https://launchpad.net/ubuntu/+source/samtools/1.19.2-1/+build/27788436 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-s390x-009 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:22 UTC 2024 s390x Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 18 Feb 05:21:25 ntpdate[1872]: adjust time server 10.211.37.1 offset 0.000016 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27788436 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-27788436 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27788436 Starting target for build PACKAGEBUILD-27788436 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27788436 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27788436 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27788436 Updating target for build PACKAGEBUILD-27788436 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x Packages [1361 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [519 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6029 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [201 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [70.6 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [961 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [408 kB] Fetched 24.4 MB in 5s (4557 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc-13-s390x-linux-gnu gcc-14-base gcc-s390x-linux-gnu libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-s390x-linux-gnu bsdextrautils bsdutils ca-certificates coreutils cpp cpp-13 debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers krb5-locales libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 152 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 75.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3 [73.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc6-dev s390x 2.39-0ubuntu1 [1629 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc-dev-bin s390x 2.39-0ubuntu1 [20.1 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-dev s390x 1.3.4+ds-1build1 [225 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libgssapi-krb5-2 s390x 1.20.1-5build1 [146 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5-3 s390x 1.20.1-5build1 [354 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libk5crypto3 s390x 1.20.1-5build1 [89.1 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5support0 s390x 1.20.1-5build1 [34.1 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3 [9448 B] Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libssl3 s390x 3.0.10-1ubuntu4 [1648 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc3 s390x 1.3.4+ds-1build1 [100 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libnsl2 s390x 1.3.0-3 [44.4 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt1 s390x 1:4.4.36-4 [102 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-libc-dev s390x 6.8.0-11.11 [1590 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc6 s390x 2.39-0ubuntu1 [2843 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc-bin s390x 2.39-0ubuntu1 [654 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x gcc-14-base s390x 14-20240201-3ubuntu1 [46.4 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-s1 s390x 14-20240201-3ubuntu1 [35.9 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x base-files s390x 13ubuntu6 [84.6 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.16 [94.6 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x bash s390x 5.2.21-2ubuntu1 [855 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x bsdutils s390x 1:2.39.2-6ubuntu1 [95.2 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main s390x coreutils s390x 9.4-2ubuntu3 [1512 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x diffutils s390x 1:3.10-1 [187 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error-l10n all 1.47-3build1 [8024 B] Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error0 s390x 1.47-3build1 [75.6 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libgcrypt20 s390x 1.10.3-2 [499 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x liblzma5 s390x 5.4.5-0.3 [149 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++6 s390x 14-20240201-3ubuntu1 [908 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libacl1 s390x 2.3.1-4ubuntu1 [20.2 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libapparmor1 s390x 4.0.0~alpha4-0ubuntu1 [50.2 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libaudit-common all 1:3.1.2-2 [5594 B] Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libcap-ng0 s390x 0.8.4-2 [15.7 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libaudit1 s390x 1:3.1.2-2 [49.2 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libblkid1 s390x 2.39.2-6ubuntu1 [126 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libzstd1 s390x 1.5.5+dfsg2-2 [336 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libkmod2 s390x 30+20230601-2ubuntu1 [54.5 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-8-0 s390x 10.42-4ubuntu1 [243 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libselinux1 s390x 3.5-2build1 [84.2 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libmount1 s390x 2.39.2-6ubuntu1 [137 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libperl5.38 s390x 5.38.2-3 [5013 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x perl s390x 5.38.2-3 [231 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main s390x perl-base s390x 5.38.2-3 [1961 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main s390x liblocale-gettext-perl s390x 1.07-6build1 [15.6 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libtext-iconv-perl s390x 1.7-8build1 [13.7 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main s390x libtext-charwidth-perl s390x 0.04-11build1 [9432 B] Get:50 http://ftpmaster.internal/ubuntu noble/main s390x perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libperl5.36 s390x 5.36.0-10ubuntu1 [4899 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libdb5.3 s390x 5.3.28+dfsg2-4 [752 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm6 s390x 1.23-5 [35.5 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm-compat4 s390x 1.23-5 [6538 B] Get:55 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g s390x 1:1.3.dfsg-3ubuntu1 [75.3 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x debconf-i18n all 1.5.86 [205 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x debconf all 1.5.86 [124 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main s390x libpam0g s390x 1.5.2-9.1ubuntu2 [66.8 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main s390x libseccomp2 s390x 2.5.5-1ubuntu1 [53.3 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main s390x systemd-sysv s390x 255.2-3ubuntu2 [11.9 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main s390x systemd-dev all 255.2-3ubuntu2 [101 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main s390x systemd s390x 255.2-3ubuntu2 [3532 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libsystemd-shared s390x 255.2-3ubuntu2 [2134 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x libargon2-1 s390x 0~20190702+dfsg-4 [53.1 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main s390x libuuid1 s390x 2.39.2-6ubuntu1 [34.4 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main s390x libcryptsetup12 s390x 2:2.6.1-6ubuntu1 [243 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main s390x libfdisk1 s390x 2.39.2-6ubuntu1 [149 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main s390x mount s390x 2.39.2-6ubuntu1 [118 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main s390x libsystemd0 s390x 255.2-3ubuntu2 [443 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main s390x libudev1 s390x 255.2-3ubuntu2 [176 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x libxxhash0 s390x 0.8.2-2 [23.6 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x libapt-pkg6.0 s390x 2.7.11 [1011 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main s390x tar s390x 1.35+dfsg-3 [269 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg s390x 1.22.4ubuntu3 [1280 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x grep s390x 3.11-4 [189 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x login s390x 1:4.13+dfsg1-3ubuntu1 [202 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ncurses-bin s390x 6.4+20240113-1ubuntu1 [198 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main s390x sed s390x 4.9-2 [207 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x util-linux s390x 2.39.2-6ubuntu1 [1137 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x libdebconfclient0 s390x 0.271ubuntu1 [11.3 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main s390x base-passwd s390x 3.6.3 [51.1 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main s390x sysvinit-utils s390x 3.08-3ubuntu1 [34.3 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x apt s390x 2.7.11 [1386 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x apt-utils s390x 2.7.11 [214 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgv s390x 2.4.4-2ubuntu3 [163 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main s390x libffi8 s390x 3.4.4-2 [22.6 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main s390x libp11-kit0 s390x 0.25.3-4ubuntu1 [318 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main s390x libunistring5 s390x 1.1-2 [544 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main s390x libidn2-0 s390x 2.3.7-2 [67.2 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main s390x libgnutls30 s390x 3.8.3-1ubuntu1 [944 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules-bin s390x 1.5.2-9.1ubuntu2 [53.1 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules s390x 1.5.2-9.1ubuntu2 [292 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main s390x init s390x 1.66ubuntu1 [6188 B] Get:97 http://ftpmaster.internal/ubuntu noble/main s390x libsmartcols1 s390x 2.39.2-6ubuntu1 [66.3 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main s390x uuid-runtime s390x 2.39.2-6ubuntu1 [33.2 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main s390x libattr1 s390x 1:2.5.2-1 [11.7 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main s390x libmd0 s390x 1.1.0-2 [24.7 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main s390x libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage-common all 3.5-1build2 [10.0 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main s390x libsepol2 s390x 3.5-2 [308 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage2 s390x 3.5-1build2 [96.7 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libncursesw6 s390x 6.4+20240113-1ubuntu1 [161 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtinfo6 s390x 6.4+20240113-1ubuntu1 [117 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main s390x passwd s390x 1:4.13+dfsg1-3ubuntu1 [855 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-13ubuntu1 [14.0 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-13ubuntu1 [463 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-13ubuntu1 [1030 B] Get:111 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-13ubuntu1 [9928 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 14-20240201-3ubuntu1 [50.0 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.42-2ubuntu1 [98.4 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.42-2ubuntu1 [99.7 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.42-2ubuntu1 [13.