b3, test:1, [B@35ac9ebd, 7)
   [testng] PASSED: testpEvidenceGivenPriorFromGLs(picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@53cb0bcb, [test:1], [false], [[D@51fe7f15])
   [testng] PASSED: testpEvidenceGivenPriorFromGLs(picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@5873f3f0, [test:1], [true], [[D@684372d0])
   [testng] PASSED: testpEvidenceGivenPriorFromGLs(picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@63dda940, [test:1, test:2], [false, false], [[D@41f964f9, [D@652e345])
   [testng] PASSED: testpEvidenceGivenPriorFromGLs(picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@7574d4ad, [test:1, test:2], [false, false], [[D@7bede4ea, [D@713999c2])
   [testng] PASSED: testpEvidenceGivenPriorFromGLs(picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@6060146b, [test:1, test:2], [false, false], [[D@33627576, [D@27bc1d44])
   [testng] PASSED: testGetLikelihoods(0.0, [D@1192c925, [D@615b5480)
   [testng] PASSED: testGetLikelihoods(0.0, [D@24691c5, [D@7b91d9f)
   [testng] PASSED: testGetLikelihoods(0.0, [D@6537ac, [D@3b218c74)
   [testng] PASSED: testGetLikelihoods(0.0, [D@ddffa6c, [D@42c54bad)
   [testng] PASSED: testGetLikelihoods(0.0, [D@6bb4cc0e, [D@5cc1bf20)
   [testng] PASSED: testGetLikelihoods(0.1, [D@2e3f324e, [D@46cf8c07)
   [testng] PASSED: testGetLikelihoods(0.2, [D@b56ec6c, [D@5abf6a99)
   [testng] PASSED: testGetLikelihoods(0.3, [D@dc59ec2, [D@375084c9)
   [testng] PASSED: testGetLikelihoods(0.1, [D@bd93bc3, [D@2a136383)
   [testng] PASSED: testGetLikelihoods(0.1, [D@b01cb8d, [D@38c460e8)
   [testng] PASSED: testGetLikelihoods(0.1, [D@7a814310, [D@4bbf38b8)
   [testng] PASSED: testDeMultiplexed
   [testng] PASSED: testDeMultiplexedWithIndex
   [testng] PASSED: testDeMultiplexedWithtwoIndexes
   [testng] PASSED: testDualBarcodes
   [testng] PASSED: testMultiplexWithIlluminaReadNameHeaders
   [testng] PASSED: testNonBarcoded
   [testng] PASSED: testBasic("1", "125T125T")
   [testng] PASSED: testBasic("2", "125T125T")
   [testng] PASSED: testMultiplexed
   [testng] PASSED: testMultiplexedWith4M4MIndex
   [testng] PASSED: testMultiplexedWith4MIndex
   [testng] PASSED: testMultiplexedWithAlternateBarcodeName
   [testng] PASSED: testNonBarcoded
   [testng] PASSED: testNonBarcodedWithDualMoleclarIndex
   [testng] PASSED: testNonBarcodedWithMoleclarIndex
   [testng] PASSED: testTileNumberComparator
   [testng] PASSED: barcodeParsingTest
   [testng] PASSED: testIlluminaDataProviderBclMethod("Bustard Parsing Test(25T8B25T) w/Clocs", 1, 180, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@56c0a61e, "25T8B25T", 0, 0, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderBclMethod("Bustard Parsing Test(25T8S25T) w/Clocs", 1, 180, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@421ead7e, "25T8S25T", 0, 0, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderBclMethod("Bustard Parsing Test(25T8S25T) w/Clocs with ending skip", 1, 180, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@5dcf0772, "25T8B1S", 0, 0, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderBclMethod("Bustard Parsing Test(25S8S25T) w/Clocs", 1, 180, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@c472300, "25S8S25T", 0, 0, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderBclMethod("Bustard Parsing Test(25T8B25T) w/Clocs And Seeking", 1, 61, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@5f6494c0, "25T8B25T", 2101, 4631, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderMissingDatas("Bad Lane(5)", 5, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@6826b70f, "25T8B25T", testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderMissingDatas("Bad Read Structure(25TB25T)", 4, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@781dac73, "25TB25T", testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderMissingDatas("Bad Read Structure(25T0B25T)", 4, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@781dac73, "25T0B25T", testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderMissingDatas("Bad Read Structure(-225T0B25T)", 4, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@781dac73, "-25T0B25T", testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderMissingDatas("Missing Barcodes File", 9, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@38c761e9, "25T8B25T", testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderMissingDatas("Missing Cycle File", 9, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@7f4e5a39, "25T8B25T", testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: testIlluminaDataProviderMissingDatas("Missing Filter File", 9, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@30159886, "25T8B24T", testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)
   [testng] PASSED: invalidLaneForLTRegex(-1000)
   [testng] PASSED: invalidLaneForLTRegex(-10)
   [testng] PASSED: invalidLaneForLTRegex(-1)
   [testng] PASSED: missingTileTest(1, [Bcl, Barcode], [Bcl, Barcode], [BaseCalls/s_1_0007_barcode.txt.gz], ".gz")
   [testng] PASSED: missingTileTest(2, [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [BaseCalls/L002/C1.1/s_2_2.bcl, BaseCalls/L002/C2.1/s_2_2.bcl, BaseCalls/L002/C3.1/s_2_2.bcl, BaseCalls/L002/C4.1/s_2_2.bcl, BaseCalls/L002/C5.1/s_2_2.bcl, BaseCalls/L002/C6.1/s_2_2.bcl, BaseCalls/L002/C7.1/s_2_2.bcl, BaseCalls/L002/C8.1/s_2_2.bcl, BaseCalls/L002/C9.1/s_2_2.bcl, BaseCalls/L002/C10.1/s_2_2.bcl, BaseCalls/L002/C11.1/s_2_2.bcl, BaseCalls/L002/C12.1/s_2_2.bcl, BaseCalls/L002/C13.1/s_2_2.bcl, BaseCalls/L002/C14.1/s_2_2.bcl, BaseCalls/L002/C15.1/s_2_2.bcl, BaseCalls/L002/C16.1/s_2_2.bcl, BaseCalls/L002/C17.1/s_2_2.bcl, BaseCalls/L002/C18.1/s_2_2.bcl, BaseCalls/L002/C19.1/s_2_2.bcl, BaseCalls/L002/C20.1/s_2_2.bcl], ".gz")
   [testng] PASSED: missingTileTest(3, [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [BaseCalls/L003/C1.1/s_3_2.bcl], ".bz2")
   [testng] PASSED: missingTileTest(4, [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [Pos, Locs], [s_4_10_pos.txt, L004/s_4_2.locs], null)
   [testng] PASSED: notMatchingRegexTest(0, "s_-0_111")
   [testng] PASSED: notMatchingRegexTest(1, "s_1_A3")
   [testng] PASSED: notMatchingRegexTest(10, "s_-100_1")
   [testng] PASSED: notMatchingRegexTest(20, "s_21_1")
   [testng] PASSED: passNewUtilTest
   [testng] PASSED: passingVerifyTest
   [testng] PASSED: perTileFileUtilsTest(Locs, null, false, "L007")
   [testng] PASSED: perTileFileUtilsTest(Clocs, null, false, "L007")
   [testng] PASSED: perTileFileUtilsTest(Pos, ".gz", false, null)
   [testng] PASSED: perTileFileUtilsTest(Pos, null, false, null)
   [testng] PASSED: perTileFileUtilsTest(Filter, null, true, "BaseCalls/L007")
   [testng] PASSED: perTileFileUtilsTest(Barcode, ".bz2", true, "BaseCalls")
   [testng] PASSED: perTilePerCycleFileUtilsMissingCycleTest([Range(10, 15, 6)])
   [testng] PASSED: perTilePerCycleFileUtilsMissingCycleTest([Range(9, 12, 4), Range(14, 15, 2)])
   [testng] PASSED: perTilePerCycleFileUtilsTest(Bcl, "BaseCalls/L007", [I@4e974b9e, false, false)
   [testng] PASSED: perTilePerCycleFileUtilsTest(Bcl, "BaseCalls/L007", [I@370c7cc5, true, true)
   [testng] PASSED: regexTests(0, "s_0_1111.test")
   [testng] PASSED: regexTests(1, "s_1_23.test")
   [testng] PASSED: regexTests(10, "s_10_1.test")
   [testng] PASSED: testCollectIlluminaLaneMetrics("A7LE0", 25T8B8B25T)
   [testng] PASSED: testCollectIlluminaLaneMetrics("C2MFAACXX", 95T101T)
   [testng] PASSED: testCollectIlluminaLaneMetrics("H7BATADXX", 76T8B76T)
   [testng] PASSED: testCollectIlluminaLaneMetrics("H7H7RADXX", 101T8B8B101T)
   [testng] PASSED: testCollectIlluminaLaneMetrics("A67HY", 8B8B)
   [testng] PASSED: testWriteLaneMetrics("130321_SL-MAK_0035_FC000000000-A306B")
   [testng] PASSED: testWriteLaneMetrics("130318_SL-HBB_0226_BFCC1WYMACXX")
   [testng] PASSED: testWriteLaneMetrics("130401_SL-HAC_0022_BH07PBADXX")
   [testng] PASSED: performanceTestGetTileFromReadName
   [testng] PASSED: testFindTileInReadName("300WFAAXX:1:119:1024:978#0/1", 119)
   [testng] PASSED: testFindTileInReadName("300WFAAXX090909:1:1:1024:978#0/1", 1)
   [testng] PASSED: testFindTileInReadName("FOO", null)
   [testng] PASSED: testFindTileInReadName("FOO:BAR_splat", null)
   [testng] PASSED: testScatter(Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})
