https://launchpad.net/ubuntu/+source/samtools/1.11-1/+build/20209978 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-023 4.15.0-121-generic #123-Ubuntu SMP Mon Oct 5 16:16:24 UTC 2020 ppc64le Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 29 Oct 14:56:42 ntpdate[1949]: adjust time server 10.211.37.1 offset 0.032562 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20209978 --image-type chroot /home/buildd/filecache-default/562b8b0d733db483afe9600af35c69ac54075a74 Creating target for build PACKAGEBUILD-20209978 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20209978 Starting target for build PACKAGEBUILD-20209978 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20209978 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20209978 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20209978 Updating target for build PACKAGEBUILD-20209978 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [88.4 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [88.4 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [114 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main ppc64el Packages [1340 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el Packages [12.4 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5318 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el Packages [206 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [82.1 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe ppc64el Packages [782 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [582 kB] Fetched 21.7 MB in 4s (5026 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files base-passwd binutils binutils-common binutils-powerpc64le-linux-gnu cpp-10 fakeroot g++-10 gcc-10 gcc-10-base libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libaudit-common libaudit1 libbinutils libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdebconfclient0 libfakeroot libgcc-10-dev libgcc-s1 libgomp1 libitm1 liblsan0 libmpc3 libncurses6 libncursesw6 libnpth0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-10-dev libstdc++6 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 linux-libc-dev ncurses-base ncurses-bin sysvinit-utils tzdata 53 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 198 MB of archives. After this operation, 760 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libcrypt-dev ppc64el 1:4.4.17-1ubuntu1 [131 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libcrypt1 ppc64el 1:4.4.17-1ubuntu1 [99.8 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main ppc64el base-files ppc64el 11ubuntu16 [60.7 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libncursesw6 ppc64el 6.2+20200918-1 [153 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libncurses6 ppc64el 6.2+20200918-1 [122 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libtinfo6 ppc64el 6.2+20200918-1 [104 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el ncurses-bin ppc64el 6.2+20200918-1 [179 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libdebconfclient0 ppc64el 0.254ubuntu1 [6156 B] Get:9 http://ftpmaster.internal/ubuntu hirsute/main ppc64el base-passwd ppc64el 3.5.48 [49.6 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el ncurses-base all 6.2+20200918-1 [18.7 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main ppc64el sysvinit-utils ppc64el 2.96-5ubuntu1 [22.8 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcc1-0 ppc64el 10.2.0-15ubuntu1 [41.8 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main ppc64el gcc-10-base ppc64el 10.2.0-15ubuntu1 [19.5 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libgcc-s1 ppc64el 10.2.0-15ubuntu1 [30.1 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libgomp1 ppc64el 10.2.0-15ubuntu1 [108 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libitm1 ppc64el 10.2.0-15ubuntu1 [28.5 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libatomic1 ppc64el 10.2.0-15ubuntu1 [9988 B] Get:18 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libasan6 ppc64el 10.2.0-15ubuntu1 [352 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main ppc64el liblsan0 ppc64el 10.2.0-15ubuntu1 [155 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libtsan0 ppc64el 10.2.0-15ubuntu1 [325 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libubsan1 ppc64el 10.2.0-15ubuntu1 [148 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libquadmath0 ppc64el 10.2.0-15ubuntu1 [149 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main ppc64el g++-10 ppc64el 10.2.0-15ubuntu1 [63.5 MB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libstdc++-10-dev ppc64el 10.2.0-15ubuntu1 [1765 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libgcc-10-dev ppc64el 10.2.0-15ubuntu1 [1251 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main ppc64el gcc-10 ppc64el 10.2.0-15ubuntu1 [64.7 MB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main ppc64el cpp-10 ppc64el 10.2.0-15ubuntu1 [57.2 MB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libstdc++6 ppc64el 10.2.0-15ubuntu1 [541 