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.42-2ubuntu1 [2271 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.42-2ubuntu1 [474 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.42-2ubuntu1 [3058 B] Get:119 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.42-2ubuntu1 [216 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-13ubuntu1 [2428 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240201-3ubuntu1 [151 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 14-20240201-3ubuntu1 [31.1 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240201-3ubuntu1 [9382 B] Get:124 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 14-20240201-3ubuntu1 [2999 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 14-20240201-3ubuntu1 [1185 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-13ubuntu1 [1003 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-13ubuntu1 [19.0 MB] Get:128 http://ftpmaster.internal/ubuntu noble/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-13ubuntu1 [11.3 MB] Get:129 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-base s390x 13.2.0-13ubuntu1 [46.6 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main s390x libproc2-0 s390x 2:4.0.4-2ubuntu1 [58.6 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main s390x mawk s390x 1.3.4.20240123-1 [133 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main s390x procps s390x 2:4.0.4-2ubuntu1 [722 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main s390x sensible-utils all 0.0.22 [22.5 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main s390x openssl s390x 3.0.10-1ubuntu4 [1005 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates all 20240203 [159 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main s390x krb5-locales all 1.20.1-5build1 [13.7 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main s390x libip4tc2 s390x 1.8.10-3ubuntu1 [24.2 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main s390x readline-common all 8.2-3 [56.2 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main s390x libreadline8 s390x 8.2-3 [167 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main s390x libsqlite3-0 s390x 3.45.1-1 [747 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main s390x tzdata all 2024a-1ubuntu1 [273 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main s390x bash-completion all 1:2.11-8 [180 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main s390x bsdextrautils s390x 2.39.2-6ubuntu1 [75.7 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main s390x libpng16-16 s390x 1.6.42-1 [200 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main s390x psmisc s390x 23.6-2 [178 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main s390x xz-utils s390x 5.4.5-0.3 [278 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] Get:148 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] Get:149 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] Get:151 http://ftpmaster.internal/ubuntu noble/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] Get:152 http://ftpmaster.internal/ubuntu noble/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg-dev all 1.22.4ubuntu3 [1078 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdpkg-perl all 1.22.4ubuntu3 [268 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 46 [12.3 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main s390x libfakeroot s390x 1.33-1 [31.9 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main s390x fakeroot s390x 1.33-1 [67.5 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main s390x pinentry-curses s390x 1.2.1-3ubuntu1 [37.1 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg s390x 2.4.4-2ubuntu3 [587 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgconf s390x 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Setting up uuid-runtime (2.39.2-6ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:s390x (1:4.4.36-4) ... Setting up libasan8:s390x (14-20240201-3ubuntu1) ... Setting up procps (2:4.0.4-2ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:s390x (1.20.1-5build1) ... Setting up libbinutils:s390x (2.42-2ubuntu1) ... Setting up libc-dev-bin (2.39-0ubuntu1) ... Setting up openssl (3.0.10-1ubuntu4) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-3) ... Setting up libcc1-0:s390x (14-20240201-3ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6build1) ... Setting up libitm1:s390x (14-20240201-3ubuntu1) ... Setting up libgdbm6:s390x (1.23-5) ... Setting up libctf0:s390x (2.42-2ubuntu1) ... Setting up pinentry-curses (1.2.1-3ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.42-2ubuntu1) ... Setting up cpp-13 (13.2.0-13ubuntu1) ... Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libreadline8:s390x (8.2-3) ... Setting up debconf-i18n (1.5.86) ... Setting up binutils (2.42-2ubuntu1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up optipng (0.7.8+ds-1) ... Setting up libgssapi-krb5-2:s390x (1.20.1-5build1) ... Setting up libgdbm-compat4:s390x (1.23-5) ... Setting up libgcc-13-dev:s390x (13.2.0-13ubuntu1) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu3) ... Setting up libperl5.36:s390x (5.36.0-10ubuntu1) ... Setting up gpg (2.4.4-2ubuntu3) ... Setting up libtirpc3:s390x (1.3.4+ds-1build1) ... Setting up gpg-agent (2.4.4-2ubuntu3) ... Setting up libperl5.38:s390x (5.38.2-3) ... Setting up perl (5.38.2-3) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1build1) ... Setting up gcc-13-s390x-linux-gnu (13.2.0-13ubuntu1) ... Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gcc-13 (13.2.0-13ubuntu1) ... Setting up libdpkg-perl (1.22.4ubuntu3) ... Setting up libnsl2:s390x (1.3.0-3) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up dpkg-dev (1.22.4ubuntu3) ... Setting up libnsl-dev:s390x (1.3.0-3) ... Setting up libc6-dev:s390x (2.39-0ubuntu1) ... Setting up libstdc++-13-dev:s390x (13.2.0-13ubuntu1) ... Setting up g++-13-s390x-linux-gnu (13.2.0-13ubuntu1) ... Setting up g++-13 (13.2.0-13ubuntu1) ... Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu1) ... Processing triggers for debianutils (5.16) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27788436 s390x noble-proposed -c chroot:build-PACKAGEBUILD-27788436 --arch=s390x --dist=noble-proposed --nolog samtools_1.19.2-1.dsc Initiating build PACKAGEBUILD-27788436 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:22 UTC 2024 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-s390x-009.buildd +==============================================================================+ | samtools 1.19.2-1 (s390x) Sun, 18 Feb 2024 05:22:36 +0000 | +==============================================================================+ Package: samtools Version: 1.19.2-1 Source Version: 1.19.2-1 Distribution: noble-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27788436/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-GyUhwR/resolver-dpXvEI' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools_1.19.2-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/samtools-GyUhwR/samtools-1.19.2' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-GyUhwR' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [459 B] Get:5 copy:/<>/apt_archive ./ Packages [535 B] Fetched 1951 B in 0s (158 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu74 libio-pty-perl libldap2 liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14 libpipeline1 libpkgconf3 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkgconf pkgconf-bin po-debconf tabix zlib1g-dev Suggested packages: gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu74 libio-pty-perl libldap2 liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14 libpipeline1 libpkgconf3 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy tabix zlib1g-dev 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 30.6 MB of archives. After this operation, 103 MB of additional disk space will be used. 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groff-base s390x 1.23.0-3 [1047 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libncurses6 s390x 6.4+20240113-1ubuntu1 [124 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libnghttp2-14 s390x 1.59.0-1 [77.6 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libpipeline1 s390x 1.5.7-1 [23.4 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libpsl5 s390x 0.21.2-1build1 [57.4 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x man-db s390x 2.12.0-3 [1246 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x m4 s390x 1.4.19-4 [255 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x autoconf all 2.71-3 [339 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x autotools-dev all 20220109.1 [44.9 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x autopoint all 0.21-14ubuntu1 [422 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libdebhelper-perl all 13.13ubuntu1 [88.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libtool all 2.4.7-7 [166 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x dh-autoreconf all 20 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libsub-override-perl all 0.10-1 [10.0 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main s390x dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libdw1 s390x 0.190-1 [282 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x debugedit s390x 1:5.0-5 [47.5 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x dwz s390x 0.15-1 [108 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x gettext s390x 0.21-14ubuntu1 [917 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main s390x debhelper all 13.13ubuntu1 [868 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libbrotli1 s390x 1.1.0-2 [374 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libbz2-dev s390x 1.0.8-5build1 [33.8 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libsasl2-modules-db s390x 2.1.28+dfsg1-4 [20.8 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libsasl2-2 s390x 2.1.28+dfsg1-4 [58.7 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libldap2 s390x 2.6.7+dfsg-1~exp1ubuntu1 [202 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build4 [56.4 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libssh-4 s390x 0.10.6-2 [221 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libcurl3-gnutls s390x 8.5.0-2ubuntu2 [356 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libcurl4-gnutls-dev s390x 8.5.0-2ubuntu2 [466 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate-dev s390x 1.19-1 [52.4 kB] Get:47 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] Get:48 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main s390x liblzma-dev s390x 5.4.5-0.3 [215 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g-dev s390x 1:1.3.dfsg-3ubuntu1 [905 kB] Get:51 http://ftpmaster.internal/ubuntu noble/universe s390x libhts-dev s390x 1.18+ds-1 [5867 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libio-pty-perl s390x 1:1.20-1 [31.2 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libncurses-dev s390x 6.4+20240113-1ubuntu1 [412 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libpkgconf3 s390x 1.8.1-2 [30.4 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf-bin s390x 1.8.1-2 [20.8 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf s390x 1.8.1-2 [16.7 kB] Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x tabix s390x 1.18+ds-1 [527 kB] Preconfiguring packages ... Fetched 30.6 MB in 4s (8279 kB/s) Selecting previously unselected package autoconf-archive. (Reading database ... 15539 files and directories currently installed.) Preparing to unpack .../00-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libelf1:s390x. Preparing to unpack .../01-libelf1_0.190-1_s390x.deb ... Unpacking libelf1:s390x (0.190-1) ... Selecting previously unselected package libicu74:s390x. Preparing to unpack .../02-libicu74_74.2-1ubuntu1_s390x.deb ... Unpacking libicu74:s390x (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../03-libxml2_2.9.14+dfsg-1.3ubuntu1_s390x.deb ... Unpacking libxml2:s390x (2.9.14+dfsg-1.3ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-2_s390x.deb ... Unpacking libmagic-mgc (1:5.45-2) ... Selecting previously unselected package libmagic1:s390x. 