   [testng] PASSED: testScatter(Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})
   [testng] PASSED: testScatter(Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})
   [testng] PASSED: testScatter(Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})
   [testng] PASSED: testScatter(Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})
   [testng] PASSED: testScatter(Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})
   [testng] PASSED: testConvertToBed
   [testng] PASSED: testDoNotFixReverseComplementedIndels
   [testng] PASSED: testFixReverseComplementedGenotypes
   [testng] PASSED: testMissingContigInReference(false, 1)
   [testng] PASSED: testMissingContigInReference(true, 0)
   [testng] PASSED: invalidFilesTest("s_1_7.locs")
   [testng] PASSED: invalidFilesTest("s_1_8.locs")
   [testng] PASSED: invalidFilesTest("s_1_9.locs")
   [testng] PASSED: invalidFilesTest("s_1_10.locs")
   [testng] PASSED: invalidFilesTest("s_f2af.locs")
   [testng] PASSED: passingFileTest
   [testng] PASSED: invalidFileSizeTests(1, 12)
   [testng] PASSED: invalidFileSizeTests(3, 11)
   [testng] PASSED: negativeHeaderTest
   [testng] PASSED: onlyHeaderTest
   [testng] PASSED: testValidConfigurations(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest$1@677cb96e)
   [testng] PASSED: testValidConfigurations(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest$2@1b1252c8)
   [testng] PASSED: testValidConfigurations(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest$3@19d53ab4)
   [testng] PASSED: tooLargeHeaderTest
   [testng] PASSED: logMathTest
   [testng] PASSED: testDivide([D@63124022, [D@591f6f83, [D@2b44605c)
   [testng] PASSED: testDivide([D@55421b8d, [D@24a04257, [D@6615237)
   [testng] PASSED: testDivide([D@eaf8427, [D@4bf4680c, [D@6d6039df)
   [testng] PASSED: testDivide([D@611c3eae, [D@13e00016, [D@7b3cbe6e)
   [testng] PASSED: testDivideFail([D@177ede17, [D@17176b18)
   [testng] PASSED: testDivideFail([D@1ab53860, [D@7b5ac347)
   [testng] PASSED: testSeqGeneration(0.0, 5.0, 1.0, [D@19ae36f4)
   [testng] PASSED: testSeqGeneration(0.0, 0.5, 0.1, [D@6735f210)
   [testng] PASSED: testSeqGeneration(0.0, 0.5, 0.11, [D@4567fb2b)
   [testng] PASSED: testSeqGeneration(50.0, 55.0, 1.25, [D@372954e1)
   [testng] PASSED: testSeqGeneration(10.0, 0.0, 2.0, [D@5fd8dd66)
   [testng] PASSED: testSeqGeneration(10.0, 0.0, -2.0, [D@173511ff)
   [testng] PASSED: testBestFragmentMapqStrategy("singleAlignmentFirstEnd", [I@57e03347, [I@2edb2f8b, 12, -1)
   [testng] PASSED: testBestFragmentMapqStrategy("singleAlignmentSecondEnd", [I@733f1395, [I@21dea711, -1, 12)
   [testng] PASSED: testBestFragmentMapqStrategy("singleAlignmentBothEnd", [I@7772d266, [I@a21c74, 13, 12)
   [testng] PASSED: testBestFragmentMapqStrategy("multipleBothEnds1", [I@b8a144e, [I@5fb8dc01, 11, 14)
   [testng] PASSED: testBestFragmentMapqStrategy("multipleBothEnds2", [I@3e38c472, [I@2ee92e7d, 255, 255)
   [testng] PASSED: testBestFragmentMapqStrategy("multipleFirstEnd", [I@759a678a, [I@6cdbe5ec, 12, -1)
   [testng] PASSED: testBestFragmentMapqStrategy("multipleSecondEnd", [I@14b8a751, [I@7345f97d, -1, 12)
   [testng] PASSED: testBestFragmentMapqStrategy("multipleFirstEndSingleSecondEnd", [I@554566a8, [I@66020d69, 12, 255)
   [testng] PASSED: testBestFragmentMapqStrategy("singleFirstEndMultipleSecondEnd", [I@3751acd7, [I@6b832551, 0, 12)
   [testng] PASSED: testContaminationDetection
   [testng] PASSED: testEarliestFragmentStrategy("simpleForward", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@72b2c5ed)
   [testng] PASSED: testEarliestFragmentStrategy("simpleReverse", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@41f785e3)
   [testng] PASSED: testEarliestFragmentStrategy("2 forward one earlier", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@6c9a3661)
   [testng] PASSED: testEarliestFragmentStrategy("forward earlier than reverse", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@727986ad)
   [testng] PASSED: testEarliestFragmentStrategy("reverse earlier than forward", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1600a8a2)
   [testng] PASSED: testEarliestFragmentStrategy("tie resolved via MAPQ", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@6b25ef1c)
   [testng] PASSED: testEarliestFragmentStrategy("tie with same MAPQ resolved arbitrarily", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@56b1e527)
   [testng] PASSED: testEarliestFragmentStrategy("one cigar with deletion and higher MAPQ", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@68c34db2)
   [testng] PASSED: testEarliestFragmentStrategy("one cigar with deletion and lower MAPQ", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@7b95bdb0)
   [testng] PASSED: testEarliestFragmentStrategy("Insertion makes alignment later", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@3f0ce0d1)
   [testng] PASSED: testEarliestFragmentStrategy("one cigar with deletion and higher MAPQ -- reverse", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@664db2ca)
   [testng] PASSED: testEarliestFragmentStrategy("one cigar with deletion and lower MAPQ -- reverse", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1491cd6c)
   [testng] PASSED: testEarliestFragmentStrategy("Insertion makes alignment later -- reverse", [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@423f8a73)
   [testng] PASSED: testEarliestFragmentStrategyPaired
   [testng] PASSED: testFragmentMultiHitWithFiltering("One secondary filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@22048bd6, picard.sam.MergeBamAlignmentTest$HitSpec@566c1e71, picard.sam.MergeBamAlignmentTest$HitSpec@2e2f20b8], -1, 2, 8)
   [testng] PASSED: testFragmentMultiHitWithFiltering("Primary filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@504497fa, picard.sam.MergeBamAlignmentTest$HitSpec@5618fc1f, picard.sam.MergeBamAlignmentTest$HitSpec@60b1ff3b], -1, 2, 11)
   [testng] PASSED: testFragmentMultiHitWithFiltering("Primary filtered, two secondaries with identical mapq", [picard.sam.MergeBamAlignmentTest$HitSpec@374c3975, picard.sam.MergeBamAlignmentTest$HitSpec@43c39321, picard.sam.MergeBamAlignmentTest$HitSpec@52aa7742], -1, 2, 11)
   [testng] PASSED: testFragmentMultiHitWithFiltering("Primary and one secondary filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@3d0d120b, picard.sam.MergeBamAlignmentTest$HitSpec@6b5c134e, picard.sam.MergeBamAlignmentTest$HitSpec@34d9df9f], -1, 1, 9)
   [testng] PASSED: testFragmentMultiHitWithFiltering("All filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@35c8be21, picard.sam.MergeBamAlignmentTest$HitSpec@60807fd9, picard.sam.MergeBamAlignmentTest$HitSpec@6bcdd6e4], null, 1, 0)
   [testng] PASSED: testMerger
   [testng] PASSED: testMergerFromMultipleFiles
   [testng] PASSED: testMergerWithSupplemental
   [testng] PASSED: testMergingFromSeparatedReadTrimmedAlignments(testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, "one file per read")
   [testng] PASSED: testMergingFromSeparatedReadTrimmedAlignments(testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, "two files per read")
   [testng] PASSED: testMostDistantStrategy("multipleAlignmentsBothEnds", [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3a38e4dc, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@41fc0084)
   [testng] PASSED: testMostDistantStrategy("multipleAlignmentsAllChimeric", [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@401788d5, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3ec9f8d)
   [testng] PASSED: testMostDistantStrategy("multipleAlignmentsFirstEnd", [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@7e0f9528, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5f56424d)
   [testng] PASSED: testMostDistantStrategy("multipleAlignmentsSecondEnd", [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@237b2852, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@448cdb47)
   [testng] PASSED: testMultiHit
   [testng] PASSED: testOldQuerynameSortFails
   [testng] PASSED: testPairedMultiHitWithFiltering("Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@7b8aebd0, picard.sam.MergeBamAlignmentTest$HitSpec@55222ee9, picard.sam.MergeBamAlignmentTest$HitSpec@3181d4de], [], -1, 1, 1, 9)
