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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update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
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Local time is now: Wed Apr 27 04:27:43 UTC 2016.
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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 │
└──────────────────────────────────────────────────────────────────────────────┘
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picard-tools_2.1.1+dfsg-1.dsc exists in .; copying to chroot
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-O8_Blx/apt_archive/sbuild-build-depends-core-dummy.deb'.
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│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
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sbuild-build-depends-core-dummy
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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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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]
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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]
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Get:173 http://ftpmaster.internal/ubuntu yakkety/main amd64 libjaxp1.3-java all 1.3.05-2ubuntu3 [450 kB]
Get:174 http://ftpmaster.internal/ubuntu yakkety/main amd64 liblapack3 amd64 3.6.0-2ubuntu2 [1938 kB]
Get:175 http://ftpmaster.internal/ubuntu yakkety/main amd64 libpaper1 amd64 1.1.24+nmu4ubuntu1 [13.7 kB]
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Get:177 http://ftpmaster.internal/ubuntu yakkety/universe amd64 libstax-java all 1.2.0-3build1 [193 kB]
Get:178 http://ftpmaster.internal/ubuntu yakkety/main amd64 libtcl8.6 amd64 8.6.5+dfsg-2 [875 kB]
Get:179 http://ftpmaster.internal/ubuntu yakkety/main amd64 libtk8.6 amd64 8.6.5-1 [693 kB]
Get:180 http://ftpmaster.internal/ubuntu yakkety/main amd64 libxt6 amd64 1:1.1.5-0ubuntu1 [160 kB]
Get:181 http://ftpmaster.internal/ubuntu yakkety/universe amd64 maven-repo-helper all 1.8.12 [133 kB]
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 libglib2.0-0:amd64 (2.48.0-1ubuntu4) ...
No schema files found: doing nothing.
Setting up libicu57:amd64 (57.1-1) ...
Setting up libxml2:amd64 (2.9.3+dfsg1-1build1) ...
Setting up shared-mime-info (1.6-1) ...
Setting up libsigsegv2:amd64 (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-4ubuntu1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2ubuntu3) ...
Setting up dctrl-tools (2.24-2) ...
Setting up libcroco3:amd64 (0.6.11-1) ...
Setting up gettext (0.19.7-2ubuntu3) ...
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...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/IlluminaBasecallsToSam.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/IlluminaLaneMetrics.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/MarkIlluminaAdapters.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/BarcodeParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/BclData.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/BclParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/ClusterData.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/ClusterIntensityFileReader.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/CycleIlluminaFileMap.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/FilterParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/FourChannelIntensityData.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaData.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaDataProvider.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaDataProviderFactory.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaDataType.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaFileMap.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaFileNotFoundException.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaFileUtil.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaMetricsCode.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IlluminaTextIterator.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/IntensityChannel.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/MultiTileBclFileUtil.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/MultiTileBclParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/MultiTileFileUtil.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/MultiTileFilterParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/MultiTileLocsParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/MultiTileParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/OutputMapping.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/ParameterizedFileUtil.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/ParameterizedFileUtil.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/PerTileCycleParser.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/PerTileCycleParser.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/PerTileFileUtil.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/PerTileFileUtil.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/PerTileParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/PerTilePerCycleFileUtil.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/PerTilePerCycleFileUtil.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/PosParser.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/Range.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/ReadData.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/ReadDescriptor.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/ReadStructure.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/ReadType.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/Tile.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/Tile.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/TileIndex.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/TileIndex.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/TileMetricsUtil.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/TileMetricsUtil.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/TilePhasingValue.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/TilePhasingValue.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/TileTemplateRead.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/TileTemplateRead.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/BarcodeFileFaker.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/BarcodeFileFaker.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/BciFileFaker.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/BclFileFaker.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/BclFileFaker.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/ClocsFileFaker.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/ClocsFileFaker.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/FileFaker.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/FileFaker.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/FilterFileFaker.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/FilterFileFaker.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/LocsFileFaker.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/LocsFileFaker.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/MultiTileBclFileFaker.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/MultiTileLocsFileFaker.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/MultiTileLocsFileFaker.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/PosFileFaker.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/fakers/PosFileFaker.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BarcodeFileReader.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BarcodeFileReader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BclIndexReader.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BclIndexReader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BclReader.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BclReader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/ClocsFileReader.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/ClocsFileReader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/FilterFileReader.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/FilterFileReader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/LocsFileReader.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/LocsFileReader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/MMapBackedIteratorFactory.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/MMapBackedIteratorFactory.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/PosFileReader.java...