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Selecting previously unselected package liblzma-dev:s390x. Preparing to unpack .../47-liblzma-dev_5.4.5-0.3_s390x.deb ... Unpacking liblzma-dev:s390x (5.4.5-0.3) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../48-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ... Selecting previously unselected package libhts-dev:s390x. Preparing to unpack .../49-libhts-dev_1.18+ds-1_s390x.deb ... Unpacking libhts-dev:s390x (1.18+ds-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../50-libio-pty-perl_1%3a1.20-1_s390x.deb ... Unpacking libio-pty-perl (1:1.20-1) ... Selecting previously unselected package libncurses-dev:s390x. Preparing to unpack .../51-libncurses-dev_6.4+20240113-1ubuntu1_s390x.deb ... Unpacking libncurses-dev:s390x (6.4+20240113-1ubuntu1) ... Selecting previously unselected package libpkgconf3:s390x. Preparing to unpack .../52-libpkgconf3_1.8.1-2_s390x.deb ... Unpacking libpkgconf3:s390x (1.8.1-2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../53-pkgconf-bin_1.8.1-2_s390x.deb ... Unpacking pkgconf-bin (1.8.1-2) ... Selecting previously unselected package pkgconf:s390x. Preparing to unpack .../54-pkgconf_1.8.1-2_s390x.deb ... Unpacking pkgconf:s390x (1.8.1-2) ... Selecting previously unselected package tabix. Preparing to unpack .../55-tabix_1.18+ds-1_s390x.deb ... Unpacking tabix (1.18+ds-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../56-sbuild-build-depends-main-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:s390x (1.6.0-1) ... Setting up libpipeline1:s390x (1.5.7-1) ... Setting up libpsl5:s390x (0.21.2-1build1) ... Setting up libio-pty-perl (1:1.20-1) ... Setting up libmagic-mgc (1:5.45-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.13ubuntu1) ... Setting up libbrotli1:s390x (1.1.0-2) ... Setting up libnghttp2-14:s390x (1.59.0-1) ... Setting up libmagic1:s390x (1:5.45-2) ... Setting up libdeflate0:s390x (1.19-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up autoconf-archive (20220903-3) ... Setting up file (1:5.45-2) ... Setting up libsasl2-modules-db:s390x (2.1.28+dfsg1-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:s390x (1.8.1-2) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libncurses6:s390x (6.4+20240113-1ubuntu1) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libsasl2-2:s390x (2.1.28+dfsg1-4) ... Setting up libssh-4:s390x (0.10.6-2) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:s390x (5.4.5-0.3) ... Setting up libicu74:s390x (74.2-1ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ... Setting up libuchardet0:s390x (0.0.8-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libdeflate-dev:s390x (1.19-1) ... Setting up tabix (1.18+ds-1) ... Setting up libelf1:s390x (0.190-1) ... Setting up libxml2:s390x (2.9.14+dfsg-1.3ubuntu1) ... Setting up libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu1) ... Setting up libbz2-dev:s390x (1.0.8-5build1) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:s390x (0.190-1) ... Setting up libncurses-dev:s390x (6.4+20240113-1ubuntu1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libtool (2.4.7-7) ... Setting up libcurl3-gnutls:s390x (8.5.0-2ubuntu2) ... Setting up libcurl4-gnutls-dev:s390x (8.5.0-2ubuntu2) ... Setting up pkgconf:s390x (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up debugedit (1:5.0-5) ... Setting up libhts3:s390x (1.18+ds-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:s390x (1.18+ds-1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up debhelper (13.13ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:22 UTC 2024 s390x (s390x) Toolchain package versions: binutils_2.42-2ubuntu1 dpkg-dev_1.22.4ubuntu3 g++-13_13.2.0-13ubuntu1 gcc-13_13.2.0-13ubuntu1 libc6-dev_2.39-0ubuntu1 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240201-3ubuntu1 linux-libc-dev_6.8.0-11.11 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.11 apt-utils_2.7.11 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu6 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.42-2ubuntu1 binutils-common_2.42-2ubuntu1 binutils-s390x-linux-gnu_2.42-2ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20240203 coreutils_9.4-2ubuntu3 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-13ubuntu1 cpp-13-s390x-linux-gnu_13.2.0-13ubuntu1 cpp-s390x-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.13ubuntu1 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.4ubuntu3 dpkg-dev_1.22.4ubuntu3 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-13ubuntu1 g++-13-s390x-linux-gnu_13.2.0-13ubuntu1 g++-s390x-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-13ubuntu1 gcc-13-base_13.2.0-13ubuntu1 gcc-13-s390x-linux-gnu_13.2.0-13ubuntu1 gcc-14-base_14-20240201-3ubuntu1 gcc-s390x-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gpg_2.4.4-2ubuntu3 gpg-agent_2.4.4-2ubuntu3 gpgconf_2.4.4-2ubuntu3 gpgv_2.4.4-2ubuntu3 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5build1 libacl1_2.3.1-4ubuntu1 libapparmor1_4.0.0~alpha4-0ubuntu1 libapt-pkg6.0_2.7.11 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240201-3ubuntu1 libassuan0_2.5.6-1 libatomic1_14-20240201-3ubuntu1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2 libaudit1_1:3.1.2-2 libbinutils_2.42-2ubuntu1 libblkid1_2.39.2-6ubuntu1 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5build1 libbz2-dev_1.0.8-5build1 libc-bin_2.39-0ubuntu1 libc-dev-bin_2.39-0ubuntu1 libc6_2.39-0ubuntu1 libc6-dev_2.39-0ubuntu1 libcap-ng0_0.8.4-2 libcap2_1:2.66-4ubuntu1 libcc1-0_14-20240201-3ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.6.1-6ubuntu1 libctf-nobfd0_2.42-2ubuntu1 libctf0_2.42-2ubuntu1 libcurl3-gnutls_8.5.0-2ubuntu2 libcurl4-gnutls-dev_8.5.0-2ubuntu2 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.13ubuntu1 libdeflate-dev_1.19-1 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.4ubuntu3 libdw1_0.190-1 libelf1_0.190-1 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-2 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-13ubuntu1 libgcc-s1_14-20240201-3ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.3-1ubuntu1 libgomp1_14-20240201-3ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgssapi-krb5-2_1.20.1-5build1 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1 libhts3_1.18+ds-1 libhtscodecs2_1.6.0-1 libicu74_74.2-1ubuntu1 libidn2-0_2.3.7-2 libio-pty-perl_1:1.20-1 libip4tc2_1.8.10-3ubuntu1 libisl23_0.26-3 libitm1_14-20240201-3ubuntu1 libjansson4_2.14-2 libjson-c5_0.17-1 libk5crypto3_1.20.1-5build1 libkeyutils1_1.6.3-3 libkmod2_30+20230601-2ubuntu1 libkrb5-3_1.20.1-5build1 libkrb5support0_1.20.1-5build1 libldap2_2.6.7+dfsg-1~exp1ubuntu1 liblocale-gettext-perl_1.07-6build1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma-dev_5.4.5-0.3 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.2-6ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses-dev_6.4+20240113-1ubuntu1 libncurses6_6.4+20240113-1ubuntu1 libncursesw6_6.4+20240113-1ubuntu1 libnettle8_3.9.1-2 libnghttp2-14_1.59.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libp11-kit0_0.25.3-4ubuntu1 libpam-modules_1.5.2-9.1ubuntu2 libpam-modules-bin_1.5.2-9.1ubuntu2 libpam-runtime_1.5.2-9.1ubuntu2 libpam0g_1.5.2-9.1ubuntu2 libpcre2-8-0_10.42-4ubuntu1 libperl5.36_5.36.0-10ubuntu1 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-2 libpng16-16_1.6.42-1 libproc2-0_2:4.0.4-2ubuntu1 libpsl5_0.21.2-1build1 libreadline8_8.2-3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.5-1ubuntu1 libselinux1_3.5-2build1 libsemanage-common_3.5-1build2 libsemanage2_3.5-1build2 libsepol2_3.5-2 libsframe1_2.42-2ubuntu1 libsmartcols1_2.39.2-6ubuntu1 libsqlite3-0_3.45.1-1 libss2_1.47.0-2ubuntu1 libssh-4_0.10.6-2 libssl3_3.0.10-1ubuntu4 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240201-3ubuntu1 libsub-override-perl_0.10-1 libsystemd-shared_255.2-3ubuntu2 libsystemd0_255.2-3ubuntu2 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11build1 libtext-iconv-perl_1.7-8build1 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1ubuntu1 libtirpc-common_1.3.4+ds-1build1 libtirpc-dev_1.3.4+ds-1build1 libtirpc3_1.3.4+ds-1build1 libtool_2.4.7-7 libubsan1_14-20240201-3ubuntu1 libuchardet0_0.0.8-1 libudev1_255.2-3ubuntu2 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6ubuntu1 libxml2_2.9.14+dfsg-1.3ubuntu1 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.0-11.11 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-3ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_46 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 mount_2.39.2-6ubuntu1 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 openssl_3.0.10-1ubuntu4 optipng_0.7.8+ds-1 passwd_1:4.13+dfsg1-3ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.36_5.36.0-10ubuntu1 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3ubuntu1 pkgbinarymangler_154 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-2ubuntu1 psmisc_23.6-2 readline-common_8.2-3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.2-3ubuntu2 systemd-dev_255.2-3ubuntu2 systemd-sysv_255.2-3ubuntu2 sysvinit-utils_3.08-3ubuntu1 tabix_1.18+ds-1 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 usrmerge_35ubuntu1 util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3ubuntu1 zlib1g-dev_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.19.2-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://www.htslib.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/samtools Vcs-Git: https://salsa.debian.org/med-team/samtools.git Testsuite: autopkgtest Testsuite-Triggers: tabix Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl , libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev Package-List: samtools deb science optional arch=any samtools-test deb science optional arch=all Checksums-Sha1: 8dff98a03e9295730b24e26cb1447b41887af669 5666279 samtools_1.19.2.orig.tar.gz ac8048d48e8883df9b4700dd4a26bccd6542cfc8 21752 samtools_1.19.2-1.debian.tar.xz Checksums-Sha256: 93b4ee042003d536a2f822a17dd5e65439f724214d5d2b5becc8a9f190ef2efd 5666279 samtools_1.19.2.orig.tar.gz ab11a07d6e8e80fadb62672ec5974867a0328f31d5b6faa7c2d8e5b7de9936a1 21752 samtools_1.19.2-1.debian.tar.xz Files: dc7d1649a27689287499876dc05785c4 5666279 samtools_1.19.2.orig.tar.gz 3eea35b7ce97c48454c4f5b378ab722a 21752 samtools_1.19.2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmXQ7ZEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqg/A//dxkPboHt/1/2CjEvRG51q7sEcs/F hBDxKGyMoAIcfHT74AYrr64GfWace3+uhytp/gq1VAhzJPXe+DZTbDry90JJ54oG ci5GjfN/JErckvf0sjp1OfdyWWfcpgQEmyTnOGj+mgZpkk4LLM5wcoGPwjQdRYlo auT+QDx1hMFqqogwEcLk49L04sFh6ECbgeEQxmUrfCiwqmodEQzppQURJ6U47LrV ht/DcOEHpwHqkVc+a4RYbzvMkGquRY+LP5W+J/iNjOo8Z212RaLK031MxqKhmQL2 6jFR4/cKB7wOqU8IA5tTHrjLqrgWCSrZRFuipMtsLZNg2qKEqS9hc+BsCNP4owkY qKZAdtko2LF8v68BqN/fgj3CGQCamH8d+tEjN9uyqYsyIdwPlvaHKgBCr3W44khX ZiWt3kRKxz0zg8f13e2aEv2G2DkHHemkUmNjbyY2JME8FKX+eu6vpPJxSVnrgTTO Y8g7vEHefMZKwIJeR6TGp9SLRYxxcN5oyhaflIRn5ASYsL5I4HJY3k5Dha4xUTX8 qfzR/04OEbWHPLa+VQy06sqiP8z34nkWIbhtNpjeg+gA9P7pIrNWNME1Hj84/r6O WlkFwUsiGfYog+9YKyXcvQNPpbu4DkvW3Ox+5tzhDTQau7YBBHa94rIYL+tsMWqu F3rea22F/v/AQOY= =ODlH -----END PGP SIGNATURE----- gpgv: Signature made Sat Feb 17 17:32:01 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./samtools_1.19.2-1.dsc: no acceptable signature found dpkg-source: info: extracting samtools in /<> dpkg-source: info: unpacking samtools_1.19.2.orig.tar.gz dpkg-source: info: unpacking samtools_1.19.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27788436 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27788436 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27788436 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.19.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x dpkg-source: info: using options from samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f config.mk touch config.mk dh_auto_clean -- make -j4 distclean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* cd test/reference && rm -f mpileup.*.fai rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS rm -rf autom4te.cache make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -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 \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=s390x-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j4 "CFLAGS=-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=3" "LDFLAGS=-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_aux.o bam_aux.