   [testng] PASSED: testPairedMultiHitWithFiltering("Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered", [], [picard.sam.MergeBamAlignmentTest$HitSpec@4f64d9cb, picard.sam.MergeBamAlignmentTest$HitSpec@639c7f9c, picard.sam.MergeBamAlignmentTest$HitSpec@270d5060], -1, 1, 1, 11)
   [testng] PASSED: testPairedMultiHitWithFiltering("Only 1st end has alignments, all are filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@1815577b, picard.sam.MergeBamAlignmentTest$HitSpec@71567f33, picard.sam.MergeBamAlignmentTest$HitSpec@71369e1a], [], null, 1, 1, 0)
   [testng] PASSED: testPairedMultiHitWithFiltering("Only 2nd end has alignments, all are filtered", [], [picard.sam.MergeBamAlignmentTest$HitSpec@3cf55e0c, picard.sam.MergeBamAlignmentTest$HitSpec@ee96866, picard.sam.MergeBamAlignmentTest$HitSpec@4c04216f], null, 1, 1, 0)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, one end of primary filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@987a0bb, picard.sam.MergeBamAlignmentTest$HitSpec@1f949ab9, picard.sam.MergeBamAlignmentTest$HitSpec@5a7b6b75], [picard.sam.MergeBamAlignmentTest$HitSpec@3719360c, picard.sam.MergeBamAlignmentTest$HitSpec@3afca2c, picard.sam.MergeBamAlignmentTest$HitSpec@3855d9b2], -1, 3, 3, 30)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, one end of primary filtered, one end of secondary filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@39f42d0e, picard.sam.MergeBamAlignmentTest$HitSpec@47a3d56a, picard.sam.MergeBamAlignmentTest$HitSpec@3a209918], [picard.sam.MergeBamAlignmentTest$HitSpec@2cae5fa7, picard.sam.MergeBamAlignmentTest$HitSpec@34aa8b61, picard.sam.MergeBamAlignmentTest$HitSpec@6d7b001b], -1, 2, 3, 30)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, both ends of primary filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@532dacf5, picard.sam.MergeBamAlignmentTest$HitSpec@da09250, picard.sam.MergeBamAlignmentTest$HitSpec@6d31f106], [picard.sam.MergeBamAlignmentTest$HitSpec@587f4f63, picard.sam.MergeBamAlignmentTest$HitSpec@660b1a9d, picard.sam.MergeBamAlignmentTest$HitSpec@6fb0261e], 1, 2, 2, 21)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq", [picard.sam.MergeBamAlignmentTest$HitSpec@d6b532f, picard.sam.MergeBamAlignmentTest$HitSpec@2f4d01b6, picard.sam.MergeBamAlignmentTest$HitSpec@112c2930], [picard.sam.MergeBamAlignmentTest$HitSpec@7f426ddd, picard.sam.MergeBamAlignmentTest$HitSpec@28e7bb31, picard.sam.MergeBamAlignmentTest$HitSpec@6fe04f2a], 1, 2, 2, 21)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq", [picard.sam.MergeBamAlignmentTest$HitSpec@1f758e4f, picard.sam.MergeBamAlignmentTest$HitSpec@733534f9, picard.sam.MergeBamAlignmentTest$HitSpec@661e279d], [picard.sam.MergeBamAlignmentTest$HitSpec@beabd6b, picard.sam.MergeBamAlignmentTest$HitSpec@38de5daf, picard.sam.MergeBamAlignmentTest$HitSpec@621624b1], -1, 2, 2, 30)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, secondary filtered on both ends", [picard.sam.MergeBamAlignmentTest$HitSpec@7523d5a1, picard.sam.MergeBamAlignmentTest$HitSpec@2bfc2f8b, picard.sam.MergeBamAlignmentTest$HitSpec@61853c7e], [picard.sam.MergeBamAlignmentTest$HitSpec@32e5af53, picard.sam.MergeBamAlignmentTest$HitSpec@5980fa73, picard.sam.MergeBamAlignmentTest$HitSpec@13ca16bf], 1, 2, 2, 40)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, secondary filtered on second end", [picard.sam.MergeBamAlignmentTest$HitSpec@5be4be74, picard.sam.MergeBamAlignmentTest$HitSpec@44641d6c, picard.sam.MergeBamAlignmentTest$HitSpec@1ae924f1], [picard.sam.MergeBamAlignmentTest$HitSpec@59d5a6fd, picard.sam.MergeBamAlignmentTest$HitSpec@27bcb4ad, picard.sam.MergeBamAlignmentTest$HitSpec@4357524b], 2, 3, 2, 40)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, secondary filtered on first end", [picard.sam.MergeBamAlignmentTest$HitSpec@104a287c, picard.sam.MergeBamAlignmentTest$HitSpec@64dc86c6, picard.sam.MergeBamAlignmentTest$HitSpec@26874f2c], [picard.sam.MergeBamAlignmentTest$HitSpec@5f3b84bd, picard.sam.MergeBamAlignmentTest$HitSpec@1e734eee, picard.sam.MergeBamAlignmentTest$HitSpec@1e191150], 2, 2, 3, 40)
   [testng] PASSED: testPairedMultiHitWithFiltering("Both ends aligned, all filtered", [picard.sam.MergeBamAlignmentTest$HitSpec@2fbd390, picard.sam.MergeBamAlignmentTest$HitSpec@166b11e, picard.sam.MergeBamAlignmentTest$HitSpec@5e68be2], [picard.sam.MergeBamAlignmentTest$HitSpec@5323999f, picard.sam.MergeBamAlignmentTest$HitSpec@f18b738, picard.sam.MergeBamAlignmentTest$HitSpec@3bc20984], null, 1, 1, 0)
   [testng] PASSED: testShortFragmentClipping
   [testng] PASSED: testSortingOnSamAlignmentMerger(testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, "Basic test with pre-sorted alignment")
   [testng] PASSED: testSortingOnSamAlignmentMerger(testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, "Basic test with unsorted alignment")
   [testng] PASSED: unsortedInputSortedOutputTest
   [testng] PASSED: testIteratorsOfUnevenLength
   [testng] PASSED: testOrderingAndCompleteness
   [testng] PASSED: testOutOfOrderIterators
   [testng] PASSED: multilevelCollectorTest([ALL_READS])
   [testng] PASSED: multilevelCollectorTest([SAMPLE, ALL_READS])
   [testng] PASSED: multilevelCollectorTest([SAMPLE, LIBRARY])
   [testng] PASSED: multilevelCollectorTest([READ_GROUP, LIBRARY])
   [testng] PASSED: multilevelCollectorTest([READ_GROUP, SAMPLE, LIBRARY])
   [testng] PASSED: multilevelCollectorTest([READ_GROUP, SAMPLE, LIBRARY, ALL_READS])
   [testng] PASSED: noIntervals
   [testng] PASSED: withIntervals
   [testng] PASSED: testDefaultRegex
   [testng] PASSED: testKeeper
   [testng] PASSED: testKeeperAtEndWithinCliqueOfAllOpticalDuplicates
   [testng] PASSED: testKeeperNotInList
   [testng] PASSED: testVeryLongReadNames
   [testng] PASSED: testFromSexMap([], [])
   [testng] PASSED: testFromSexMap([female1, female2, female3], [male1, male2, male3])
   [testng] PASSED: testFromSexMap([female1, female2, female3], [])
   [testng] PASSED: testFromSexMap([female1], [male1, male2, male3])
   [testng] PASSED: basicIterationTest
   [testng] PASSED: failVerifyTestMissingTile
   [testng] PASSED: failVerifyTestTooManyTiles
   [testng] PASSED: missingTileTest(-1)
   [testng] PASSED: missingTileTest(10)
   [testng] PASSED: missingTileTest(2147483647)
   [testng] PASSED: missingTileTest(-2147483648)
   [testng] PASSED: passVerifyTest
   [testng] PASSED: seekToTileTest(1, 4, null, null)
   [testng] PASSED: seekToTileTest(15, 1, null, null)
   [testng] PASSED: seekToTileTest(25, 3, null, null)
   [testng] PASSED: seekToTileTest(24, 5, null, null)
   [testng] PASSED: seekToTileTest(1, 3, 10, 1)
   [testng] PASSED: seekToTileTest(1, 3, 15, 2)
   [testng] PASSED: seekToTileTest(12, 2, 15, 4)
   [testng] PASSED: seekToTileTest(6, 3, 12, 5)
   [testng] PASSED: seekToTileTest(14, 5, 25, 2)
   [testng] PASSED: basicIterationTest
   [testng] PASSED: seekingIterationTest(1, 3, null, null)
   [testng] PASSED: seekingIterationTest(22, 1, null, null)
   [testng] PASSED: seekingIterationTest(38, 2, null, null)
   [testng] PASSED: seekingIterationTest(75, 4, null, null)
   [testng] PASSED: seekingIterationTest(1, 3, 70, 1)
   [testng] PASSED: seekingIterationTest(1, 3, 45, 2)
   [testng] PASSED: seekingIterationTest(12, 2, 59, 4)
   [testng] PASSED: seekingIterationTest(45, 3, 70, 3)
   [testng] PASSED: seekingIterationTest(14, 1, 5, 2)
   [testng] PASSED: TestPicardPublic
   [testng] PASSED: failingDataPosFileTest(testdata/picard/illumina/readerTests/s_1_1101_pos.txt)
   [testng] PASSED: failingDataPosFileTest(testdata/picard/illumina/readerTests/s_1_1102_pos.txt)
   [testng] PASSED: failingDataPosFileTest(testdata/picard/illumina/readerTests/s_1_1103_pos.txt)
   [testng] PASSED: failingNamePosFileTest
   [testng] PASSED: validPosFileTest
   [testng] PASSED: zeroLengthFileTest
   [testng] PASSED: multiTileDataTest([1, 2, 3], null, [testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_2_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_3_pos.txt])
   [testng] PASSED: multiTileDataTest([1, 2, 3], 1, [testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_2_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_3_pos.txt])
   [testng] PASSED: multiTileDataTest([1, 3], 0, [testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_3_pos.txt])