[javadoc] /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java:35: warning: '_' used as an identifier
[javadoc] public AtomicInteger make(final Byte _) {
[javadoc] ^
[javadoc] (use of '_' as an identifier might not be supported in releases after Java SE 8)
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/PosFileReader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/parser/readers/TileMetricsOutReader.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/metrics/GcBiasMetrics.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/metrics/MultiLevelCollector.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/metrics/MultilevelMetrics.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/metrics/PerUnitMetricCollector.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/metrics/SAMRecordAndReference.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/metrics/SAMRecordAndReferenceMultiLevelCollector.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/metrics/SAMRecordAndReferenceMultiLevelCollector.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/metrics/SAMRecordMultiLevelCollector.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/pedigree/PedFile.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/pedigree/Sex.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/reference/ExtractSequences.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/reference/NonNFastaSize.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/reference/NormalizeFasta.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/AbstractAlignmentMerger.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/AddCommentsToBam.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/AddOrReplaceReadGroups.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/BamIndexStats.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/BestEndMapqPrimaryAlignmentStrategy.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/BestMapqPrimaryAlignmentSelectionStrategy.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/BuildBamIndex.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/CalculateReadGroupChecksum.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/CheckTerminatorBlock.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/CleanSam.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/CompareSAMs.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/CreateSequenceDictionary.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/DownsampleSam.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/DuplicationMetrics.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/EarliestFragmentPrimaryAlignmentSelectionStrategy.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/EarliestFragmentPrimaryAlignmentSelectionStrategy.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/FastqToSam.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/FilterSamReads.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/FixMateInformation.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/GatherBamFiles.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/GatherBamFiles.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/HitsForInsert.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/HitsForInsert.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/MergeBamAlignment.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/MergeBamAlignment.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/MergeSamFiles.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/MergeSamFiles.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/MostDistantPrimaryAlignmentSelectionStrategy.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/MostDistantPrimaryAlignmentSelectionStrategy.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/MultiHitAlignedReadIterator.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/MultiHitAlignedReadIterator.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/PositionBasedDownsampleSam.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/PositionBasedDownsampleSam.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/PrimaryAlignmentSelectionStrategy.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/PrimaryAlignmentSelectionStrategy.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/ReorderSam.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/ReorderSam.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/ReplaceSamHeader.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/ReplaceSamHeader.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.java...
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/RevertSam.java...
[javadoc] [parsing started RegularFileObject[/«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/SamAlignmentMerger.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SamAlignmentMerger.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SamFormatConverter.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SamFormatConverter.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SamToFastq.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SamToFastq.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SortSam.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SortSam.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SplitSamByLibrary.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/SplitSamByLibrary.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/ValidateSamFile.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/ValidateSamFile.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/ViewSam.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/ViewSam.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...
[javadoc] [parsing started RegularFileObject[/«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...
[javadoc] [parsing started RegularFileObject[/«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...
[javadoc] [parsing started RegularFileObject[/«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...
[javadoc] [parsing started RegularFileObject[/«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...
[javadoc] [parsing started RegularFileObject[/«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...
[javadoc] [parsing started RegularFileObject[/«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...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/MarkQueue.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/MemoryBasedReadEndsForMarkDuplicatesMap.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/MemoryBasedReadEndsForMarkDuplicatesMap.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/OpticalDuplicateFinder.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/OpticalDuplicateFinder.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/PhysicalLocationForMateCigar.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/PhysicalLocationForMateCigar.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/PhysicalLocationForMateCigarSet.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/PhysicalLocationForMateCigarSet.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/ReadEnds.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/ReadEnds.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicates.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicates.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesCodec.java...
[javadoc] [parsing started RegularFileObject[/«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesCodec.java]]
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[javadoc] Loading source file /«BUILDDIR»/picard-tools-2.1.1+dfsg/src/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesMap.java...