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_index.o bam_index.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_view.o sam_view.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_fastq.o bam_fastq.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_cat.o bam_cat.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_md.o bam_md.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.19.2"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=3"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1"' >> version.h cc1: warning: command-line option ‘-frelease’ is valid for D but not for C echo '#define SAMTOOLS_LDFLAGS "-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/<>@«BUILDPATH»@g' version.h gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam2bcf.o bam2bcf.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sample.o sample.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cut_target.o cut_target.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o phase.o phase.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o coverage.o coverage.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o padding.o padding.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bedcov.o bedcov.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o faidx.o faidx.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o dict.o dict.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o stats.o stats.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_split.o bam_split.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_tview_curses.o bam_tview_curses.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_ampliconclip.o bam_ampliconclip.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_import.o bam_import.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o consensus_pileup.o consensus_pileup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o reference.o reference.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o reset.o reset.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram_size.o cram_size.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bedidx.o bedidx.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam.o bam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test.o test/test.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.19.2-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bamtk.o bamtk.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/<>' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} test_reference: /<>/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/iJSBnAAIOB/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/iJSBnAAIOB/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/iJSBnAAIOB/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/iJSBnAAIOB/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/iJSBnAAIOB/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/iJSBnAAIOB/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/iJSBnAAIOB/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/iJSBnAAIOB/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/iJSBnAAIOB/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/iJSBnAAIOB/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/iJSBnAAIOB/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /<>/samtools fqidx /tmp/iJSBnAAIOB/fqidx.fq 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/iJSBnAAIOB/fqidx.fq.gz 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/iJSBnAAIOB/fqidx.fq 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/iJSBnAAIOB/fqidx.fq.gz 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/iJSBnAAIOB/fqidx.fq 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/iJSBnAAIOB/fqidx.fq.gz 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/iJSBnAAIOB/fqidx.fq 1:99998-100007 .. ok .. ok /<>/samtools fqidx /tmp/iJSBnAAIOB/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /<>/test/dat/dict.fa .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/iJSBnAAIOB/dict.fa.gz .. ok test_dict: cat /<>/test/dat/dict.fa | /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /<>/samtools dict -AH < /<>/test/dat/dict.alias.fa .. ok test_dict: /<>/samtools dict -H -l /<>/test/dat/dict.alt < /<>/test/dat/dict.alias.fa .. ok test_index: /<>/samtools view /tmp/iJSBnAAIOB/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/iJSBnAAIOB/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/iJSBnAAIOB/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/iJSBnAAIOB/test_input_1_b.bam.bai .. ok test_index: /<>/samtools merge -O sam - -X -cp -R ref2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_a.bam.bai /tmp/iJSBnAAIOB/test_input_1_b.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/iJSBnAAIOB/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /<>/samtools index /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam .. ok test_index: /<>/samtools index -M /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.bam /tmp/iJSBnAAIOB/auto_indexed.csi && cat /tmp/iJSBnAAIOB/auto_indexed.csi .. ok test_index: /<>/samtools index /<>/test/dat/auto_indexed.tmp.cram /tmp/iJSBnAAIOB/auto_indexed.crai && cat /tmp/iJSBnAAIOB/auto_indexed.crai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.sam /tmp/iJSBnAAIOB/auto_indexed.csi && cat /tmp/iJSBnAAIOB/auto_indexed.csi .. ok test_index: /<>/samtools view -@ 2 /tmp/iJSBnAAIOB/large_chrom.bam ref2 .. ok test_index: /<>/samtools view -@ 2 /tmp/iJSBnAAIOB/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/iJSBnAAIOB/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/iJSBnAAIOB/test_input_1_b.bam.bai .. ok test_index: /<>/samtools merge -@ 2 -O sam - -X -cp -R ref2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_a.bam.bai /tmp/iJSBnAAIOB/test_input_1_b.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/iJSBnAAIOB/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam .. ok test_index: /<>/samtools index -@ 2 -M /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.bam /tmp/iJSBnAAIOB/auto_indexed.csi && cat /tmp/iJSBnAAIOB/auto_indexed.csi .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/auto_indexed.tmp.cram /tmp/iJSBnAAIOB/auto_indexed.crai && cat /tmp/iJSBnAAIOB/auto_indexed.crai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.sam /tmp/iJSBnAAIOB/auto_indexed.csi && cat /tmp/iJSBnAAIOB/auto_indexed.csi .. ok test_mpileup: /<>/samtools mpileup -b /tmp/iJSBnAAIOB/mpileup.bam.list -f /tmp/iJSBnAAIOB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/iJSBnAAIOB/mpileup.cram.list -f /tmp/iJSBnAAIOB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/iJSBnAAIOB/mpileup.bam.urllist -f /tmp/iJSBnAAIOB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/iJSBnAAIOB/mpileup.cram.urllist -f /tmp/iJSBnAAIOB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/iJSBnAAIOB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/iJSBnAAIOB/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/iJSBnAAIOB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/iJSBnAAIOB/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup /<>/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate .. ok test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools consensus .. ok test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools import .. ok test_usage_subcommand: samtools reference .. ok test_usage_subcommand: samtools reset .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth .. ok test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags .. ok test_usage_subcommand: samtools head .. ok test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools samples Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/iJSBnAAIOB/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/iJSBnAAIOB/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/iJSBnAAIOB/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/iJSBnAAIOB/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/iJSBnAAIOB/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/iJSBnAAIOB/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/iJSBnAAIOB/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/iJSBnAAIOB/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/iJSBnAAIOB/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/iJSBnAAIOB/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/iJSBnAAIOB/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/iJSBnAAIOB/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/iJSBnAAIOB/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/iJSBnAAIOB/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/iJSBnAAIOB/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/iJSBnAAIOB/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/iJSBnAAIOB/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/iJSBnAAIOB/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/iJSBnAAIOB/view.001.forn (SAM input) .. ok 68: Count -N /tmp/iJSBnAAIOB/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/iJSBnAAIOB/view.001.forn (BAM input) .. ok 70: Count -N /tmp/iJSBnAAIOB/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/iJSBnAAIOB/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/iJSBnAAIOB/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/iJSBnAAIOB/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/iJSBnAAIOB/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/iJSBnAAIOB/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/iJSBnAAIOB/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/iJSBnAAIOB/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/iJSBnAAIOB/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/iJSBnAAIOB/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/iJSBnAAIOB/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/iJSBnAAIOB/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/iJSBnAAIOB/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/iJSBnAAIOB/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/iJSBnAAIOB/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/iJSBnAAIOB/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/iJSBnAAIOB/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/iJSBnAAIOB/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/iJSBnAAIOB/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/iJSBnAAIOB/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/iJSBnAAIOB/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/iJSBnAAIOB/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/iJSBnAAIOB/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/iJSBnAAIOB/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/iJSBnAAIOB/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/iJSBnAAIOB/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/iJSBnAAIOB/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test115.sam -h -d TGCA /tmp/iJSBnAAIOB/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/iJSBnAAIOB/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test117.sam -h -d TGCA /tmp/iJSBnAAIOB/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/iJSBnAAIOB/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test119.sam -h -d TGCA /tmp/iJSBnAAIOB/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/iJSBnAAIOB/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/iJSBnAAIOB/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/iJSBnAAIOB/view.001.fobc" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test121.sam -h -D BClong:/tmp/iJSBnAAIOB/view.001.fobc /tmp/iJSBnAAIOB/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/iJSBnAAIOB/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/iJSBnAAIOB/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/iJSBnAAIOB/view.001.fobc /tmp/iJSBnAAIOB/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/iJSBnAAIOB/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/iJSBnAAIOB/view.001.fobc" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test123.sam -h -D