   [testng] PASSED: multiTileDataTest([3201, 3202], null, [testdata/picard/illumina/parserTests/posParser/s_9_3201_pos.txt, testdata/picard/illumina/parserTests/posParser/s_9_3202_pos.txt])
   [testng] PASSED: multiTileDataTest([3201, 3202], 1, [testdata/picard/illumina/parserTests/posParser/s_9_3201_pos.txt, testdata/picard/illumina/parserTests/posParser/s_9_3202_pos.txt])
   [testng] PASSED: singleTileDataTest(1, 1, testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt)
   [testng] PASSED: singleTileDataTest(1, null, testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt)
   [testng] PASSED: singleTileDataTest(3202, 3202, testdata/picard/illumina/parserTests/posParser/s_9_3202_pos.txt)
   [testng] PASSED: singleTileDataTest(3202, null, testdata/picard/illumina/parserTests/posParser/s_9_3202_pos.txt)
   [testng] PASSED: TestBuilder
   [testng] PASSED: TestInvalidArguments(-1.0)
   [testng] PASSED: TestInvalidArguments(-1.0E-5)
   [testng] PASSED: TestInvalidArguments(-5.0)
   [testng] PASSED: TestInvalidArguments(1.00001)
   [testng] PASSED: TestInvalidArguments(5.0)
   [testng] PASSED: TestInvalidArguments(50.0)
   [testng] PASSED: TestInvalidArguments(1.7976931348623157E308)
   [testng] PASSED: TestInvalidArguments(Infinity)
   [testng] PASSED: TestInvalidArguments(-Infinity)
   [testng] PASSED: TestInvalidTwice(true)
   [testng] PASSED: TestInvalidTwice(false)
   [testng] PASSED: testDownsampleSingleTile(0.3)
   [testng] PASSED: testDownsampleSingleTile(0.4)
   [testng] PASSED: testDownsampleSingleTile(0.5)
   [testng] PASSED: testDownsampleSingleTile(0.6)
   [testng] PASSED: testDownsampleSingleTile(0.7)
   [testng] PASSED: testDownsampleSingleTile(0.7999999999999999)
   [testng] PASSED: testDownsampleSingleTile(0.8999999999999999)
   [testng] PASSED: testDownsampleSingleTile(0.9999999999999999)
   [testng] PASSED: testBasicHalfmappedReadPair
   [testng] PASSED: testBasicPairedRead
   [testng] PASSED: testBasicUnmappedReadPair
   [testng] PASSED: testFragmentNoReadPair
   [testng] PASSED: testFailingRScript
   [testng] PASSED: testPassingRScript
   [testng] PASSED: testRScriptNotFound
   [testng] PASSED: testInvalidReadStructureFromList("", [])
   [testng] PASSED: testInvalidReadStructureFromList("0T", [0T])
   [testng] PASSED: testInvalidReadStructureFromList("-1T", [-1T])
   [testng] PASSED: testInvalidReadStructureFromList("0S", [0S])
   [testng] PASSED: testInvalidReadStructureFromList("0M", [0M])
   [testng] PASSED: testInvalidReadStructureFromList("-1B", [-1B])
   [testng] PASSED: testInvalidReadStructureFromList("-1M", [-1M])
   [testng] PASSED: testInvalidReadStructureFromList("-66S1B", [-66S, 1B])
   [testng] PASSED: testInvalidReadStructureFromList("77T82B0S", [77T, 82B, 0S])
   [testng] PASSED: testInvalidReadStructureFromString("", [])
   [testng] PASSED: testInvalidReadStructureFromString("0T", [0T])
   [testng] PASSED: testInvalidReadStructureFromString("-1T", [-1T])
   [testng] PASSED: testInvalidReadStructureFromString("0S", [0S])
   [testng] PASSED: testInvalidReadStructureFromString("0M", [0M])
   [testng] PASSED: testInvalidReadStructureFromString("-1B", [-1B])
   [testng] PASSED: testInvalidReadStructureFromString("-1M", [-1M])
   [testng] PASSED: testInvalidReadStructureFromString("8C", null)
   [testng] PASSED: testInvalidReadStructureFromString("B5", null)
   [testng] PASSED: testInvalidReadStructureFromString("SS", null)
   [testng] PASSED: testInvalidReadStructureFromString("SM", null)
   [testng] PASSED: testInvalidReadStructureFromString("75TS", null)
   [testng] PASSED: testInvalidReadStructureFromString("8*T", null)
   [testng] PASSED: testInvalidReadStructureFromString("-66S1B", [-66S, 1B])
   [testng] PASSED: testInvalidReadStructureFromString("-0T5B8C", null)
   [testng] PASSED: testInvalidReadStructureFromString("77T82B0S", [77T, 82B, 0S])
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@1002d192)
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@36ad5f2a)
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@55c50f52)
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@4044589a)
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@216f01)
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@1e721583)
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@722787b5)
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@8b41ad, "10T10T")
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@541d4d9f, "10T10T")
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@1a497286, "10T8B10T")
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@48dff674, "10T8B5M10T")
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@120350eb, "10T8B10T")
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@2ccc9681, "8S8S")
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@7d401cdc, "8S8S")
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@4a9b3956, "8B")
   [testng] PASSED: testSubstructureToReadStructure(picard.illumina.parser.ReadStructure$Substructure@4217bce6, "8M")
   [testng] PASSED: testValidStructuresFromList("2T", [2T], 1, 0, 0, 0)
   [testng] PASSED: testValidStructuresFromList("1234B", [1234B], 0, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromList("2147483647S", [2147483647S], 0, 0, 1, 0)
   [testng] PASSED: testValidStructuresFromList("2147483647M", [2147483647M], 0, 0, 0, 1)
   [testng] PASSED: testValidStructuresFromList("76T76T", [76T, 76T], 2, 0, 0, 0)
   [testng] PASSED: testValidStructuresFromList("76T1B", [76T, 1B], 1, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromList("76B1T", [76B, 1T], 1, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromList("1S1B", [1S, 1B], 0, 1, 1, 0)
   [testng] PASSED: testValidStructuresFromList("1S1B1M", [1S, 1B, 1M], 0, 1, 1, 1)
   [testng] PASSED: testValidStructuresFromList("1T999S", [1T, 999S], 1, 0, 1, 0)
   [testng] PASSED: testValidStructuresFromList("100T20T100T", [100T, 20T, 100T], 3, 0, 0, 0)
   [testng] PASSED: testValidStructuresFromList("2S50S10S", [2S, 50S, 10S], 0, 0, 3, 0)
   [testng] PASSED: testValidStructuresFromList("10T1B11T", [10T, 1B, 11T], 2, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromList("201T13T111B", [201T, 13T, 111B], 2, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromList("15B1T1T", [15B, 1T, 1T], 2, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromList("99B7T6B", [99B, 7T, 6B], 1, 2, 0, 0)
   [testng] PASSED: testValidStructuresFromList("631B776S638T", [631B, 776S, 638T], 1, 1, 1, 0)
   [testng] PASSED: testValidStructuresFromList("631M776S638T", [631M, 776S, 638T], 1, 0, 1, 1)
   [testng] PASSED: testValidStructuresFromList("3T7B60S2T", [3T, 7B, 60S, 2T], 2, 1, 1, 0)
   [testng] PASSED: testValidStructuresFromList("20B9S100T1T", [20B, 9S, 100T, 1T], 2, 1, 1, 0)
   [testng] PASSED: testValidStructuresFromList("33T42B9T81B", [33T, 42B, 9T, 81B], 2, 2, 0, 0)
   [testng] PASSED: testValidStructuresFromList("28B56B13T123S", [28B, 56B, 13T, 123S], 1, 2, 1, 0)
   [testng] PASSED: testValidStructuresFromList("92S8B8B32B", [92S, 8B, 8B, 32B], 0, 3, 1, 0)
   [testng] PASSED: testValidStructuresFromList("92S8M8M32M", [92S, 8M, 8M, 32M], 0, 0, 1, 3)
   [testng] PASSED: testValidStructuresFromList("2S88B7T8S9T9T84B100S2S4B3B", [2S, 88B, 7T, 8S, 9T, 9T, 84B, 100S, 2S, 4B, 3B], 3, 4, 4, 0)
   [testng] PASSED: testValidStructuresFromList("2S88B7T8S9T9T84B3M100S2S4B3M3B", [2S, 88B, 7T, 8S, 9T, 9T, 84B, 3M, 100S, 2S, 4B, 3M, 3B], 3, 4, 4, 2)
   [testng] PASSED: testValidStructuresFromString("2T", [2T], 1, 0, 0, 0)
   [testng] PASSED: testValidStructuresFromString("1234B", [1234B], 0, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromString("2147483647S", [2147483647S], 0, 0, 1, 0)
   [testng] PASSED: testValidStructuresFromString("2147483647M", [2147483647M], 0, 0, 0, 1)
   [testng] PASSED: testValidStructuresFromString("76T76T", [76T, 76T], 2, 0, 0, 0)
   [testng] PASSED: testValidStructuresFromString("76T1B", [76T, 1B], 1, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromString("76B1T", [76B, 1T], 1, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromString("1S1B", [1S, 1B], 0, 1, 1, 0)
   [testng] PASSED: testValidStructuresFromString("1S1B1M", [1S, 1B, 1M], 0, 1, 1, 1)