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libmpc3 ppc64el 1.2.0-1 [47.1 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libctf-nobfd0 ppc64el 2.35.1-2ubuntu1 [54.4 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libctf0 ppc64el 2.35.1-2ubuntu1 [53.5 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libbinutils ppc64el 2.35.1-2ubuntu1 [531 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el binutils-common ppc64el 2.35.1-2ubuntu1 [212 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el binutils ppc64el 2.35.1-2ubuntu1 [3376 B] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.35.1-2ubuntu1 [1805 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libapt-pkg6.0 ppc64el 2.1.11 [927 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libseccomp2 ppc64el 2.4.3-1ubuntu5 [48.0 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el apt ppc64el 2.1.11 [1319 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libaudit-common all 1:2.8.5-3ubuntu2 [4092 B] Get:40 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libaudit1 ppc64el 1:2.8.5-3ubuntu2 [42.5 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libselinux1 ppc64el 3.1-2build1 [81.9 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsemanage-common all 3.1-1build1 [10.1 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsemanage1 ppc64el 3.1-1build1 [97.0 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libtirpc-common all 1.2.6-3 [7444 B] Get:45 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libtirpc-dev ppc64el 1.2.6-3 [208 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libtirpc3 ppc64el 1.2.6-3 [89.2 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libapparmor1 ppc64el 3.0.0-0ubuntu2 [40.3 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libcap2 ppc64el 1:2.44-1 [19.8 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main ppc64el tzdata all 2020d-1ubuntu1 [293 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libfakeroot ppc64el 1.25.3-1 [28.5 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el fakeroot ppc64el 1.25.3-1 [66.4 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libnpth0 ppc64el 1.6-3 [8640 B] Get:53 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el linux-libc-dev ppc64el 5.8.0-26.27 [1161 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 198 MB in 3s (58.5 MB/s) (Reading database ... 12922 files and directories currently installed.) 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(Reading database ... 12920 files and directories currently installed.) Preparing to unpack .../libtirpc-dev_1.2.6-3_ppc64el.deb ... Unpacking libtirpc-dev:ppc64el (1.2.6-3) over (1.2.6-1build1) ... Preparing to unpack .../libtirpc3_1.2.6-3_ppc64el.deb ... Unpacking libtirpc3:ppc64el (1.2.6-3) over (1.2.6-1build1) ... Setting up libtirpc3:ppc64el (1.2.6-3) ... (Reading database ... 12920 files and directories currently installed.) Preparing to unpack .../0-libapparmor1_3.0.0-0ubuntu2_ppc64el.deb ... Unpacking libapparmor1:ppc64el (3.0.0-0ubuntu2) over (3.0.0-0ubuntu1) ... Preparing to unpack .../1-libcap2_1%3a2.44-1_ppc64el.deb ... Unpacking libcap2:ppc64el (1:2.44-1) over (1:2.43-1) ... Preparing to unpack .../2-tzdata_2020d-1ubuntu1_all.deb ... Unpacking tzdata (2020d-1ubuntu1) over (2020b-1ubuntu1) ... Preparing to unpack .../3-libfakeroot_1.25.3-1_ppc64el.deb ... Unpacking libfakeroot:ppc64el (1.25.3-1) over (1.25.2-1) ... 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.25.3-1) ... Setting up libtirpc-dev:ppc64el (1.2.6-3) ... Setting up libncurses6:ppc64el (6.2+20200918-1) ... Setting up libquadmath0:ppc64el (10.2.0-15ubuntu1) ... Setting up libmpc3:ppc64el (1.2.0-1) ... Setting up libatomic1:ppc64el (10.2.0-15ubuntu1) ... Setting up libncursesw6:ppc64el (6.2+20200918-1) ... Setting up libubsan1:ppc64el (10.2.0-15ubuntu1) ... Setting up libcrypt-dev:ppc64el (1:4.4.17-1ubuntu1) ... Setting up libbinutils:ppc64el (2.35.1-2ubuntu1) ... Setting up libcc1-0:ppc64el (10.2.0-15ubuntu1) ... Setting up liblsan0:ppc64el (10.2.0-15ubuntu1) ... Setting up cpp-10 (10.2.0-15ubuntu1) ... Setting up libitm1:ppc64el (10.2.0-15ubuntu1) ... Setting up libtsan0:ppc64el (10.2.0-15ubuntu1) ... Setting up libctf0:ppc64el (2.35.1-2ubuntu1) ... Setting up libgcc-10-dev:ppc64el (10.2.0-15ubuntu1) ... Setting up binutils-powerpc64le-linux-gnu (2.35.1-2ubuntu1) ... Setting up libstdc++-10-dev:ppc64el (10.2.0-15ubuntu1) ... Setting up binutils (2.35.1-2ubuntu1) ... Setting up gcc-10 (10.2.0-15ubuntu1) ... Setting up g++-10 (10.2.0-15ubuntu1) ... Processing triggers for libc-bin (2.32-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20209978 ppc64el hirsute-proposed -c chroot:build-PACKAGEBUILD-20209978 --arch=ppc64el --dist=hirsute-proposed --nolog samtools_1.11-1.dsc Initiating build PACKAGEBUILD-20209978 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-121-generic #123-Ubuntu SMP Mon Oct 5 16:16:24 UTC 2020 ppc64le sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-ppc64el-023.buildd +==============================================================================+ | samtools 1.11-1 (ppc64el) Thu, 29 Oct 2020 14:57:25 +0000 | +==============================================================================+ Package: samtools Version: 1.11-1 Source Version: 1.11-1 Distribution: hirsute-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20209978/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools_1.11-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/samtools-NKB6ol/samtools-1.11' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-NKB6ol' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-xJQJEw/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-xJQJEw/apt_archive ./ InRelease Get:2 copy:/<>/resolver-xJQJEw/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-xJQJEw/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-xJQJEw/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-xJQJEw/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (105 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 860 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-xJQJEw/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [860 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 860 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12920 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.11), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.11), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<>/resolver-xJQJEw/apt_archive/sbuild-build-depends-samtools-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-samtools-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-xJQJEw/apt_archive ./ InRelease Get:2 copy:/<>/resolver-xJQJEw/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-xJQJEw/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-xJQJEw/apt_archive ./ Sources [592 B] Get:5 copy:/<>/resolver-xJQJEw/apt_archive ./ Packages [665 B] Fetched 2220 B in 0s (90.5 kB/s) Reading package lists... Reading package lists... Install samtools build dependencies (apt-based resolver) -------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libio-pty-perl libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db pkg-config po-debconf tabix zlib1g-dev Suggested packages: gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-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 libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libio-pty-perl libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 26.9 MB of archives. After this operation, 106 MB of additional disk space will be used. Get:1 copy:/<>/resolver-xJQJEw/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [956 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main ppc64el bsdextrautils ppc64el 2.36-3ubuntu1 [83.7 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libuchardet0 ppc64el 0.0.7-1 [71.0 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main ppc64el groff-base ppc64el 1.22.4-5 [922 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libpipeline1 ppc64el 1.5.3-1 [29.6 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main ppc64el man-db ppc64el 2.9.3-2 [1148 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el autoconf-archive all 20190106-2.1ubuntu1 [665 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libmagic-mgc ppc64el 1:5.38-5 [218 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libmagic1 ppc64el 1:5.38-5 [93.2 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main ppc64el file ppc64el 1:5.38-5 [24.2 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libelf1 ppc64el 0.181-1 [52.0 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libglib2.0-0 ppc64el 2.66.1-2 [1406 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libicu67 ppc64el 67.1-4 [8812 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libxml2 ppc64el 2.9.10+dfsg-6.1 [656 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main ppc64el bash-completion all 1:2.11-2ubuntu1 [179 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main ppc64el gettext-base ppc64el 0.19.8.1-10build1 [52.5 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libpsl5 ppc64el 0.21.0-1.1ubuntu1 [54.0 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsigsegv2 ppc64el 2.12-2build1 [14.4 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main ppc64el m4 ppc64el 1.4.18-4 [210 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main ppc64el autoconf all 2.69-11.1 [321 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main ppc64el autotools-dev all 20180224.1 [39.6 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main ppc64el automake all 1:1.16.2-4ubuntu1 [548 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main ppc64el autopoint all 0.19.8.1-10build1 [412 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libtool all 2.4.6-14 [161 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dh-autoreconf all 19 [16.1 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libdebhelper-perl all 13.2.1ubuntu1 [63.6 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsub-override-perl all 0.09-2 [9532 B] Get:29 