BClong:/tmp/iJSBnAAIOB/view.001.fobc /tmp/iJSBnAAIOB/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/iJSBnAAIOB/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/iJSBnAAIOB/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/iJSBnAAIOB/view.001.fobc /tmp/iJSBnAAIOB/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/iJSBnAAIOB/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/iJSBnAAIOB/view.001.fobc" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test125.sam -h -D BClong:/tmp/iJSBnAAIOB/view.001.fobc /tmp/iJSBnAAIOB/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/iJSBnAAIOB/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/iJSBnAAIOB/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/iJSBnAAIOB/view.001.fobc /tmp/iJSBnAAIOB/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/iJSBnAAIOB/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/iJSBnAAIOB/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/iJSBnAAIOB/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/iJSBnAAIOB/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/iJSBnAAIOB/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/iJSBnAAIOB/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/iJSBnAAIOB/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa,ha (SAM input) .. ok 188: Count -x fa,ha (SAM input) .. ok 189: Filter -x fa,ha (BAM input) .. ok 190: Count -x fa,ha (BAM input) .. ok 191: Filter -x fa,ha (CRAM input) .. ok 192: Count -x fa,ha (CRAM input) .. ok 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 205: Filter -x fa -r grp2 (SAM input) .. ok 206: Count -x fa -r grp2 (SAM input) .. ok 207: Filter -x fa -r grp2 (BAM input) .. ok 208: Count -x fa -r grp2 (BAM input) .. ok 209: Filter -x fa -r grp2 (CRAM input) .. ok 210: Count -x fa -r grp2 (CRAM input) .. ok 211: Filter -x RG -r grp2 (SAM input) .. ok 212: Count -x RG -r grp2 (SAM input) .. ok 213: Filter -x RG -r grp2 (BAM input) .. ok 214: Count -x RG -r grp2 (BAM input) .. ok 215: Filter -x RG -r grp2 (CRAM input) .. ok 216: Count -x RG -r grp2 (CRAM input) .. ok 217: Filter -m 10 (SAM input) .. ok 218: Count -m 10 (SAM input) .. ok 219: Filter -m 10 (BAM input) .. ok 220: Count -m 10 (BAM input) .. ok 221: Filter -m 10 (CRAM input) .. ok 222: Count -m 10 (CRAM input) .. ok 223: Filter -m 11 (SAM input) .. ok 224: Count -m 11 (SAM input) .. ok 225: Filter -m 11 (BAM input) .. ok 226: Count -m 11 (BAM input) .. ok 227: Filter -m 11 (CRAM input) .. ok 228: Count -m 11 (CRAM input) .. ok 229: Filter -m 15 (SAM input) .. ok 230: Count -m 15 (SAM input) .. ok 231: Filter -m 15 (BAM input) .. ok 232: Count -m 15 (BAM input) .. ok 233: Filter -m 15 (CRAM input) .. ok 234: Count -m 15 (CRAM input) .. ok 235: Filter -m 16 (SAM input) .. ok 236: Count -m 16 (SAM input) .. ok 237: Filter -m 16 (BAM input) .. ok 238: Count -m 16 (BAM input) .. ok 239: Filter -m 16 (CRAM input) .. ok 240: Count -m 16 (CRAM input) .. ok 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247: Filter -e [BC] (SAM input) .. ok 248: Count -e [BC] (SAM input) .. ok 249: Filter -e [BC] (BAM input) .. ok 250: Count -e [BC] (BAM input) .. ok 251: Filter -e [BC] (CRAM input) .. ok 252: Count -e [BC] (CRAM input) .. ok 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 259: Filter -e mapq >= 50 (SAM input) .. ok 260: Count -e mapq >= 50 (SAM input) .. ok 261: Filter -e mapq >= 50 (BAM input) .. ok 262: Count -e mapq >= 50 (BAM input) .. ok 263: Filter -e mapq >= 50 (CRAM input) .. ok 264: Count -e mapq >= 50 (CRAM input) .. ok 265: Filter -e mapq >= 99 (SAM input) .. ok 266: Count -e mapq >= 99 (SAM input) .. ok 267: Filter -e mapq >= 99 (BAM input) .. ok 268: Count -e mapq >= 99 (BAM input) .. ok 269: Filter -e mapq >= 99 (CRAM input) .. ok 270: Count -e mapq >= 99 (CRAM input) .. ok 271: Filter -e mapq >= 100 (SAM input) .. ok 272: Count -e mapq >= 100 (SAM input) .. ok 273: Filter -e mapq >= 100 (BAM input) .. ok 274: Count -e mapq >= 100 (BAM input) .. ok 275: Filter -e mapq >= 100 (CRAM input) .. ok 276: Count -e mapq >= 100 (CRAM input) .. ok 277: 1bp reads file SAM -> BAM -> SAM .. ok 278: 1bp reads file SAM -> CRAM -> SAM .. ok 278: Region Z (BAM input) .. ok 279: Count Z (BAM input) .. ok 280: Region Z (CRAM input) .. ok 281: Count Z (CRAM input) .. ok 282: Region Z:30 (BAM input) .. ok 283: Count Z:30 (BAM input) .. ok 284: Region Z:30 (CRAM input) .. ok 285: Count Z:30 (CRAM input) .. ok 286: Region Z:20-40 (BAM input) .. ok 287: Count Z:20-40 (BAM input) .. ok 288: Region Z:20-40 (CRAM input) .. ok 289: Count Z:20-40 (CRAM input) .. ok 290: Region ref1 (BAM input) .. ok 291: Count ref1 (BAM input) .. ok 292: Region ref1 (CRAM input) .. ok 293: Count ref1 (CRAM input) .. ok 294: Region ref1:15 (BAM input) .. ok 295: Count ref1:15 (BAM input) .. ok 296: Region ref1:15 (CRAM input) .. ok 297: Count ref1:15 (CRAM input) .. ok 298: Region ref1:15-45 (BAM input) .. ok 299: Count ref1:15-45 (BAM input) .. ok 300: Region ref1:15-45 (CRAM input) .. ok 301: Count ref1:15-45 (CRAM input) .. ok 302: Region ref1:15-45 ref2 (BAM input) .. ok 303: Count ref1:15-45 ref2 (BAM input) .. ok 304: Region ref1:15-45 ref2 (CRAM input) .. ok 305: Count ref1:15-45 ref2 (CRAM input) .. ok 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 318: Region -f 128 ref1 (BAM input) .. ok 319: Count -f 128 ref1 (BAM input) .. ok 320: Region -f 128 ref1 (CRAM input) .. ok 321: Count -f 128 ref1 (CRAM input) .. ok 322: Region -q 50 ref1:15-45 (BAM input) .. ok 323: Count -q 50 ref1:15-45 (BAM input) .. ok 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 330: Region * (BAM input) .. ok 331: Count * (BAM input) .. ok 332: Region * (CRAM input) .. ok 333: Count * (CRAM input) .. ok 334: Region -L /<>/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /<>/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /<>/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /<>/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /<>/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /<>/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /<>/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /<>/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /<>/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /<>/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /<>/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /<>/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /<>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /<>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /<>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /<>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 406: Make BAM with no M5/UR tags .. ok 407: Add @SQ with -t (SAM -> SAM) .. ok 408: Add @SQ with -T (SAM -> SAM) .. ok 409: Add @SQ with -t (BAM -> SAM) .. ok 410: Add @SQ with -T (BAM -> SAM) .. ok 411: Add @SQ with -t (SAM -> BAM) .. ok 412: Add @SQ with -T (SAM -> BAM) .. ok 413: Add @SQ with -t (BAM -> BAM) .. ok 414: Add @SQ with -T (BAM -> BAM) .. ok 415: Add @SQ with -t (SAM -> CRAM) .. ok 416: Add @SQ with -T (SAM -> CRAM) .. ok 417: Add @SQ with -t (BAM -> CRAM) .. ok 418: Add @SQ with -T (BAM -> CRAM) .. ok 419: Make CRAM with no UR field .. ok 420: Decoding CRAM with no UR field via -T .. ok 421: CIGAR B-operator removal .. ok 422: Big SAM -> BAM .. ok 423: Big SAM -> BAM (2 threads) .. ok 424: Big SAM -> BAM (4 threads) .. ok 425: Big SAM -> CRAM .. ok 426: Big SAM -> CRAM (2 threads) .. ok 427: Big SAM -> CRAM (4 threads) .. ok 428: Subsample 0.2 (SAM input) ............ ok 429: Subsample 0.5 (SAM input) ............ ok 430: Subsample 0.8 (SAM input) ............ ok 431: Subsample 0.2 (BAM input) ............ ok 432: Subsample 0.5 (BAM input) ............ ok 433: Subsample 0.8 (BAM input) ............ ok 434: Subsample 0.2 (CRAM input) ............ ok 435: Subsample 0.5 (CRAM input) ............ ok 436: Subsample 0.8 (CRAM input) ............ ok 437: SAM add PG .. ok 438: Unset dup flag, remove dt and do tags .. ok 439: Unmap dup flagged reads. .. ok 440: Unmap dup flagged reads. .. ok 441: fetch pairs .. ok 442: fetch pairs .. ok 443: fetch pairs .. ok test_head: /<>/samtools head /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 0 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 1 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 5 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 29 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 30 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 0 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 1 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 5 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 5 -n 5 < /<>/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_import: /<>/samtools import -0 test/bam2fq/1.1.fq.expected | /<>/samtools fastq -0 /<>/test/0.fq .. ok test_import: /<>/samtools import -s test/bam2fq/1.1.fq.expected | /<>/samtools fastq -0 /<>/test/0.fq .. ok test_import: /<>/samtools import -s test/bam2fq/5.s.fq.expected | /<>/samtools fastq -s /<>/test/s.fq .. ok test_import: /<>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /<>/samtools fastq -N -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<>/samtools fastq -i --index-format 'i*i*' -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<>/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /<>/samtools fastq -N -T RG,BC,QT -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /<>/samtools fastq -N -T RG,BC,QT,MD,ia -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /<>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /<>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /<>/samtools import test/import/2.interleaved.fq -T "" .. ok test_import: /<>/samtools import test/import/3.interleaved.fq -i .. ok test_import: /<>/samtools import test/import/4.aux.fq -T "*" .. ok test_import: /<>/samtools import test/import/4.aux.fq -T "" .. ok test_import: /<>/samtools import test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /<>/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /<>/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.010.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -T MD,ia -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -i --index-format 'i*i*' -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.703.sam .. ok test_bam2fq: /<>/samtools fastq -N -1 /<>/test/o.fq -2 /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fasta -N -1 /<>/test/o.fa -2 /<>/test/o.fa /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -s /tmp/iJSBnAAIOB/bam2fq.discard.s.fq -0 /tmp/iJSBnAAIOB/bam2fq.discard.0.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -T ba,bb,bc,bd,be,bf,bg /<>/test/dat/bam2fq.013.sam .. ok test_bam2fq: /<>/samtools fastq --index-format 'i8n1i8' --i1 /<>/test/i1.fq --i2 /<>/test/i2.fq -0 /<>/test/0.fq /<>/test/dat/bam2fq.014.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -T '*' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '*' -d MD:10 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '*' -d NM:0 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '*' -d ia /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.010.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -T MD,ia -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -i --index-format 'i*i*' -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.703.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -1 /<>/test/o.fq -2 /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fasta -@ 2 -N -1 /<>/test/o.fa -2 /<>/test/o.fa /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -s /tmp/iJSBnAAIOB/bam2fq.discard.s.fq -0 /tmp/iJSBnAAIOB/bam2fq.discard.0.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /<>/test/dat/bam2fq.013.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /<>/test/i1.fq --i2 /<>/test/i2.fq -0 /<>/test/0.fq /<>/test/dat/bam2fq.014.