   [testng] PASSED: testValidStructuresFromString("1T999S", [1T, 999S], 1, 0, 1, 0)
   [testng] PASSED: testValidStructuresFromString("100T20T100T", [100T, 20T, 100T], 3, 0, 0, 0)
   [testng] PASSED: testValidStructuresFromString("2S50S10S", [2S, 50S, 10S], 0, 0, 3, 0)
   [testng] PASSED: testValidStructuresFromString("10T1B11T", [10T, 1B, 11T], 2, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromString("201T13T111B", [201T, 13T, 111B], 2, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromString("15B1T1T", [15B, 1T, 1T], 2, 1, 0, 0)
   [testng] PASSED: testValidStructuresFromString("99B7T6B", [99B, 7T, 6B], 1, 2, 0, 0)
   [testng] PASSED: testValidStructuresFromString("631B776S638T", [631B, 776S, 638T], 1, 1, 1, 0)
   [testng] PASSED: testValidStructuresFromString("631M776S638T", [631M, 776S, 638T], 1, 0, 1, 1)
   [testng] PASSED: testValidStructuresFromString("3T7B60S2T", [3T, 7B, 60S, 2T], 2, 1, 1, 0)
   [testng] PASSED: testValidStructuresFromString("20B9S100T1T", [20B, 9S, 100T, 1T], 2, 1, 1, 0)
   [testng] PASSED: testValidStructuresFromString("33T42B9T81B", [33T, 42B, 9T, 81B], 2, 2, 0, 0)
   [testng] PASSED: testValidStructuresFromString("28B56B13T123S", [28B, 56B, 13T, 123S], 1, 2, 1, 0)
   [testng] PASSED: testValidStructuresFromString("92S8B8B32B", [92S, 8B, 8B, 32B], 0, 3, 1, 0)
   [testng] PASSED: testValidStructuresFromString("92S8M8M32M", [92S, 8M, 8M, 32M], 0, 0, 1, 3)
   [testng] PASSED: testValidStructuresFromString("2S88B7T8S9T9T84B100S2S4B3B", [2S, 88B, 7T, 8S, 9T, 9T, 84B, 100S, 2S, 4B, 3B], 3, 4, 4, 0)
   [testng] PASSED: testValidStructuresFromString("2S88B7T8S9T9T84B3M100S2S4B3M3B", [2S, 88B, 7T, 8S, 9T, 9T, 84B, 3M, 100S, 2S, 4B, 3M, 3B], 3, 4, 4, 2)
   [testng] PASSED: basicNegativeTest("NewSample", null)
   [testng] PASSED: basicNegativeTest(null, "NewLibrary")
   [testng] PASSED: basicNegativeTest("NewSample", "NewLibrary")
   [testng] PASSED: basicPositiveTests(null, true, true, true, null, null, [])
   [testng] PASSED: basicPositiveTests(queryname, true, true, true, "Hey,Dad!", null, [XT])
   [testng] PASSED: basicPositiveTests(null, false, true, false, "Hey,Dad!", "NewLibraryName", [XT])
   [testng] PASSED: basicPositiveTests(null, false, false, false, null, null, [])
   [testng] PASSED: testBAMToCRAM
   [testng] PASSED: testBAMToSAM
   [testng] PASSED: testCRAMToBAM
   [testng] PASSED: testCRAMToSAM
   [testng] PASSED: testSAMToBAM
   [testng] PASSED: testSAMToCRAM
   [testng] PASSED: testBadFile("bad/unpaired-mate.sam")
   [testng] PASSED: testBadGroupedFile("bad/grouped-unpaired-mate.sam", null, null, [Ljava.lang.String;@6eda012b)
   [testng] PASSED: testClipping(null, "AAAAAAAAAA", "1111111111", "AAAAAAAAAA", "1111111111", "CCCCCCCCCC", "2222222222", "GGGGGGGGGG", "2222222222", "No clipping test")
   [testng] PASSED: testClipping("X", "AAAAAAA", "1111111", "AAAAAA", "111111", "CCCCCCCC", "22222222", "GGGGGG", "222222", "Cut clipped bases test")
   [testng] PASSED: testClipping("N", "AAAAAAANNN", "1111111111", "AAAAAANNNN", "1111111111", "CCCCCCCCNN", "2222222222", "GGGGGGNNNN", "2222222222", "Mask clipped bases test")
   [testng] PASSED: testClipping("2", "AAAAAAAAAA", "1111111###", "AAAAAAAAAA", "111111####", "CCCCCCCCCC", "22222222##", "GGGGGGGGGG", "222222####", "Change clipped qualities test")
   [testng] PASSED: testOkFile("ok/sorted-pair.sam")
   [testng] PASSED: testOkFile("ok/sorted-pair-no-rg.sam")
   [testng] PASSED: testOkFile("ok/last-pair-mates-flipped.sam")
   [testng] PASSED: testOkFile("ok/first-mate-bof-last-mate-eof.sam")
   [testng] PASSED: testOkGroupedFiles("ok/grouped-last-pair-mates-flipped.sam", null, null, [Ljava.lang.String;@721bf7ad)
   [testng] PASSED: testOkInterleavedFile("ok/sorted-pair.sam")
   [testng] PASSED: testOkInterleavedFile("ok/sorted-pair-no-rg.sam")
   [testng] PASSED: testOkInterleavedFile("ok/last-pair-mates-flipped.sam")
   [testng] PASSED: testOkInterleavedFile("ok/first-mate-bof-last-mate-eof.sam")
   [testng] PASSED: testTrimming("ok/sorted-pair.sam", 6, 7, 7, 5, 8, 8)
   [testng] PASSED: testTrimming("ok/sorted-pair.sam", 7, 7, 6, 3, 8, 8)
   [testng] PASSED: testSegregateReference("NNNNNAAAAANNNNNN", 1, [fake1:1-5	+	., fake1:6-10	+	., fake1:11-16	+	.])
   [testng] PASSED: testSegregateReference("NNNNNAAAAANNNNNN", 5, [fake1:1-5	+	., fake1:6-10	+	., fake1:11-16	+	.])
   [testng] PASSED: testSegregateReference("NNNNNAAAnANNNNNN", 6, [fake1:1-5	+	., fake1:6-10	+	., fake1:11-16	+	.])
   [testng] PASSED: testSegregateReference("AnTGCNNNNNACGTCG", 1, [fake1:1-5	+	., fake1:6-10	+	., fake1:11-16	+	.])
   [testng] PASSED: testSegregateReference("ACTGCNNNNNACGTCG", 4, [fake1:1-5	+	., fake1:6-10	+	., fake1:11-16	+	.])
   [testng] PASSED: testSegregateReference("ACTGCNNNNNACgctG", 5, [fake1:1-16	+	.])
   [testng] PASSED: testSegregateReference("ACNGCNNNNNACnTNG", 5, [fake1:1-16	+	.])
   [testng] PASSED: testSegregateReference("ACNGCNNNNNACnTNG", 0, [fake1:1-2	+	., fake1:3-3	+	., fake1:4-5	+	., fake1:6-10	+	., fake1:11-12	+	., fake1:13-13	+	., fake1:14-14	+	., fake1:15-15	+	., fake1:16-16	+	.])
   [testng] PASSED: testSegregateReference("AAAAAAAAAAACnTNG", 0, [fake1:1-12	+	., fake1:13-13	+	., fake1:14-14	+	., fake1:15-15	+	., fake1:16-16	+	.])
   [testng] PASSED: testSegregateReference("AAAAAAAAAAACATNG", 0, [fake1:1-14	+	., fake1:15-15	+	., fake1:16-16	+	.])
   [testng] PASSED: testSegregateReference("ANCNNGCNNNNNACNTNGN", 1, [fake1:1-3	+	., fake1:4-5	+	., fake1:6-7	+	., fake1:8-12	+	., fake1:13-18	+	., fake1:19-19	+	.])
   [testng] PASSED: testSegregateReference("ANCNNGCNNNNNACNTNGN", 0, [fake1:1-1	+	., fake1:2-2	+	., fake1:3-3	+	., fake1:4-5	+	., fake1:6-7	+	., fake1:8-12	+	., fake1:13-14	+	., fake1:15-15	+	., fake1:16-16	+	., fake1:17-17	+	., fake1:18-18	+	., fake1:19-19	+	.])
   [testng] PASSED: basicPositiveTest
   [testng] PASSED: testNoLibrarySpecified
   [testng] PASSED: testNoUnknownFile
   [testng] PASSED: testSplit
   [testng] PASSED: basicParsingTest
   [testng] PASSED: parsingWithColumnHeadersTest
   [testng] PASSED: testAbFiltering
   [testng] PASSED: testCombinedFiltering
   [testng] PASSED: testDpFiltering
   [testng] PASSED: testDpFilteringToVcf
   [testng] PASSED: testFilteringToVcfWithNoSequenceDictionary
   [testng] PASSED: testFsFiltering
   [testng] PASSED: testGqFiltering
   [testng] PASSED: testJavaScript
   [testng] PASSED: testNoFiltering
   [testng] PASSED: testMultiFileParsing(testdata/picard/util/whitespace_text_file.txt, testdata/picard/util/whitespace_text_file.txt)
   [testng] PASSED: testMultiFileParsing(sun.nio.ch.ChannelInputStream@4628a02b, sun.nio.ch.ChannelInputStream@2b01c689)
   [testng] PASSED: testTabbedFileParser(testdata/picard/util/tabbed_text_file.txt)
   [testng] PASSED: testTabbedFileParser(sun.nio.ch.ChannelInputStream@aa752bb)
   [testng] PASSED: testTextFileParser(testdata/picard/util/whitespace_text_file.txt)
   [testng] PASSED: testTextFileParser(sun.nio.ch.ChannelInputStream@77fc19cf)
   [testng] PASSED: testTextFileParserLeadingWhitespace(testdata/picard/util/all_ones_text_file.txt)
   [testng] PASSED: testTextFileParserLeadingWhitespace(sun.nio.ch.ChannelInputStream@643ecfef)
   [testng] PASSED: testTextFileParserNoGrouping(testdata/picard/util/no_grouping_file.txt)
   [testng] PASSED: testTextFileParserNoGrouping(sun.nio.ch.ChannelInputStream@1b31af02)
   [testng] PASSED: testTooManyWords(testdata/picard/util/whitespace_text_file.txt)
   [testng] PASSED: testTooManyWords(sun.nio.ch.ChannelInputStream@389a5022)
   [testng] PASSED: testWordCountCalculation("1	2	3", false, "Tabs with all fields filled.")
   [testng] PASSED: testWordCountCalculation("1	2	", false, "Tabs with no final field.")
   [testng] PASSED: testWordCountCalculation("	2	3", false, "Tabs with no first field.")
   [testng] PASSED: testWordCountCalculation("	2	", false, "Tabs with no first or final field.")
   [testng] PASSED: testWordCountCalculation("1  2  3", true, "Spaces with all fields filled  (grouping on).")
   [testng] PASSED: testWordCountCalculation("1  2  3  ", true, "Spaces with no final field (grouping on).")
   [testng] PASSED: testWordCountCalculation("   2   3   4", true, "Spaces with no first field (grouping on).")
   [testng] PASSED: testWordCountCalculation(" 2 ", false, "Spaces with no first or final field.")