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[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/SortedSet.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMRecordIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMUtils.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/FormatUtil.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/RuntimeIOException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/PrintWriter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Deprecated.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/CloseableIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/ConcurrentModificationException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/NoSuchElementException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/InputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/BufferedLineReader.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/AbstractIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/Closeable.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/AutoCloseable.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/net/URL.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/net/URLClassLoader.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/net/URI.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/net/URISyntaxException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/zip/ZipEntry.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/zip/ZipFile.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/ClassLoader.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/annotation/Documented.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/reflect/Modifier.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/TreeMap.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/filter/FilteringIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/filter/TagFilter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/filter/WholeReadClippedFilter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/BinaryCodec.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/variant/utils/SAMSequenceDictionaryExtractor.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/BamFileIoUtils.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/TimeUnit.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/math/BigDecimal.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/NavigableMap.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/SortedMap.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/AbstractMap.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMFileReader.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/variant/variantcontext/Allele.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/variant/variantcontext/Genotype.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/variant/variantcontext/GenotypeLikelihoods.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/atomic/AtomicInteger.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMTextHeaderCodec.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/StringLineReader.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/tribble/readers/LineIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/tribble/readers/LineIteratorImpl.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/tribble/readers/LineReaderUtil.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/variant/vcf/VCFCodec.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/BufferedInputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/ProcessExecutor.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/FileOutputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/OutputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/nio/ByteBuffer.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/nio/ByteOrder.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/nio/channels/Channels.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/nio/channels/WritableByteChannel.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/zip/GZIPOutputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/filter/SolexaNoiseFilter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/PeekIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/SortingCollection.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/LinkedList.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/Queue.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/Timer.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/TimerTask.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/ExecutorService.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/PriorityBlockingQueue.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/ThreadPoolExecutor.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/atomic/AtomicBoolean.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/BAMRecordCodec.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMFileWriter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMRecordQueryNameComparator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/Iso8601Date.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/SolexaQualityConverter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/atomic/AtomicReference.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/SortingCollection$Codec.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/CollectionUtil$DefaultingMap.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Byte.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Override.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/StringBuilder.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/FileNotFoundException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Float.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/BufferedWriter.class)]]
[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)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Runnable.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Thread.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/InterruptedException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/fastq/BasicFastqWriter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/fastq/FastqReader.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/fastq/FastqRecord.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/fastq/FastqWriter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/fastq/FastqWriterFactory.class)]]
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[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/FileInputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/nio/MappedByteBuffer.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/nio/channels/FileChannel.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/BlockCompressedInputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/zip/GZIPInputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/IterableAdapter.class)]]
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[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Number.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/ReferenceSequenceMask.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/Cigar.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMProgramRecord.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMRecordCoordinateComparator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMRecordUtil.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/filter/OverclippedReadFilter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/CigarUtil.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SamInputResource.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/BAMIndex.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/BAMIndexMetaData.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/BAMIndexer.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/FileWriter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/BlockCompressedInputStream$FileTermination.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/math/BigInteger.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/security/MessageDigest.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/security/NoSuchAlgorithmException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/DownsamplingIteratorFactory.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/DownsamplingIteratorFactory$Strategy.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/DownsamplingIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/fastq/FastqConstants.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/fastq/FastqConstants$FastqExtensions.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/FastqQualityFormat.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/QualityEncodingDetector.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/filter/JavascriptSamRecordFilter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/filter/ReadNameFilter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/MergingSamRecordIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SamFileHeaderMerger.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/SamRecordIntervalIteratorFactory.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/Map$Entry.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/CollectionUtil$DefaultingMap$Factory.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Short.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/NumberFormatException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/DelegatingIterator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMValidationError.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/Lazy.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/TrimmingUtil.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Character.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SamFileValidator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/BamIndexValidator.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/BamIndexValidator$IndexValidationStringency.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/SAMValidationError$Type.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/AsciiWriter.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/DataInputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/DataOutputStream.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/io/EOFException.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/SortingLongCollection.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/DuplicateScoringStrategy.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/DuplicateScoringStrategy$ScoringStrategy.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/SamRecordWithOrdinal.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/util/SamRecordTrackingBuffer.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/CoordinateSortedPairInfoMap.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/CoordinateSortedPairInfoMap$Codec.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/ArrayBlockingQueue.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/concurrent/BlockingQueue.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/guava.jar(com/google/common/base/Optional.class)]]
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[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/tribble/bed/BEDCodec.class)]]
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[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/Thread$UncaughtExceptionHandler.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/util/ArrayDeque.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/samtools/liftover/LiftOver.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/lib/tools.jar(com/sun/javadoc/ClassDoc.class)]]
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[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/lib/tools.jar(com/sun/javadoc/Tag.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/testng.jar(org/testng/annotations/DataProvider.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/testng.jar(org/testng/annotations/Test.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/testng.jar(org/testng/Assert.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/variant/variantcontext/VariantContextUtils.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/htsjdk.jar(htsjdk/variant/vcf/VCFHeader.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/guava.jar(com/google/common/base/Function.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/guava.jar(com/google/common/base/Joiner.class)]]
[javadoc] [loading ZipFileIndexFileObject[/usr/share/java/guava.jar(com/google/common/collect/FluentIterable.class)]]
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[javadoc] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/rt.jar(java/lang/IllegalStateException.class)]]
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[javadoc] [done in 2991 ms]
[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 ' '-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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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 '' 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= 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 '' 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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 '' 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= 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 '' 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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 '' 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= 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 '' 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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 '' 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= 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 '' 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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= 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=