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -T '*' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '*' -d MD:10 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '*' -d NM:0 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '*' -d ia /<>/test/dat/bam2fq.001.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa -i 0 /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -t /<>/test/stat/11.stats.targets /<>/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /<>/samtools stats -g 4 -t /<>/test/stat/11.stats.targets /<>/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -g 4 /<>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -t /<>/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -p -t /<>/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -t /<>/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -p -t /<>/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats -I s1 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I grp2 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I grp3 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I Sample /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/mpileup/ce.fa /<>/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -s 1 -O sam -b /tmp/k82ZUrLoHv - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -r -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -cp -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -o - -s 1 -O sam /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/iJSBnAAIOB/merge.tag.1.bam /tmp/iJSBnAAIOB/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/iJSBnAAIOB/merge.tag.3.bam /tmp/iJSBnAAIOB/merge.tag.4.bam .. ok test_merge: /<>/samtools merge --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge --no-PG -O SAM -L /<>/test/merge/merge.bed - /tmp/iJSBnAAIOB/merge.bed.1.bam /tmp/iJSBnAAIOB/merge.bed.2.bam .. ok test_merge: /<>/samtools merge --no-PG -r -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam -b /tmp/SSBYawyeps - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -@ 2 -r -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -cp -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -@ 2 -o - -s 1 -O sam /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/iJSBnAAIOB/merge.tag.1.bam /tmp/iJSBnAAIOB/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/iJSBnAAIOB/merge.tag.3.bam /tmp/iJSBnAAIOB/merge.tag.4.bam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM -L /<>/test/merge/merge.bed - /tmp/iJSBnAAIOB/merge.bed.1.bam /tmp/iJSBnAAIOB/merge.bed.2.bam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -r -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_sort: /<>/samtools sort /<>/test/dat/test_input_1_a.bam /tmp/iJSBnAAIOB/sortout .. ok test_sort: /<>/samtools sort -f /<>/test/dat/test_input_1_a.bam /tmp/iJSBnAAIOB/sortout.bam .. ok test_sort: /<>/samtools sort -o /<>/test/dat/test_input_1_a.bam /tmp/iJSBnAAIOB/sorttmp .. ok test_sort: /<>/samtools sort -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -N -m 10M /<>/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t AS -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -t FI -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort --template-coordinate -m 10M /<>/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -M -K10 -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -M -K10 -I /<>/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -MH -K10 -I /<>/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 /<>/test/dat/test_input_1_a.bam /tmp/iJSBnAAIOB/sortout .. ok test_sort: /<>/samtools sort -@ 2 -f /<>/test/dat/test_input_1_a.bam /tmp/iJSBnAAIOB/sortout.bam .. ok test_sort: /<>/samtools sort -@ 2 -o /<>/test/dat/test_input_1_a.bam /tmp/iJSBnAAIOB/sorttmp .. ok test_sort: /<>/samtools sort -@ 2 -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -N -m 10M /<>/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t AS -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t FI -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 --template-coordinate -m 10M /<>/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -@ 2 -M -K10 -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -@ 2 -M -K10 -I /<>/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -@ 2 -MH -K10 -I /<>/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /<>/samtools collate --output-fmt=sam -O /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -o /<>/test/collate/collate1.tmp.sam /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -o /<>/test/collate/collate2.tmp.sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate2.tmp .. ok test_collate: /<>/samtools collate --output-fmt=sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate3.tmp .. ok test_collate: /<>/samtools collate --output-fmt=sam -f /<>/test/collate/fast_collate.sam -o /<>/test/collate/1_fast_collate.sam .. ok test_collate: /<>/samtools collate --output-fmt=sam -f -r 4 /<>/test/collate/fast_collate.sam -o /<>/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -O /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -@ 2 -o /<>/test/collate/collate1.tmp.sam /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -@ 2 -o /<>/test/collate/collate2.tmp.sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate2.tmp .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate3.tmp .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -f /<>/test/collate/fast_collate.sam -o /<>/test/collate/1_fast_collate.sam .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -f -r 4 /<>/test/collate/fast_collate.sam -o /<>/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/sanitize.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/sanitize.sam - .. ok /<>/samtools calmd -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok /<>/samtools calmd -@ 2 -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.bam .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.cram .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.sam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /<>/samtools quickcheck -v /<>/test/quickcheck/1.quickcheck.badeof.bam /<>/test/quickcheck/2.quickcheck.badheader.bam /<>/test/quickcheck/3.quickcheck.ok.bam /<>/test/quickcheck/4.quickcheck.ok.bam /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<>/test/quickcheck/6.quickcheck.cram21.ok.cram /<>/test/quickcheck/7.quickcheck.cram30.ok.cram /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram /<>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /<>/samtools quickcheck -uv /<>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram && /<>/samtools view -h --no-PG /<>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram && /<>/samtools view -h --no-PG /<>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -R '1#9' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -R '1#9' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<>/test/addrprg/1_fixup.sam .. ok test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/5_markdup.sam - .. ok test_markdup: /<>/samtools markdup -O sam -r --no-PG /<>/test/markdup/6_remove_dups.sam - .. ok test_markdup: /<>/samtools markdup -S -O sam --no-PG /<>/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /<>/test/markdup/8_optical_dup.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<>/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<>/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<>/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<>/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /<>/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /<>/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /<>/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /<>/test/markdup/17_read_group.sam - .. ok test_markdup: /<>/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /<>/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/5_markdup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -O sam -r --no-PG /<>/test/markdup/6_remove_dups.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -O sam --no-PG /<>/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /<>/test/markdup/8_optical_dup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<>/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<>/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<>/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<>/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /<>/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /<>/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /<>/test/markdup/17_read_group.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /<>/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /<>/samtools bedcov /<>/test/bedcov/bedcov.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -j /<>/test/bedcov/bedcov.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -g512 -G2048 /<>/test/bedcov/bedcov_gG.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -c /<>/test/bedcov/bedcov_gG.bed /<>/test/bedcov/bedcov.bam .. ok test_split: /<>/samtools split --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -d RG -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -d an -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -d an -M 3 -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -d RG -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -d an -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/iJSBnAAIOB/longref.sam.gz .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/iJSBnAAIOB/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /<>/samtools view -h --no-PG -L /<>/test/large_pos/test.bed /tmp/iJSBnAAIOB/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -m 10M /<>/test/large_pos/longref_name.sam .. ok test_large_positions: /<>/samtools merge -O sam --no-PG - /<>/test/large_pos/longref.sam /<>/test/large_pos/longref2.sam .. ok test_large_positions: /<>/samtools depth /<>/test/large_pos/longref.sam .. ok test_large_positions: /<>/samtools depth -b /<>/test/large_pos/test.bed /<>/test/large_pos/longref.sam .. ok test_large_positions: /<>/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/iJSBnAAIOB/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /<>/samtools fixmate -O sam --no-PG - - | /<>/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test2.bed /<>/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test2.bed /<>/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_hard_clipped.expected.sam /<>/test/ampliconclip/1_soft_clipped.expected.sam /<>/test/ampliconclip/1_soft_clipped_strand.expected.sam /<>/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -c 0 /<>/test/ampliconclip/multi_ref.bed /<>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -c 0 /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /<>/test/dat/mpileup.1.sam | /<>/samtools reset | /<>/samtools view .. ok test_reset: /<>/samtools reset < /<>/test/dat/mpileup.1.sam | /<>/samtools view .. ok test_reset: /<>/samtools reset /<>/test/dat/mpileup.1.sam | /<>/samtools view .. ok test_reset: cat /<>/test/dat/mpileup.1.sam | /<>/samtools reset -o /<>/test/reset/output.tmp.sam .. ok test_reset: /<>/samtools reset -o /<>/test/reset/output.tmp.sam /<>/test/dat/test_input_1_a.bam .. ok test_reset: /<>/samtools reset -o /<>/test/reset/output.tmp.sam /<>/test/dat/test_input_1_a.cram .. ok test_reset: /<>/samtools reset --reject-PG bwa_index /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.tmp.sam; grep /<>/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /<>/samtools reset --reject-PG sam_to_fixed_bam /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.tmp.sam; grep /<>/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /<>/samtools reset --reject-PG bwa_index --no-PG /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.tmp.sam; grep /<>/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset /<>/test/reset/seq.sam -o /<>/test/reset/output .. ok Number of tests: total .. 933 passed .. 889 failed .. 0 expected failure .. 