   [testng] PASSED: testCentralLimitTheorem
   [testng] PASSED: testDeterministicQualityAndDepth
   [testng] PASSED: testHetAltDepthDistribution
   [testng] PASSED: testHetSensDistributions
   [testng] PASSED: testHetSensTargeted(0.913, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics)
   [testng] PASSED: testHetSensTargeted(0.9784, testdata/picard/analysis/TheoreticalSensitivity/test_NexPond-359781.hsMetrics)
   [testng] PASSED: testHetSensTargeted(0.9562, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics)
   [testng] PASSED: testHetSensTargeted(0.9892, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-316269_sampled.wgs_metrics)
   [testng] PASSED: testProportionsAboveThresholds
   [testng] PASSED: testRouletteWheel
   [testng] PASSED: ensureSameVariantsReadAsSimpleVcfFileIterator
   [testng] PASSED: ensureTestDataActuallyHasWideVariantAtTenMillion
   [testng] PASSED: ensureUniqueVariantObservationsEspeciallyMultiAllelicOnesThatAppearAtChunkingBoundaries
   [testng] PASSED: uByteToIntTest(-1, 255)
   [testng] PASSED: uByteToIntTest(-2, 254)
   [testng] PASSED: uByteToIntTest(-128, 128)
   [testng] PASSED: uByteToIntTest(127, 127)
   [testng] PASSED: uByteToIntTest(112, 112)
   [testng] PASSED: uByteToIntTest(2, 2)
   [testng] PASSED: uByteToIntTest(1, 1)
   [testng] PASSED: uByteToIntTest(0, 0)
   [testng] PASSED: uByteToShortTest(-1, 255)
   [testng] PASSED: uByteToShortTest(-2, 254)
   [testng] PASSED: uByteToShortTest(-128, 128)
   [testng] PASSED: uByteToShortTest(127, 127)
   [testng] PASSED: uByteToShortTest(112, 112)
   [testng] PASSED: uByteToShortTest(2, 2)
   [testng] PASSED: uByteToShortTest(1, 1)
   [testng] PASSED: uByteToShortTest(0, 0)
   [testng] PASSED: uIntToLongTest(-1, 4294967295)
   [testng] PASSED: uIntToLongTest(-2, 4294967294)
   [testng] PASSED: uIntToLongTest(-2130624512, 2164342784)
   [testng] PASSED: uIntToLongTest(2147483647, 2147483647)
   [testng] PASSED: uIntToLongTest(273686784, 273686784)
   [testng] PASSED: uIntToLongTest(2, 2)
   [testng] PASSED: uIntToLongTest(1, 1)
   [testng] PASSED: uIntToLongTest(0, 0)
   [testng] PASSED: uShortToIntTest(-1, 65535)
   [testng] PASSED: uShortToIntTest(-2, 65534)
   [testng] PASSED: uShortToIntTest(-32735, 32801)
   [testng] PASSED: uShortToIntTest(32767, 32767)
   [testng] PASSED: uShortToIntTest(21829, 21829)
   [testng] PASSED: uShortToIntTest(2, 2)
   [testng] PASSED: uShortToIntTest(1, 1)
   [testng] PASSED: uShortToIntTest(0, 0)
   [testng] PASSED: testUpdateVcfSequenceDictionary
   [testng] PASSED: testCombinationOne
   [testng] PASSED: testCombinationTwo
   [testng] PASSED: testContigs
   [testng] PASSED: testIdentical
   [testng] PASSED: testPositions
   [testng] PASSED: testThrowsOnDuplicateContig
   [testng] PASSED: ensureOverlapExclusionTest
   [testng] PASSED: testBcfToBcf
   [testng] PASSED: testBcfToVcf
   [testng] PASSED: testVcfToBcf
   [testng] PASSED: testVcfToVcf
   [testng] PASSED: testVcfToVcfGz
   [testng] PASSED: testHeaderVersion
   [testng] PASSED: testIntervals
   [testng] PASSED: testForVcf
   [testng] 
   [testng] ===============================================
   [testng]     Ant test
   [testng]     Tests run: 1625, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 
   [testng] 
   [testng] ===============================================
   [testng] picard-tests
   [testng] Total tests run: 1625, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 
   [testng] [TestNG] Time taken by org.testng.reporters.SuiteHTMLReporter@6ae40994: 237 ms
   [testng] [TestNG] Time taken by org.testng.reporters.EmailableReporter2@7e774085: 42 ms
   [testng] [TestNG] Time taken by org.testng.reporters.JUnitReportReporter@58d25a40: 54 ms
   [testng] [TestNG] Time taken by [FailedReporter passed=0 failed=0 skipped=0]: 0 ms
   [testng] [TestNG] Time taken by org.testng.reporters.XMLReporter@4c98385c: 118 ms
   [testng] [TestNG] Time taken by org.testng.reporters.jq.Main@61e717c2: 226 ms
[junitreport] the file /«BUILDDIR»/picard-tools-2.1.1+dfsg/dist/test/testng-results.xml is not a valid testsuite XML document
[junitreport] Processing /«BUILDDIR»/picard-tools-2.1.1+dfsg/dist/test/TESTS-TestSuites.xml to /«BUILDDIR»/picard-tools-2.1.1+dfsg/dist/test/junit-noframes.html
[junitreport] Loading stylesheet /«BUILDDIR»/picard-tools-2.1.1+dfsg/etc/test/junit-noframes.xsl
[junitreport] Transform time: 298ms
     [copy] Copying 1 file to /«BUILDDIR»/picard-tools-2.1.1+dfsg/dist/test

BUILD SUCCESSFUL
Total time: 3 minutes 25 seconds
make[1]: Leaving directory '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
 fakeroot debian/rules binary
dh  binary --with javahelper
   dh_testroot
   dh_prep
	rm -f debian/picard-tools.substvars
	rm -f debian/picard-tools.*.debhelper
	rm -rf debian/picard-tools/
	rm -f debian/libpicard-java.substvars
	rm -f debian/libpicard-java.*.debhelper
	rm -rf debian/libpicard-java/
	rm -f debian/libpicard-java-doc.substvars
	rm -f debian/libpicard-java-doc.*.debhelper
	rm -rf debian/libpicard-java-doc/
   dh_auto_install
	install -d debian/picard-tools
	install -d debian/libpicard-java
	install -d debian/libpicard-java-doc
   dh_install
	install -d debian/picard-tools/usr/bin
	cp --reflink=auto -a ./debian/bin/PicardCommandLine debian/picard-tools/usr/bin/
   jh_installjavadoc
Installing javadoc from javadoc/picard into package libpicard-java-doc
   dh_installdocs
	install -d debian/picard-tools/usr/share/doc/picard-tools
	install -p -m0644 debian/copyright debian/picard-tools/usr/share/doc/picard-tools/copyright
	install -d debian/libpicard-java/usr/share/doc/libpicard-java
	install -p -m0644 debian/copyright debian/libpicard-java/usr/share/doc/libpicard-java/copyright
	install -d debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc
	install -p -m0644 debian/copyright debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc/copyright
	install -d debian/libpicard-java-doc/usr/share/doc-base/
	install -p -m0644 debian/libpicard-java-doc.doc-base.javadoc debian/libpicard-java-doc/usr/share/doc-base/libpicard-java-doc
   dh_installchangelogs
	install -p -m0644 debian/changelog debian/picard-tools/usr/share/doc/picard-tools/changelog.Debian
	install -p -m0644 debian/changelog debian/libpicard-java/usr/share/doc/libpicard-java/changelog.Debian
	install -p -m0644 debian/changelog debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc/changelog.Debian
   dh_installman
	install -d debian/picard-tools/usr/share/man/man1/
	install -p -m0644 debian/PicardCommandLine.1 debian/picard-tools/usr/share/man/man1/PicardCommandLine.1
	man --recode UTF-8 ./PicardCommandLine\.1 > PicardCommandLine\.1\.new
	chmod 644 PicardCommandLine.1.new
	mv -f PicardCommandLine.1.new PicardCommandLine.1
   dh_perl
   dh_link
	rm -f debian/picard-tools/usr/share/man/man1/picard-tools.1
	ln -sf PicardCommandLine.1 debian/picard-tools/usr/share/man/man1/picard-tools.1
	rm -f debian/picard-tools/usr/bin/picard-tools
	ln -sf PicardCommandLine debian/picard-tools/usr/bin/picard-tools
   debian/rules override_jh_installlibs
make[1]: Entering directory '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
jh_installlibs --version-strip='[+]dfsg\.[0-9]*'
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/picard-tools for picard-tools
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java for libpicard-java
Installing library dist/picard.jar into package libpicard-java
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java-doc for libpicard-java-doc
make[1]: Leaving directory '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
   jh_classpath
Setting classpath on debian/libpicard-java/usr/share/java/picard.jar to /usr/share/java/htsjdk.jar /usr/share/java/guava.jar /usr/share/java/testng.jar
	Updating symlinked /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.1.1+dfsg.jar (via debian/libpicard-java/usr/share/java/picard.jar)
	Reading manifest from /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.1.1+dfsg.jar
	Updating manifest in /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.1.1+dfsg.jar
   jh_manifest
	find debian/picard-tools  -name '*.jar'
	find debian/libpicard-java  -name '*.jar'
	Found symlink usr/share/java/picard.jar
	Found usr/share/java/picard-2.1.1+dfsg.jar
	Reading manifest from debian/libpicard-java/usr/share/java/picard-2.1.1+dfsg.jar
	No update of debian/libpicard-java/usr/share/java/picard-2.1.1+dfsg.jar required.