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:31 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dwz ppc64el 0.13-5 [136 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcroco3 ppc64el 0.6.13-1 [92.1 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main ppc64el gettext ppc64el 0.19.8.1-10build1 [959 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main ppc64el po-debconf all 1.0.21 [233 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main ppc64el debhelper all 13.2.1ubuntu1 [879 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libroken18-heimdal ppc64el 7.7.0+dfsg-2 [46.4 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libasn1-8-heimdal ppc64el 7.7.0+dfsg-2 [176 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libbrotli1 ppc64el 1.0.9-2build1 [297 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libbz2-dev ppc64el 1.0.8-4ubuntu2 [44.5 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libheimbase1-heimdal ppc64el 7.7.0+dfsg-2 [32.4 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libhcrypto4-heimdal ppc64el 7.7.0+dfsg-2 [108 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libwind0-heimdal ppc64el 7.7.0+dfsg-2 [48.9 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libhx509-5-heimdal ppc64el 7.7.0+dfsg-2 [120 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libkrb5-26-heimdal ppc64el 7.7.0+dfsg-2 [234 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libheimntlm0-heimdal ppc64el 7.7.0+dfsg-2 [17.4 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libgssapi3-heimdal ppc64el 7.7.0+dfsg-2 [105 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsasl2-modules-db ppc64el 2.1.27+dfsg-2ubuntu1 [16.8 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsasl2-2 ppc64el 2.1.27+dfsg-2ubuntu1 [60.0 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libldap-2.4-2 ppc64el 2.4.53+dfsg-1ubuntu1 [178 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libnghttp2-14 ppc64el 1.41.0-3 [78.1 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build2 [59.2 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libssh-4 ppc64el 0.9.4-1ubuntu3 [195 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcurl3-gnutls ppc64el 7.68.0-1ubuntu4 [254 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcurl4-gnutls-dev ppc64el 7.68.0-1ubuntu4 [357 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el libdeflate0 ppc64el 1.6-1 [64.0 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el libdeflate-dev ppc64el 1.6-1 [48.0 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute-proposed/universe ppc64el libhts3 ppc64el 1.11-2 [426 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main ppc64el liblzma-dev ppc64el 5.2.4-1ubuntu1 [164 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-2ubuntu4 [166 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute-proposed/universe ppc64el libhts-dev ppc64el 1.11-2 [3963 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libio-pty-perl ppc64el 1:1.12-1 [32.5 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libncurses-dev ppc64el 6.2+20200918-1 [420 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libncurses5-dev ppc64el 6.2+20200918-1 [992 B] Get:65 http://ftpmaster.internal/ubuntu hirsute/main ppc64el pkg-config ppc64el 0.29.2-1ubuntu1 [49.5 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute-proposed/universe ppc64el tabix ppc64el 1.11-2 [401 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 26.9 MB in 1s (24.8 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12920 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36-3ubuntu1_ppc64el.deb ... Unpacking bsdextrautils (2.36-3ubuntu1) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../01-libuchardet0_0.0.7-1_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_ppc64el.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../03-libpipeline1_1.5.3-1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_ppc64el.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package autoconf-archive. Preparing to unpack .../05-autoconf-archive_20190106-2.1ubuntu1_all.deb ... Unpacking autoconf-archive (20190106-2.1ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.38-5_ppc64el.deb ... Unpacking libmagic-mgc (1:5.38-5) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../07-libmagic1_1%3a5.38-5_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.38-5) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.38-5_ppc64el.deb ... Unpacking file (1:5.38-5) ... Selecting previously unselected package libelf1:ppc64el. Preparing to unpack .../09-libelf1_0.181-1_ppc64el.deb ... Unpacking libelf1:ppc64el (0.181-1) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../10-libglib2.0-0_2.66.1-2_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.66.1-2) ... Selecting previously unselected package libicu67:ppc64el. Preparing to unpack .../11-libicu67_67.1-4_ppc64el.deb ... Unpacking libicu67:ppc64el (67.1-4) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../12-libxml2_2.9.10+dfsg-6.1_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.10+dfsg-6.1) ... Selecting