44 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 118 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 53 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 65 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS make[2]: Leaving directory '/<>' rm -fr -- /tmp/dh-xdg-rundir-zVnwCYyF make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a rm -f -- debian/samtools.substvars rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/ rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- \ prefix=/usr install -m0755 -d /<>/debian/tmp make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/share/man/man1 install -p samtools /<>/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<>/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /<>/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /<>/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/<>' make clean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* cd test/reference && rm -f mpileup.*.fai rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install install -m0755 -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -m0755 -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -m0755 -d debian/samtools/usr/share/commonwl/ cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl// install -m0755 -d debian/samtools/usr/share/man/man1 cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done # Disable the executable bit on a dataset. if [ -d debian/samtools-test ] \ ; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \ ; fi make[1]: Leaving directory '/<>' dh_installdocs -a install -m0755 -d debian/samtools/usr/share/doc/samtools install -m0755 -d debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./debian/README.test debian/samtools/usr/share/doc/samtools chmod -R u\+rw,go=rX debian/samtools/usr/share/doc install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright rm -f debian/samtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS.md install -m0755 -d debian/samtools/usr/share/doc/samtools install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/<>' dh_installexamples -a install -m0755 -d debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples rm -f debian/samtools.debhelper.log debian/rules execute_before_dh_installman make[1]: Entering directory '/<>' # Fix whatis entries for subcommands; "samtools subcommand \- desc." # will confuse the lexer, but "samtools-subcommand \- desc." will work. sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \ debian/*/usr/share/man/man*/*.* # .EX expects a indentation width. sed -i 's/^.EX$/.EX 8/' debian/*/usr/share/man/man*/*.* make[1]: Leaving directory '/<>' dh_installman -a rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 dh_lintian -a install -m0755 -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl -a mv debian/samtools.substvars.new debian/samtools.substvars dh_link -a rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 dh_strip_nondeterminism -a Using 1708190561 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip dh_compress -a cd debian/samtools chmod a-x usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/<>' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms -a find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -a dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/s390x-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/s390x-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/s390x-linux-gnu/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 697517 new size 703310 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/s390x-linux-gnu/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/s390x-linux-gnu/samtools.debug dh_strip -a debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/md5fa debugedit: debian/samtools/usr/bin/md5fa: Unknown DWARF DW_FORM_0x1f20 9cf2b97f6344e8a333edce8182e62f59dec155be install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c/f2b97f6344e8a333edce8182e62f59dec155be.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c/f2b97f6344e8a333edce8182e62f59dec155be.debug strip --remove-section=.comment --remove-section=.note -o /tmp/TWynPdspva/strip1eVgfh debian/samtools/usr/bin/md5fa chmod --reference debian/samtools/usr/bin/md5fa /tmp/TWynPdspva/strip1eVgfh cat '/tmp/TWynPdspva/strip1eVgfh' > 'debian/samtools/usr/bin/md5fa' chmod --reference /tmp/TWynPdspva/strip1eVgfh debian/samtools/usr/bin/md5fa objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c/f2b97f6344e8a333edce8182e62f59dec155be.debug debian/samtools/usr/bin/md5fa /tmp/TWynPdspva/objcopySMIgUV chmod --reference debian/samtools/usr/bin/md5fa /tmp/TWynPdspva/objcopySMIgUV cat '/tmp/TWynPdspva/objcopySMIgUV' > 'debian/samtools/usr/bin/md5fa' chmod --reference /tmp/TWynPdspva/objcopySMIgUV debian/samtools/usr/bin/md5fa debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/ace2sam debugedit: debian/samtools/usr/bin/ace2sam: Unknown DWARF DW_FORM_0x1f20 1374812232d09a7496bbcc9a18222ae32b9120c6 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/13/74812232d09a7496bbcc9a18222ae32b9120c6.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/13/74812232d09a7496bbcc9a18222ae32b9120c6.debug strip --remove-section=.comment --remove-section=.note -o /tmp/TWynPdspva/strip9bVhRI debian/samtools/usr/bin/ace2sam chmod --reference debian/samtools/usr/bin/ace2sam /tmp/TWynPdspva/strip9bVhRI cat '/tmp/TWynPdspva/strip9bVhRI' > 'debian/samtools/usr/bin/ace2sam' chmod --reference /tmp/TWynPdspva/strip9bVhRI debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/13/74812232d09a7496bbcc9a18222ae32b9120c6.debug debian/samtools/usr/bin/ace2sam /tmp/TWynPdspva/objcopy71ZURN chmod --reference debian/samtools/usr/bin/ace2sam /tmp/TWynPdspva/objcopy71ZURN cat '/tmp/TWynPdspva/objcopy71ZURN' > 'debian/samtools/usr/bin/ace2sam' chmod --reference /tmp/TWynPdspva/objcopy71ZURN debian/samtools/usr/bin/ace2sam debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/maq2sam-short debugedit: debian/samtools/usr/bin/maq2sam-short: Unknown DWARF DW_FORM_0x1f20 9da13029f4b20725d3b6caca72f8ea2852371d25 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9d/a13029f4b20725d3b6caca72f8ea2852371d25.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9d/a13029f4b20725d3b6caca72f8ea2852371d25.debug strip --remove-section=.comment --remove-section=.note -o /tmp/TWynPdspva/stripWXdzl0 debian/samtools/usr/bin/maq2sam-short chmod --reference debian/samtools/usr/bin/maq2sam-short /tmp/TWynPdspva/stripWXdzl0 cat '/tmp/TWynPdspva/stripWXdzl0' > 'debian/samtools/usr/bin/maq2sam-short' chmod --reference /tmp/TWynPdspva/stripWXdzl0 debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9d/a13029f4b20725d3b6caca72f8ea2852371d25.debug debian/samtools/usr/bin/maq2sam-short /tmp/TWynPdspva/objcopyiUnqjI chmod --reference debian/samtools/usr/bin/maq2sam-short /tmp/TWynPdspva/objcopyiUnqjI cat '/tmp/TWynPdspva/objcopyiUnqjI' > 'debian/samtools/usr/bin/maq2sam-short' chmod --reference /tmp/TWynPdspva/objcopyiUnqjI debian/samtools/usr/bin/maq2sam-short debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/maq2sam-long debugedit: debian/samtools/usr/bin/maq2sam-long: Unknown DWARF DW_FORM_0x1f20 752e4c99fbaff23428fc64ae3c4a854c38e25138 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/75 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/75/2e4c99fbaff23428fc64ae3c4a854c38e25138.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/75/2e4c99fbaff23428fc64ae3c4a854c38e25138.debug strip --remove-section=.comment --remove-section=.note -o /tmp/TWynPdspva/stripbuMFGM debian/samtools/usr/bin/maq2sam-long chmod --reference debian/samtools/usr/bin/maq2sam-long /tmp/TWynPdspva/stripbuMFGM cat '/tmp/TWynPdspva/stripbuMFGM' > 'debian/samtools/usr/bin/maq2sam-long' chmod --reference /tmp/TWynPdspva/stripbuMFGM debian/samtools/usr/bin/maq2sam-long objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/75/2e4c99fbaff23428fc64ae3c4a854c38e25138.debug debian/samtools/usr/bin/maq2sam-long /tmp/TWynPdspva/objcopynKAQo3 chmod --reference debian/samtools/usr/bin/maq2sam-long /tmp/TWynPdspva/objcopynKAQo3 cat '/tmp/TWynPdspva/objcopynKAQo3' > 'debian/samtools/usr/bin/maq2sam-long' chmod --reference /tmp/TWynPdspva/objcopynKAQo3 debian/samtools/usr/bin/maq2sam-long debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/md5sum-lite debugedit: debian/samtools/usr/bin/md5sum-lite: Unknown DWARF DW_FORM_0x1f21 b3e58198ea43b4d6b67b6ac9f13b0397eb958d19 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b3 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b3/e58198ea43b4d6b67b6ac9f13b0397eb958d19.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b3/e58198ea43b4d6b67b6ac9f13b0397eb958d19.debug strip --remove-section=.comment --remove-section=.note -o /tmp/TWynPdspva/stripEY0yaj debian/samtools/usr/bin/md5sum-lite chmod --reference debian/samtools/usr/bin/md5sum-lite /tmp/TWynPdspva/stripEY0yaj cat '/tmp/TWynPdspva/stripEY0yaj' > 'debian/samtools/usr/bin/md5sum-lite' chmod --reference /tmp/TWynPdspva/stripEY0yaj debian/samtools/usr/bin/md5sum-lite objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b3/e58198ea43b4d6b67b6ac9f13b0397eb958d19.debug debian/samtools/usr/bin/md5sum-lite /tmp/TWynPdspva/objcopyOZki_Q chmod --reference debian/samtools/usr/bin/md5sum-lite /tmp/TWynPdspva/objcopyOZki_Q cat '/tmp/TWynPdspva/objcopyOZki_Q' > 'debian/samtools/usr/bin/md5sum-lite' chmod --reference /tmp/TWynPdspva/objcopyOZki_Q debian/samtools/usr/bin/md5sum-lite debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/wgsim debugedit: debian/samtools/usr/bin/wgsim: Unknown DWARF DW_FORM_0x1f21 1700b85bd1ef1d2b72f5cb2d7484616970838e3d install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/17 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/17/00b85bd1ef1d2b72f5cb2d7484616970838e3d.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/17/00b85bd1ef1d2b72f5cb2d7484616970838e3d.debug strip --remove-section=.comment --remove-section=.note -o /tmp/TWynPdspva/stripyBrk5Y debian/samtools/usr/bin/wgsim chmod --reference debian/samtools/usr/bin/wgsim /tmp/TWynPdspva/stripyBrk5Y cat '/tmp/TWynPdspva/stripyBrk5Y' > 'debian/samtools/usr/bin/wgsim' chmod --reference /tmp/TWynPdspva/stripyBrk5Y debian/samtools/usr/bin/wgsim objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/17/00b85bd1ef1d2b72f5cb2d7484616970838e3d.debug debian/samtools/usr/bin/wgsim /tmp/TWynPdspva/objcopy6vwPCE chmod --reference debian/samtools/usr/bin/wgsim /tmp/TWynPdspva/objcopy6vwPCE cat '/tmp/TWynPdspva/objcopy6vwPCE' > 'debian/samtools/usr/bin/wgsim' chmod --reference /tmp/TWynPdspva/objcopy6vwPCE debian/samtools/usr/bin/wgsim debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/samtools 1ca155a20d3dc3bda26f8b2437a1c414130f5c7d install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/a155a20d3dc3bda26f8b2437a1c414130f5c7d.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/a155a20d3dc3bda26f8b2437a1c414130f5c7d.debug strip --remove-section=.comment --remove-section=.note -o /tmp/TWynPdspva/stripyLMs1l debian/samtools/usr/bin/samtools chmod --reference debian/samtools/usr/bin/samtools /tmp/TWynPdspva/stripyLMs1l cat '/tmp/TWynPdspva/stripyLMs1l' > 'debian/samtools/usr/bin/samtools' chmod --reference /tmp/TWynPdspva/stripyLMs1l debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/a155a20d3dc3bda26f8b2437a1c414130f5c7d.debug debian/samtools/usr/bin/samtools /tmp/TWynPdspva/objcopyuWWbmC chmod --reference debian/samtools/usr/bin/samtools /tmp/TWynPdspva/objcopyuWWbmC cat '/tmp/TWynPdspva/objcopyuWWbmC' > 'debian/samtools/usr/bin/samtools' chmod --reference /tmp/TWynPdspva/objcopyuWWbmC debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/s390x-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools dh_installdeb -a install -m0755 -d debian/samtools/DEBIAN dh_gencontrol -a install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=1374812232d09a7496bbcc9a18222ae32b9120c6 1700b85bd1ef1d2b72f5cb2d7484616970838e3d 1ca155a20d3dc3bda26f8b2437a1c414130f5c7d 752e4c99fbaff23428fc64ae3c4a854c38e25138 9cf2b97f6344e8a333edce8182e62f59dec155be 9da13029f4b20725d3b6caca72f8ea2852371d25 b3e58198ea43b4d6b67b6ac9f13b0397eb958d19" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums -a install -m0755 -d debian/samtools/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root debian/.debhelper/scratch-space/build-samtools INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing samtools (in debian/samtools); do_strip: , oemstrip: pkgstriptranslations: processing samtools-dbgsym (in debian/.debhelper/samtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools pkgstripfiles: processing control file: debian/.debhelper/samtools/dbgsym-root/DEBIAN/control, package samtools-dbgsym, directory debian/.debhelper/samtools/dbgsym-root .. removing usr/share/doc/samtools/changelog.gz dpkg-deb: building package 'samtools-dbgsym' in 'debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.19.2-1_s390x.