	find debian/libpicard-java-doc  -name '*.jar'
   jh_exec
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/picard-tools for picard-tools
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java for libpicard-java
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java-doc for libpicard-java-doc
   jh_depends
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/picard-tools for picard-tools
Searching
Found Jars:
Found Debs:
Adding substvars: java:Depends= java:Recommends=
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java for libpicard-java
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.1.1+dfsg.jar
Found Jars: /usr/share/java/guava.jar /usr/share/java/htsjdk.jar /usr/share/java/testng.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/picard-tools/usr/share/java/guava.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java/usr/share/java/guava.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java-doc/usr/share/java/guava.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/picard-tools/usr/share/java/htsjdk-2.1.1.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java/usr/share/java/htsjdk-2.1.1.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java-doc/usr/share/java/htsjdk-2.1.1.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/picard-tools/usr/share/java/testng.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java/usr/share/java/testng.jar
Checking:  /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java-doc/usr/share/java/testng.jar
Found Debs: libguava-java libhtsjdk-java testng
Adding substvars: java:Depends=libguava-java,  libhtsjdk-java,  testng java:Recommends=
Searching /«BUILDDIR»/picard-tools-2.1.1+dfsg/debian/libpicard-java-doc for libpicard-java-doc
Searching
Found Jars:
Found Debs:
Adding substvars: java:Depends= java:Recommends=default-jdk-doc, libguava-java-doc, libhtsjdk-java-doc
   dh_strip_nondeterminism
   dh_compress
	cd debian/picard-tools
	chmod a-x usr/share/doc/picard-tools/changelog.Debian usr/share/man/man1/PicardCommandLine.1
	gzip -9nf usr/share/doc/picard-tools/changelog.Debian usr/share/man/man1/PicardCommandLine.1
	cd '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
	rm -f debian/picard-tools/usr/share/man/man1/picard-tools.1
	ln -sf PicardCommandLine.1.gz debian/picard-tools/usr/share/man/man1/picard-tools.1.gz
	cd debian/libpicard-java
	chmod a-x usr/share/doc/libpicard-java/changelog.Debian
	gzip -9nf usr/share/doc/libpicard-java/changelog.Debian
	cd '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
	cd debian/libpicard-java-doc
	chmod a-x usr/share/doc/libpicard-java-doc/changelog.Debian
	gzip -9nf usr/share/doc/libpicard-java-doc/changelog.Debian
	cd '/«BUILDDIR»/picard-tools-2.1.1+dfsg'
   dh_fixperms
	find debian/picard-tools  -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
	find debian/picard-tools ! -type l  -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/picard-tools/usr/share/doc -type f  ! -regex 'debian/picard-tools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/picard-tools/usr/share/doc -type d  -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/picard-tools/usr/share/man debian/picard-tools/usr/man/ debian/picard-tools/usr/X11*/man/ -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/picard-tools/usr/include -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/picard-tools/usr/share/applications -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/picard-tools/usr/lib/x86_64-linux-gnu/perl5/5.22 debian/picard-tools/usr/share/perl5 -type f -perm -5 -name '*.pm'  -print0 2>/dev/null | xargs -0r chmod a-X
	find debian/picard-tools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \)  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/picard-tools/usr/bin -type f  -print0 2>/dev/null | xargs -0r chmod a+x
	find debian/picard-tools/usr/lib -type f -name '*.ali'  -print0 2>/dev/null | xargs -0r chmod uga-w
	find debian/libpicard-java  -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
	find debian/libpicard-java ! -type l  -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/libpicard-java/usr/share/doc -type f  ! -regex 'debian/libpicard-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java/usr/share/doc -type d  -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libpicard-java/usr/share/man debian/libpicard-java/usr/man/ debian/libpicard-java/usr/X11*/man/ -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java/usr/include -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java/usr/share/applications -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java/usr/lib/x86_64-linux-gnu/perl5/5.22 debian/libpicard-java/usr/share/perl5 -type f -perm -5 -name '*.pm'  -print0 2>/dev/null | xargs -0r chmod a-X
	find debian/libpicard-java -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \)  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java/usr/lib -type f -name '*.ali'  -print0 2>/dev/null | xargs -0r chmod uga-w
	find debian/libpicard-java-doc  -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
	find debian/libpicard-java-doc ! -type l  -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/libpicard-java-doc/usr/share/doc -type f  ! -regex 'debian/libpicard-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java-doc/usr/share/doc -type d  -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libpicard-java-doc/usr/share/man debian/libpicard-java-doc/usr/man/ debian/libpicard-java-doc/usr/X11*/man/ -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java-doc/usr/include -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java-doc/usr/share/applications -type f  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java-doc/usr/lib/x86_64-linux-gnu/perl5/5.22 debian/libpicard-java-doc/usr/share/perl5 -type f -perm -5 -name '*.pm'  -print0 2>/dev/null | xargs -0r chmod a-X
	find debian/libpicard-java-doc -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \)  -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libpicard-java-doc/usr/lib -type f -name '*.ali'  -print0 2>/dev/null | xargs -0r chmod uga-w
   dh_installdeb
	install -d debian/picard-tools/DEBIAN
	install -d debian/libpicard-java/DEBIAN
	install -d debian/libpicard-java-doc/DEBIAN
   dh_gencontrol
	echo misc:Depends= >> debian/picard-tools.substvars
	echo misc:Pre-Depends= >> debian/picard-tools.substvars
	dpkg-gencontrol -ppicard-tools -ldebian/changelog -Tdebian/picard-tools.substvars -Pdebian/picard-tools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
	chmod 0644 debian/picard-tools/DEBIAN/control
	chown 0:0 debian/picard-tools/DEBIAN/control
	echo misc:Depends= >> debian/libpicard-java.substvars
	echo misc:Pre-Depends= >> debian/libpicard-java.substvars
	dpkg-gencontrol -plibpicard-java -ldebian/changelog -Tdebian/libpicard-java.substvars -Pdebian/libpicard-java
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
	chmod 0644 debian/libpicard-java/DEBIAN/control
	chown 0:0 debian/libpicard-java/DEBIAN/control
	echo misc:Depends= >> debian/libpicard-java-doc.substvars
	echo misc:Pre-Depends= >> debian/libpicard-java-doc.substvars
	dpkg-gencontrol -plibpicard-java-doc -ldebian/changelog -Tdebian/libpicard-java-doc.substvars -Pdebian/libpicard-java-doc
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
	chmod 0644 debian/libpicard-java-doc/DEBIAN/control
	chown 0:0 debian/libpicard-java-doc/DEBIAN/control
dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform amd64: 
dh_gencontrol debug symbol wrapper: packages to act on: 
dh_gencontrol debug symbol wrapper: ignored packages: 
   dh_md5sums
	(cd debian/picard-tools >/dev/null ; find . -type f  ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
	chmod 0644 debian/picard-tools/DEBIAN/md5sums
	chown 0:0 debian/picard-tools/DEBIAN/md5sums
	(cd debian/libpicard-java >/dev/null ; find . -type f  ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
	chmod 0644 debian/libpicard-java/DEBIAN/md5sums
	chown 0:0 debian/libpicard-java/DEBIAN/md5sums
	(cd debian/libpicard-java-doc >/dev/null ; find . -type f  ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
	chmod 0644 debian/libpicard-java-doc/DEBIAN/md5sums
	chown 0:0 debian/libpicard-java-doc/DEBIAN/md5sums
   dh_builddeb
	dpkg-deb --build debian/picard-tools ..
	dpkg-deb --build debian/libpicard-java ..
	dpkg-deb --build debian/libpicard-java-doc ..
INFO: pkgstriptranslations version 129
INFO: pkgstriptranslations version 129
INFO: pkgstriptranslations version 129
pkgstriptranslations: processing libpicard-java (in debian/libpicard-java); do_strip: , oemstrip: 
pkgstriptranslations: processing picard-tools (in debian/picard-tools); do_strip: , oemstrip: 
pkgstriptranslations: processing libpicard-java-doc (in debian/libpicard-java-doc); do_strip: , oemstrip: 
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/libpicard-java-doc/DEBIAN/control, package libpicard-java-doc, directory debian/libpicard-java-doc
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/libpicard-java/DEBIAN/control, package libpicard-java, directory debian/libpicard-java
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
INFO: pkgstripfiles: waiting for lock (libpicard-java) ...
INFO: pkgstripfiles: waiting for lock (libpicard-java-doc) ...
pkgstripfiles: processing control file: debian/picard-tools/DEBIAN/control, package picard-tools, directory debian/picard-tools
Searching for duplicated docs in dependency libpicard-java...
  symlinking changelog.Debian.gz in picard-tools to file in libpicard-java
pkgstripfiles: Running PNG optimization (using 4 cpus) for package picard-tools ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'picard-tools' in '../picard-tools_2.1.1+dfsg-1_all.deb'.
pkgstripfiles: Truncating usr/share/doc/libpicard-java/changelog.Debian.gz to topmost ten records
pkgstripfiles: Truncating usr/share/doc/libpicard-java-doc/changelog.Debian.gz to topmost ten records
pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpicard-java ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'libpicard-java' in '../libpicard-java_2.1.1+dfsg-1_all.deb'.
pkgstripfiles: Disabled PNG optimization for -doc package libpicard-java-doc (to save build time)
dpkg-deb: building package 'libpicard-java-doc' in '../libpicard-java-doc_2.1.1+dfsg-1_all.deb'.
 dpkg-genchanges -b -mLaunchpad Build Daemon <buildd@lgw01-16.buildd> >../picard-tools_2.1.1+dfsg-1_amd64.changes
dpkg-genchanges: binary-only upload (no source code included)
 dpkg-source --after-build picard-tools-2.1.1+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20160427-0433

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot                                                            │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


picard-tools_2.1.1+dfsg-1_amd64.changes:
────────────────────────────────────────

Format: 1.8
Date: Tue, 05 Apr 2016 09:59:27 +0200
Source: picard-tools
Binary: picard-tools libpicard-java libpicard-java-doc
Architecture: all
Version: 2.1.1+dfsg-1
Distribution: yakkety-proposed
Urgency: medium
Maintainer: Launchpad Build Daemon <buildd@lgw01-16.buildd>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 libpicard-java - Java library to manipulate SAM and BAM files
 libpicard-java-doc - Documentation for the java picard library
 picard-tools - Command line tools to manipulate SAM and BAM files
Changes:
 picard-tools (2.1.1+dfsg-1) unstable; urgency=medium
 .
   * New upstream version
   * Adapt debian/watch to use xz compression
   * Remove Shaun Jackman and add myself as Uploader
   * cme fix dpkg-control
 .