previously unselected package bash-completion. Preparing to unpack .../13-bash-completion_1%3a2.11-2ubuntu1_all.deb ... Unpacking bash-completion (1:2.11-2ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../14-gettext-base_0.19.8.1-10build1_ppc64el.deb ... Unpacking gettext-base (0.19.8.1-10build1) ... Selecting previously unselected package libpsl5:ppc64el. Preparing to unpack .../15-libpsl5_0.21.0-1.1ubuntu1_ppc64el.deb ... Unpacking libpsl5:ppc64el (0.21.0-1.1ubuntu1) ... Selecting previously unselected package libsigsegv2:ppc64el. Preparing to unpack .../16-libsigsegv2_2.12-2build1_ppc64el.deb ... Unpacking libsigsegv2:ppc64el (2.12-2build1) ... Selecting previously unselected package m4. Preparing to unpack .../17-m4_1.4.18-4_ppc64el.deb ... Unpacking m4 (1.4.18-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../18-autoconf_2.69-11.1_all.deb ... Unpacking autoconf (2.69-11.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../19-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../20-automake_1%3a1.16.2-4ubuntu1_all.deb ... Unpacking automake (1:1.16.2-4ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../21-autopoint_0.19.8.1-10build1_all.deb ... Unpacking autopoint (0.19.8.1-10build1) ... Selecting previously unselected package libtool. Preparing to unpack .../22-libtool_2.4.6-14_all.deb ... Unpacking libtool (2.4.6-14) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../23-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libdebhelper-perl. 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Selecting previously unselected package libcroco3:ppc64el. Preparing to unpack .../30-libcroco3_0.6.13-1_ppc64el.deb ... Unpacking libcroco3:ppc64el (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../31-gettext_0.19.8.1-10build1_ppc64el.deb ... Unpacking gettext (0.19.8.1-10build1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../32-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../33-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../34-debhelper_13.2.1ubuntu1_all.deb ... Unpacking debhelper (13.2.1ubuntu1) ... Selecting previously unselected package libroken18-heimdal:ppc64el. Preparing to unpack .../35-libroken18-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libroken18-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libasn1-8-heimdal:ppc64el. Preparing to unpack .../36-libasn1-8-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libasn1-8-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libbrotli1:ppc64el. Preparing to unpack .../37-libbrotli1_1.0.9-2build1_ppc64el.deb ... Unpacking libbrotli1:ppc64el (1.0.9-2build1) ... Selecting previously unselected package libbz2-dev:ppc64el. Preparing to unpack .../38-libbz2-dev_1.0.8-4ubuntu2_ppc64el.deb ... Unpacking libbz2-dev:ppc64el (1.0.8-4ubuntu2) ... Selecting previously unselected package libheimbase1-heimdal:ppc64el. Preparing to unpack .../39-libheimbase1-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libheimbase1-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libhcrypto4-heimdal:ppc64el. Preparing to unpack .../40-libhcrypto4-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libhcrypto4-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libwind0-heimdal:ppc64el. Preparing to unpack .../41-libwind0-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libwind0-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libhx509-5-heimdal:ppc64el. Preparing to unpack .../42-libhx509-5-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libhx509-5-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libkrb5-26-heimdal:ppc64el. Preparing to unpack .../43-libkrb5-26-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libkrb5-26-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libheimntlm0-heimdal:ppc64el. Preparing to unpack .../44-libheimntlm0-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libheimntlm0-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libgssapi3-heimdal:ppc64el. Preparing to unpack .../45-libgssapi3-heimdal_7.7.0+dfsg-2_ppc64el.deb ... Unpacking libgssapi3-heimdal:ppc64el (7.7.0+dfsg-2) ... Selecting previously unselected package libsasl2-modules-db:ppc64el. Preparing to unpack .../46-libsasl2-modules-db_2.1.27+dfsg-2ubuntu1_ppc64el.deb ... Unpacking libsasl2-modules-db:ppc64el (2.1.27+dfsg-2ubuntu1) ... Selecting previously unselected package libsasl2-2:ppc64el. Preparing to unpack .../47-libsasl2-2_2.1.27+dfsg-2ubuntu1_ppc64el.deb ... Unpacking libsasl2-2:ppc64el (2.1.27+dfsg-2ubuntu1) ... Selecting previously unselected package libldap-2.4-2:ppc64el. Preparing to unpack .../48-libldap-2.4-2_2.4.53+dfsg-1ubuntu1_ppc64el.deb ... Unpacking libldap-2.4-2:ppc64el (2.4.53+dfsg-1ubuntu1) ... Selecting previously unselected package libnghttp2-14:ppc64el. Preparing to unpack .../49-libnghttp2-14_1.41.0-3_ppc64el.deb ... Unpacking libnghttp2-14:ppc64el (1.41.0-3) ... Selecting previously unselected package librtmp1:ppc64el. Preparing to unpack .../50-librtmp1_2.4+20151223.gitfa8646d.1-2build2_ppc64el.deb ... Unpacking librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build2) ... Selecting previously unselected package libssh-4:ppc64el. Preparing to unpack .../51-libssh-4_0.9.4-1ubuntu3_ppc64el.deb ... Unpacking libssh-4:ppc64el (0.9.4-1ubuntu3) ... Selecting previously unselected package libcurl3-gnutls:ppc64el. Preparing to unpack .../52-libcurl3-gnutls_7.68.0-1ubuntu4_ppc64el.deb ... Unpacking libcurl3-gnutls:ppc64el (7.68.0-1ubuntu4) ... Selecting previously unselected package libcurl4-gnutls-dev:ppc64el. Preparing to unpack .../53-libcurl4-gnutls-dev_7.68.0-1ubuntu4_ppc64el.deb ... Unpacking libcurl4-gnutls-dev:ppc64el (7.68.0-1ubuntu4) ... Selecting previously unselected package libdeflate0:ppc64el. Preparing to unpack .../54-libdeflate0_1.6-1_ppc64el.deb ... Unpacking libdeflate0:ppc64el (1.6-1) ... Selecting previously unselected package libdeflate-dev:ppc64el. Preparing to unpack .../55-libdeflate-dev_1.6-1_ppc64el.deb ... Unpacking libdeflate-dev:ppc64el (1.6-1) ... Selecting previously unselected package libhts3:ppc64el. Preparing to unpack .../56-libhts3_1.11-2_ppc64el.deb ... Unpacking libhts3:ppc64el (1.11-2) ... Selecting previously unselected package liblzma-dev:ppc64el. Preparing to unpack .../57-liblzma-dev_5.2.4-1ubuntu1_ppc64el.deb ... Unpacking liblzma-dev:ppc64el (5.2.4-1ubuntu1) ... Selecting previously unselected package zlib1g-dev:ppc64el. Preparing to unpack .../58-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu4_ppc64el.deb ... Unpacking zlib1g-dev:ppc64el (1:1.2.11.dfsg-2ubuntu4) ... Selecting previously unselected package libhts-dev:ppc64el. Preparing to unpack .../59-libhts-dev_1.11-2_ppc64el.deb ... Unpacking libhts-dev:ppc64el (1.11-2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../60-libio-pty-perl_1%3a1.12-1_ppc64el.deb ... Unpacking libio-pty-perl (1:1.12-1) ... Selecting previously unselected package libncurses-dev:ppc64el. Preparing to unpack .../61-libncurses-dev_6.2+20200918-1_ppc64el.deb ... Unpacking libncurses-dev:ppc64el (6.2+20200918-1) ... Selecting previously unselected package libncurses5-dev:ppc64el. Preparing to unpack .../62-libncurses5-dev_6.2+20200918-1_ppc64el.deb ... Unpacking libncurses5-dev:ppc64el (6.2+20200918-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../63-pkg-config_0.29.2-1ubuntu1_ppc64el.deb ... Unpacking pkg-config (0.29.2-1ubuntu1) ... Selecting previously unselected package tabix. Preparing to unpack .../64-tabix_1.11-2_ppc64el.deb ... Unpacking tabix (1.11-2) ... Selecting previously unselected package sbuild-build-depends-samtools-dummy. Preparing to unpack .../65-sbuild-build-depends-samtools-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ... Setting up libpipeline1:ppc64el (1.5.3-1) ... Setting up libncurses-dev:ppc64el (6.2+20200918-1) ... Setting up libpsl5:ppc64el (0.21.0-1.1ubuntu1) ... Setting up bsdextrautils (2.36-3ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:ppc64el (67.1-4) ... Setting up libio-pty-perl (1:1.12-1) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:ppc64el (2.66.1-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.2.1ubuntu1) ... Setting up libbrotli1:ppc64el (1.0.9-2build1) ... Setting up libnghttp2-14:ppc64el (1.41.0-3) ... Setting up libmagic1:ppc64el (1:5.38-5) ... Setting up libdeflate0:ppc64el (1.6-1) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up autoconf-archive (20190106-2.1ubuntu1) ... Setting up file (1:5.38-5) ... Setting up libsasl2-modules-db:ppc64el (2.1.27+dfsg-2ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build2) ... Setting up bash-completion (1:2.11-2ubuntu1) ... Setting up libsigsegv2:ppc64el (2.12-2build1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up libsasl2-2:ppc64el (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:ppc64el (0.9.4-1ubuntu3) ... Setting up libroken18-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up liblzma-dev:ppc64el (5.2.4-1ubuntu1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-2ubuntu4) ... Setting up libuchardet0:ppc64el (0.0.7-1) ... Setting up libncurses5-dev:ppc64el (6.2+20200918-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:ppc64el (1.6-1) ... Setting up tabix (1.11-2) ... Setting up libelf1:ppc64el (0.181-1) ... Setting up libxml2:ppc64el (2.9.10+dfsg-6.1) ... Setting up libheimbase1-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libbz2-dev:ppc64el (1.0.8-4ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-4) ... Setting up libhcrypto4-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libwind0-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libcroco3:ppc64el (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up automake (1:1.16.2-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10build1) ... Setting up libhx509-5-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libkrb5-26-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:ppc64el (2.4.53+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:ppc64el (7.68.0-1ubuntu4) ... Setting up libcurl4-gnutls-dev:ppc64el (7.68.0-1ubuntu4) ... Setting up libhts3:ppc64el (1.11-2) ... Setting up libhts-dev:ppc64el (1.11-2) ... Setting up debhelper (13.2.1ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-121-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.35.1-2ubuntu1 dpkg-dev_1.20.5ubuntu2 g++-10_10.2.0-15ubuntu1 gcc-10_10.2.0-15ubuntu1 libc6-dev_2.32-0ubuntu3 libstdc++-10-dev_10.2.0-15ubuntu1 libstdc++6_10.2.0-15ubuntu1 linux-libc-dev_5.8.0-26.27 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.11 autoconf_2.69-11.1 autoconf-archive_20190106-2.1ubuntu1 automake_1:1.16.2-4ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.0-6ubuntu2 bash-completion_1:2.11-2ubuntu1 binutils_2.35.1-2ubuntu1 binutils-common_2.35.1-2ubuntu1 binutils-powerpc64le-linux-gnu_2.35.1-2ubuntu1 bsdextrautils_2.36-3ubuntu1 bsdutils_1:2.36-3ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.32-3ubuntu1 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.0-15ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1ubuntu1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.5ubuntu2 dpkg-dev_1.20.5ubuntu2 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1 file_1:5.38-5 findutils_4.7.0-1ubuntu2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.0-15ubuntu1 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.0-15ubuntu1 gcc-10-base_10.2.0-15ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_3.0.0-0ubuntu2 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.0-15ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.2.0-15ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3ubuntu2 libaudit1_1:2.8.5-3ubuntu2 libbinutils_2.35.1-2ubuntu1 libblkid1_2.36-3ubuntu1 libbrotli1_1.0.9-2build1 libbz2-1.0_1.0.8-4ubuntu2 libbz2-dev_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu3 libc-dev-bin_2.32-0ubuntu3 libc6_2.32-0ubuntu3 libc6-dev_2.32-0ubuntu3 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcc1-0_10.2.0-15ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.3-1ubuntu6 libctf-nobfd0_2.35.1-2ubuntu1 libctf0_2.35.1-2ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu4 libcurl4-gnutls-dev_7.68.0-1ubuntu4 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.254ubuntu1 libdebhelper-perl_13.2.1ubuntu1 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.20.5ubuntu2 libelf1_0.181-1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.3-1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-15ubuntu1 libgcc-s1_10.2.0-15ubuntu1 libgcrypt20_1.8.5-5ubuntu2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.1-2 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.6.15-4ubuntu2 libgomp1_10.2.0-15ubuntu1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libhx509-5-heimdal_7.7.0+dfsg-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libio-pty-perl_1:1.12-1 libip4tc2_1.8.5-3ubuntu1 libisl22_0.22.1-1 libitm1_10.2.0-15ubuntu1 libjson-c5_0.15-1 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libldap-2.4-2_2.4.53+dfsg-1ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.2.0-15ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3ubuntu1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20200918-1 libncurses5-dev_6.2+20200918-1 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-3 libnsl-dev_1.3.0-0ubuntu3 libnsl2_1.3.0-0ubuntu3 libnss-nis_3.1-0ubuntu4 libnss-nisplus_1.3-0ubuntu4 libp11-kit0_0.23.21-2build1 libpam-modules_1.3.1-5ubuntu6 libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpsl5_0.21.0-1.1ubuntu1 libquadmath0_10.2.0-15ubuntu1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27+dfsg-2ubuntu1 libseccomp2_2.4.3-1ubuntu5 libselinux1_3.1-2build1 libsemanage-common_3.1-1build1 libsemanage1_3.1-1build1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.36-3ubuntu1 libsqlite3-0_3.33.0-1 libss2_1.45.6-1ubuntu1 libssh-4_0.9.4-1ubuntu3 libssl1.1_1.1.1f-1ubuntu4 libstdc++-10-dev_10.2.0-15ubuntu1 libstdc++6_10.2.0-15ubuntu1 libsub-override-perl_0.09-2 libsystemd0_246.6-1ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libtsan0_10.2.0-15ubuntu1 libubsan1_10.2.0-15ubuntu1 libuchardet0_0.0.7-1 libudev1_246.6-1ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36-3ubuntu1 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-6.1 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.0-26.27 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3ubuntu1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 openssl_1.1.1f-1ubuntu4 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 readline-common_8.0-4 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 systemd_246.6-1ubuntu1 systemd-sysv_246.6-1ubuntu1 systemd-timesyncd_246.6-1ubuntu1 sysvinit-utils_2.96-5ubuntu1 tabix_1.11-2 tar_1.30+dfsg-7 tzdata_2020d-1ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.36-3ubuntu1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Oct 1 14:52:01 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./samtools_1.11-1.dsc dpkg-source: info: extracting samtools in /<> dpkg-source: info: unpacking samtools_1.11.orig.tar.gz dpkg-source: info: unpacking samtools_1.11-1.debian.tar.xz 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-20209978 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20209978 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20209978 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.11-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el dpkg-source: info: using options from samtools-1.11/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 -- install -d /<>/debian/.debhelper/generated/_source/home 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 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* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) 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.