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'samtools' in '../samtools_1.19.2-1_s390x.deb'. Renaming samtools-dbgsym_1.19.2-1_s390x.deb to samtools-dbgsym_1.19.2-1_s390x.ddeb mv debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.19.2-1_s390x.deb ../samtools-dbgsym_1.19.2-1_s390x.ddeb dpkg-genbuildinfo --build=any -O../samtools_1.19.2-1_s390x.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../samtools_1.19.2-1_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-02-18T05:24:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools_1.19.2-1_s390x.changes: -------------------------------- Format: 1.8 Date: Sat, 17 Feb 2024 18:22:41 +0100 Source: samtools Binary: samtools Built-For-Profiles: noudeb Architecture: s390x Version: 1.19.2-1 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats Changes: samtools (1.19.2-1) unstable; urgency=medium . * [3f34445] New upstream version 1.19.2 * [e0d4f37] d/control: replace pkg-config by pkgconf. 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wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: samtools Binary: samtools samtools-dbgsym Architecture: s390x Version: 1.19.2-1 Checksums-Md5: 679d542b760818befba313c08095b58c 834686 samtools-dbgsym_1.19.2-1_s390x.ddeb 3717ae05c038eca489c9bde0cdf702dd 612882 samtools_1.19.2-1_s390x.deb Checksums-Sha1: 8ca902736bf05c0e3aa4c380a9e82d422641d09e 834686 samtools-dbgsym_1.19.2-1_s390x.ddeb 9f1bead46ad19ef8dd5fd728b9c40104a86c8f82 612882 samtools_1.19.2-1_s390x.deb Checksums-Sha256: 9c756baeea02409633cb69603f0e42238975caf9acd53e4dd99ddda5e91c7202 834686 samtools-dbgsym_1.19.2-1_s390x.ddeb f5513f0082c51e67e900631f80b48266e17675a867b3ca059d72f5e2eb2f73a2 612882 samtools_1.19.2-1_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Sun, 18 Feb 2024 05:24:55 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), autoconf-archive (= 20220903-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu6), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), bash-completion (= 1:2.11-8), binutils (= 2.42-2ubuntu1), binutils-common (= 2.42-2ubuntu1), binutils-s390x-linux-gnu (= 2.42-2ubuntu1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), coreutils (= 9.4-2ubuntu3), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-13ubuntu1), cpp-13-s390x-linux-gnu (= 13.2.0-13ubuntu1), cpp-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.86), debhelper (= 13.13ubuntu1), debianutils (= 5.16), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.4ubuntu3), dpkg-dev (= 1.22.4ubuntu3), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-13ubuntu1), g++-13-s390x-linux-gnu (= 13.2.0-13ubuntu1), g++-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-13ubuntu1), gcc-13-base (= 13.2.0-13ubuntu1), gcc-13-s390x-linux-gnu (= 13.2.0-13ubuntu1), gcc-14-base (= 14-20240201-3ubuntu1), gcc-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-4ubuntu1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240201-3ubuntu1), libatomic1 (= 14-20240201-3ubuntu1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2), libaudit1 (= 1:3.1.2-2), libbinutils (= 2.42-2ubuntu1), libblkid1 (= 2.39.2-6ubuntu1), libbrotli1 (= 1.1.0-2), libbz2-1.0 (= 1.0.8-5build1), libbz2-dev (= 1.0.8-5build1), libc-bin (= 2.39-0ubuntu1), libc-dev-bin (= 2.39-0ubuntu1), libc6 (= 2.39-0ubuntu1), libc6-dev (= 2.39-0ubuntu1), libcap-ng0 (= 0.8.4-2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 14-20240201-3ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-2ubuntu1), libctf0 (= 2.42-2ubuntu1), libcurl3-gnutls (= 8.5.0-2ubuntu2), libcurl4-gnutls-dev (= 8.5.0-2ubuntu2), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.13ubuntu1), libdeflate-dev (= 1.19-1), libdeflate0 (= 1.19-1), libdpkg-perl (= 1.22.4ubuntu3), libdw1 (= 0.190-1), libelf1 (= 0.190-1), libffi8 (= 3.4.4-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-13ubuntu1), libgcc-s1 (= 14-20240201-3ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.3-1ubuntu1), libgomp1 (= 14-20240201-3ubuntu1), libgpg-error0 (= 1.47-3build1), libgssapi-krb5-2 (= 1.20.1-5build1), libhogweed6 (= 3.9.1-2), libhts-dev (= 1.18+ds-1), libhts3 (= 1.18+ds-1), libhtscodecs2 (= 1.6.0-1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.7-2), libio-pty-perl (= 1:1.20-1), libisl23 (= 0.26-3), libitm1 (= 14-20240201-3ubuntu1), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu1), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.5-0.3), liblzma5 (= 5.4.5-0.3), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-2), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncurses-dev (= 6.4+20240113-1ubuntu1), libncurses6 (= 6.4+20240113-1ubuntu1), libncursesw6 (= 6.4+20240113-1ubuntu1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.59.0-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libp11-kit0 (= 0.25.3-4ubuntu1), libpam-modules (= 1.5.2-9.1ubuntu2), libpam-modules-bin (= 1.5.2-9.1ubuntu2), libpam-runtime (= 1.5.2-9.1ubuntu2), libpam0g (= 1.5.2-9.1ubuntu2), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1), libpkgconf3 (= 1.8.1-2), libpsl5 (= 0.21.2-1build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.5-1ubuntu1), libselinux1 (= 3.5-2build1), libsframe1 (= 2.42-2ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libssh-4 (= 0.10.6-2), libssl3 (= 3.0.10-1ubuntu4), libstdc++-13-dev (= 13.2.0-13ubuntu1), libstdc++6 (= 14-20240201-3ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.2-3ubuntu2), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1ubuntu1), libtirpc-common (= 1.3.4+ds-1build1), libtirpc-dev (= 1.3.4+ds-1build1), libtirpc3 (= 1.3.4+ds-1build1), libtool (= 2.4.7-7), libubsan1 (= 14-20240201-3ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.2-3ubuntu2), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libxml2 (= 2.9.14+dfsg-1.3ubuntu1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-11.11), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 46), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-3ubuntu1), tabix (= 1.18+ds-1), tar (= 1.35+dfsg-3), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1708190561" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ samtools_1.19.2-1_s390x.deb --------------------------- new Debian package, version 2.0. size 612882 bytes: control archive=2913 bytes. 913 bytes, 18 lines control 5605 bytes, 82 lines md5sums Package: samtools Version: 1.19.2-1 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1348 Depends: libc6 (>= 2.34), libhts3 (>= 1.17), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.1.4) Suggests: cwltool Section: science Priority: optional Homepage: https://www.htslib.org/ Description: processing sequence alignments in SAM, BAM and CRAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing, and allows one to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP or HTTP server. drwxr-xr-x root/root 0 2024-02-17 17:22 ./ drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/ drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/bin/ -rwxr-xr-x root/root 22608 2024-02-17 17:22 ./usr/bin/ace2sam -rwxr-xr-x root/root 5443 2024-02-17 17:22 ./usr/bin/blast2sam.pl -rwxr-xr-x root/root 3360 2024-02-17 17:22 ./usr/bin/bowtie2sam.pl -rwxr-xr-x root/root 17996 2024-02-17 17:22 ./usr/bin/export2sam.pl -rwxr-xr-x root/root 3300 2024-02-17 17:22 ./usr/bin/fasta-sanitize.pl -rwxr-xr-x root/root 6121 2024-02-17 17:22 ./usr/bin/interpolate_sam.pl -rwxr-xr-x root/root 10320 2024-02-17 17:22 ./usr/bin/maq2sam-long -rwxr-xr-x root/root 10320 2024-02-17 17:22 ./usr/bin/maq2sam-short -rwxr-xr-x root/root 14416 2024-02-17 17:22 ./usr/bin/md5fa -rwxr-xr-x root/root 10320 2024-02-17 17:22 ./usr/bin/md5sum-lite -rwxr-xr-x root/root 7969 2024-02-17 17:22 ./usr/bin/novo2sam.pl -rwxr-xr-x root/root 44331 2024-02-17 17:22 ./usr/bin/plot-ampliconstats -rwxr-xr-x root/root 55292 2024-02-17 17:22 ./usr/bin/plot-bamstats -rwxr-xr-x root/root 3204 2024-02-17 17:22 ./usr/bin/psl2sam.pl -rwxr-xr-x root/root 8957 2024-02-17 17:22 ./usr/bin/sam2vcf.pl -rwxr-xr-x root/root 718200 2024-02-17 17:22 ./usr/bin/samtools -rwxr-xr-x root/root 16474 2024-02-17 17:22 ./usr/bin/samtools.pl -rwxr-xr-x root/root 11333 2024-02-17 17:22 ./usr/bin/seq_cache_populate.pl -rwxr-xr-x root/root 3905 2024-02-17 17:22 ./usr/bin/soap2sam.pl -rwxr-xr-x root/root 22648 2024-02-17 17:22 ./usr/bin/wgsim -rwxr-xr-x root/root 12542 2024-02-17 17:22 ./usr/bin/wgsim_eval.pl -rwxr-xr-x root/root 3579 2024-02-17 17:22 ./usr/bin/zoom2sam.pl drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/ drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/commonwl/ -rwxr-xr-x root/root 1906 2023-12-15 15:06 ./usr/share/commonwl/samtools-faidx.cwl -rwxr-xr-x root/root 1979 2023-12-15 15:06 ./usr/share/commonwl/samtools-index.cwl -rwxr-xr-x root/root 1627 2023-12-15 15:06 ./usr/share/commonwl/samtools-rmdup.cwl -rwxr-xr-x root/root 2834 2023-12-15 15:06 ./usr/share/commonwl/samtools-sort.cwl -rwxr-xr-x root/root 6224 2023-12-15 15:06 ./usr/share/commonwl/samtools-view.cwl drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/doc/samtools/ -rw-r--r-- root/root 828 2024-01-24 09:34 ./usr/share/doc/samtools/AUTHORS -rw-r--r-- root/root 497 2023-12-15 15:06 ./usr/share/doc/samtools/README.Debian -rw-r--r-- root/root 2482 2024-01-24 09:34 ./usr/share/doc/samtools/README.gz -rw-r--r-- root/root 313 2023-12-15 15:06 ./usr/share/doc/samtools/README.test -rw-r--r-- root/root 1973 2024-02-17 17:22 ./usr/share/doc/samtools/changelog.Debian.gz -rw-r--r-- root/root 2250 2024-02-17 17:08 ./usr/share/doc/samtools/copyright drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/doc/samtools/examples/ -rw-r--r-- root/root 1315 2024-01-24 09:34 ./usr/share/doc/samtools/examples/00README.txt -rw-r--r-- root/root 3225 2024-01-24 09:34 ./usr/share/doc/samtools/examples/ex1.fa -rw-r--r-- root/root 114565 2024-02-17 17:22 ./usr/share/doc/samtools/examples/ex1.sam.gz -rw-r--r-- root/root 98 2024-01-24 09:34 ./usr/share/doc/samtools/examples/toy.fa -rw-r--r-- root/root 786 2024-01-24 09:34 ./usr/share/doc/samtools/examples/toy.sam drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 168 2023-12-15 15:06 ./usr/share/lintian/overrides/samtools drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/man/ drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/man/man1/ -rw-r--r-- root/root 462 2024-02-17 17:22 ./usr/share/man/man1/ace2sam.1.gz -rw-r--r-- root/root 1641 2024-02-17 17:22 ./usr/share/man/man1/samtools-addreplacerg.1.gz -rw-r--r-- root/root 2358 2024-02-17 17:22 ./usr/share/man/man1/samtools-ampliconclip.1.gz -rw-r--r-- 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: 30560 Build-Time: 124 Distribution: noble-proposed Host Architecture: s390x Install-Time: 14 Job: samtools_1.19.2-1.dsc Machine Architecture: s390x Package: samtools Package-Time: 139 Source-Version: 1.19.2-1 Space: 30560 Status: successful Version: 1.19.2-1 -------------------------------------------------------------------------------- Finished at 2024-02-18T05:24:55Z Build needed 00:02:19, 30560k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27788436 Scanning for processes to kill in build PACKAGEBUILD-27788436