   [ Steffen Moeller and Jon Ison ]
   * Added EDAM annotation to debian/upstream/edam
Checksums-Sha1:
 1e215bf0b0368625376845fbd3d057532718634d 466354 libpicard-java-doc_2.1.1+dfsg-1_all.deb
 f7316597fa251b3f752bf99bab749d11b8cd589e 557062 libpicard-java_2.1.1+dfsg-1_all.deb
 cc14815a63a725c189cc49d7354b6ae3967796c1 4032 picard-tools_2.1.1+dfsg-1_all.deb
Checksums-Sha256:
 ab8fbdacf594f02303d7804a70a4c6df6a2d68c841239e0cc6158488d13e6d1c 466354 libpicard-java-doc_2.1.1+dfsg-1_all.deb
 f6dd955551d485f56393b3d576d3fd48f449a90d42624440d3cbc0c8e36f216b 557062 libpicard-java_2.1.1+dfsg-1_all.deb
 26c40324b4b06fe48f8fc6981d02659635e7299bbee2fd2a55c81fc896b4c441 4032 picard-tools_2.1.1+dfsg-1_all.deb
Files:
 04edd34358cc3f807f1e63be3d5c492f 466354 doc optional libpicard-java-doc_2.1.1+dfsg-1_all.deb
 9d4c7d3c326b9940acc6f6df8f5896c5 557062 java optional libpicard-java_2.1.1+dfsg-1_all.deb
 52c2e452d3be43ec3c51cb9bd5389925 4032 science optional picard-tools_2.1.1+dfsg-1_all.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


libpicard-java-doc_2.1.1+dfsg-1_all.deb
───────────────────────────────────────

 new debian package, version 2.0.
 size 466354 bytes: control archive=25990 bytes.
     728 bytes,    17 lines      control              
  105337 bytes,   903 lines      md5sums              
 Package: libpicard-java-doc
 Source: picard-tools
 Version: 2.1.1+dfsg-1
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 13598
 Recommends: default-jdk-doc, libguava-java-doc, libhtsjdk-java-doc
 Section: doc
 Priority: optional
 Homepage: http://broadinstitute.github.io/picard/
 Description: Documentation for the java picard library
  SAM (Sequence Alignment/Map) format is a generic format for storing
  large nucleotide sequence alignments. The picard java library provides classes
  to manipulate SAM and BAM files.
  .
  This package contains the javadoc of the picard java library.

drwxr-xr-x root/root         0 2016-04-27 04:32 ./
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/doc-base/
-rw-r--r-- root/root       303 2016-04-27 04:32 ./usr/share/doc-base/libpicard-java-doc
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/doc/libpicard-java-doc/
-rw-r--r-- root/root      1106 2016-04-27 04:33 ./usr/share/doc/libpicard-java-doc/changelog.Debian.gz
-rw-r--r-- root/root      2513 2016-04-05 08:00 ./usr/share/doc/libpicard-java-doc/copyright
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/doc/libpicard-java/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/
-rw-r--r-- root/root     57309 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/allclasses-frame.html
-rw-r--r-- root/root     49729 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/allclasses-noframe.html
-rw-r--r-- root/root     62867 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/constant-values.html
-rw-r--r-- root/root      8152 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/deprecated-list.html
-rw-r--r-- root/root      8747 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/help-doc.html
-rw-r--r-- root/root   1240986 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/index-all.html
-rw-r--r-- root/root      2804 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/index.html
-rw-r--r-- root/root      3400 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/overview-frame.html
-rw-r--r-- root/root      8144 2016-04-27 04:32 ./usr/share/doc/libpicard-java/api/overview-summary.html
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libpicard-java_2.1.1+dfsg-1_all.deb
───────────────────────────────────

 new debian package, version 2.0.
 size 557062 bytes: control archive=766 bytes.
     840 bytes,    22 lines      control              
     227 bytes,     3 lines      md5sums              
 Package: libpicard-java
 Source: picard-tools
 Version: 2.1.1+dfsg-1
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2365
 Depends: libguava-java, libhtsjdk-java (>= 2.1.1), testng
 Recommends: r-base-core
 Suggests: picard-tools
 Breaks: picard-tools (<< 1.114)
 Replaces: picard-tools (<< 1.114)
 Section: java
 Priority: optional
 Homepage: http://broadinstitute.github.io/picard/
 Description: Java library to manipulate SAM and BAM files
  SAM (Sequence Alignment/Map) format is a generic format for storing
  large nucleotide sequence alignments. This library provides classes to
  manipulate SAM and BAM files.
  .
  A command line wrapper for this library is provided in the picard-tools
  package.

drwxr-xr-x root/root         0 2016-04-27 04:32 ./
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/doc/libpicard-java/
-rw-r--r-- root/root      1103 2016-04-27 04:33 ./usr/share/doc/libpicard-java/changelog.Debian.gz
-rw-r--r-- root/root      2513 2016-04-05 08:00 ./usr/share/doc/libpicard-java/copyright
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/java/
-rw-r--r-- root/root   2407971 2016-04-27 04:32 ./usr/share/java/picard-2.1.1+dfsg.jar
lrwxrwxrwx root/root         0 2016-04-27 04:32 ./usr/share/java/picard.jar -> picard-2.1.1+dfsg.jar


picard-tools_2.1.1+dfsg-1_all.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 4032 bytes: control archive=1420 bytes.
    2723 bytes,    53 lines      control              
     207 bytes,     3 lines      md5sums              
 Package: picard-tools
 Version: 2.1.1+dfsg-1
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 18
 Depends: default-jre | java6-runtime, libpicard-java (= 2.1.1+dfsg-1)
 Section: science
 Priority: optional
 Homepage: http://broadinstitute.github.io/picard/
 Description: Command line tools to manipulate SAM and BAM files
  SAM (Sequence Alignment/Map) format is a generic format for storing
  large nucleotide sequence alignments. Picard Tools includes these
  utilities to manipulate SAM and BAM files:
   AddCommentsToBam                  FifoBuffer
   AddOrReplaceReadGroups            FilterSamReads
   BaitDesigner                      FilterVcf
   BamIndexStats                     FixMateInformation
   BamToBfq                          GatherBamFiles
   BedToIntervalList                 GatherVcfs
   BuildBamIndex                     GenotypeConcordance
   CalculateHsMetrics                IlluminaBasecallsToFastq
   CalculateReadGroupChecksum        IlluminaBasecallsToSam
   CheckIlluminaDirectory            LiftOverIntervalList
   CheckTerminatorBlock              LiftoverVcf
   CleanSam                          MakeSitesOnlyVcf
   CollectAlignmentSummaryMetrics    MarkDuplicates
   CollectBaseDistributionByCycle    MarkDuplicatesWithMateCigar
   CollectGcBiasMetrics              MarkIlluminaAdapters
   CollectHiSeqXPfFailMetrics        MeanQualityByCycle
   CollectIlluminaBasecallingMetrics MergeBamAlignment
   CollectIlluminaLaneMetrics        MergeSamFiles
   CollectInsertSizeMetrics          MergeVcfs
   CollectJumpingLibraryMetrics      NormalizeFasta
   CollectMultipleMetrics            PositionBasedDownsampleSam
   CollectOxoGMetrics                QualityScoreDistribution
   CollectQualityYieldMetrics        RenameSampleInVcf
   CollectRawWgsMetrics              ReorderSam
   CollectRnaSeqMetrics              ReplaceSamHeader
   CollectRrbsMetrics                RevertOriginalBaseQualitiesAndAddMateCigar
   CollectSequencingArtifactMetrics  RevertSam
   CollectTargetedPcrMetrics         SamFormatConverter
   CollectVariantCallingMetrics      SamToFastq
   CollectWgsMetrics                 ScatterIntervalsByNs
   CompareMetrics                    SortSam
   CompareSAMs                       SortVcf
   ConvertSequencingArtifactToOxoG   SplitSamByLibrary
   CreateSequenceDictionary          SplitVcfs
   DownsampleSam                     UpdateVcfSequenceDictionary
   EstimateLibraryComplexity         ValidateSamFile
   ExtractIlluminaBarcodes           VcfFormatConverter
   ExtractSequences                  VcfToIntervalList
   FastqToSam                        ViewSam

drwxr-xr-x root/root         0 2016-04-27 04:32 ./
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/bin/
-rwxr-xr-x root/root       311 2016-04-05 08:00 ./usr/bin/PicardCommandLine
lrwxrwxrwx root/root         0 2016-04-27 04:32 ./usr/bin/picard-tools -> PicardCommandLine
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-04-27 04:33 ./usr/share/doc/picard-tools/
lrwxrwxrwx root/root         0 2016-04-27 04:33 ./usr/share/doc/picard-tools/changelog.Debian.gz -> ../libpicard-java/changelog.Debian.gz
-rw-r--r-- root/root      2513 2016-04-05 08:00 ./usr/share/doc/picard-tools/copyright
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/man/
drwxr-xr-x root/root         0 2016-04-27 04:32 ./usr/share/man/man1/
-rw-r--r-- root/root       469 2016-04-27 04:32 ./usr/share/man/man1/PicardCommandLine.1.gz
lrwxrwxrwx root/root         0 2016-04-27 04:32 ./usr/share/man/man1/picard-tools.1.gz -> PicardCommandLine.1.gz


┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Not removing build depends: as requested
Keeping session: 

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Build Architecture: amd64
Build-Space: 76788
Build-Time: 259
Distribution: yakkety-proposed
Host Architecture: amd64
Install-Time: 67
Job: picard-tools_2.1.1+dfsg-1.dsc
Machine Architecture: amd64
Package: picard-tools
Package-Time: 327
Source-Version: 2.1.1+dfsg-1
Space: 76788
Status: successful
Version: 2.1.1+dfsg-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20160427-0433
Build needed 00:05:27, 76788k disc space
RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-9645758']
Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-9645758/chroot-autobuild...
RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-9645758']
Unmounting chroot for build PACKAGEBUILD-9645758...
RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-9645758']
Removing build PACKAGEBUILD-9645758