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: 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 configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level autoconf configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: 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 install -d /<>/debian/.debhelper/generated/_source/home ./configure --build=powerpc64le-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/powerpc64le-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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c bam_plcmd.c: In function ‘mpileup’: bam_plcmd.c:621:20: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 621 | bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ; | ~~~~~~~~~~~^~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c bam_fastq.c: In function ‘main_bam2fq’: bam_fastq.c:998:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 998 | int main_bam2fq(int argc, char *argv[]) | ^~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.11"' > version.h gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c stats.c: In function ‘replicate_regions’: stats.c:1997:61: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1997 | stats->regions[tid].mpos = stats->regions[tid].npos = iter->reg_list[i].count; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c bedidx.c: In function ‘bed_hash_regions’: bedidx.c:473:18: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 473 | p->n = new_n; | ~~~~~^~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -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 -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 -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 -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 -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 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.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 bam2bcf_indel.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 ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -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 -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 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 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:-} /usr/bin/bgzip -c -b 65272 -s 5 /tmp/mFb3u6qHYf/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/mFb3u6qHYf/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/mFb3u6qHYf/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/mFb3u6qHYf/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/mFb3u6qHYf/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/mFb3u6qHYf/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/mFb3u6qHYf/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/mFb3u6qHYf/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/mFb3u6qHYf/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/mFb3u6qHYf/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/mFb3u6qHYf/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /<>/samtools fqidx /tmp/mFb3u6qHYf/fqidx.fq 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/mFb3u6qHYf/fqidx.fq.gz 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/mFb3u6qHYf/fqidx.fq 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/mFb3u6qHYf/fqidx.fq.gz 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/mFb3u6qHYf/fqidx.fq 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/mFb3u6qHYf/fqidx.fq.gz 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/mFb3u6qHYf/fqidx.fq 1:99998-100007 .. ok .. ok /<>/samtools fqidx /tmp/mFb3u6qHYf/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/mFb3u6qHYf/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_index: /<>/samtools view /tmp/mFb3u6qHYf/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/mFb3u6qHYf/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/mFb3u6qHYf/test_input_1_b.bam.bai ref2 .. 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/mFb3u6qHYf/test_input_1_b.bam.bai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.bam /tmp/mFb3u6qHYf/auto_indexed.csi && cat /tmp/mFb3u6qHYf/auto_indexed.csi .. ok test_index: /<>/samtools index /<>/test/dat/auto_indexed.tmp.cram /tmp/mFb3u6qHYf/auto_indexed.crai && cat /tmp/mFb3u6qHYf/auto_indexed.crai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.sam /tmp/mFb3u6qHYf/auto_indexed.csi && cat /tmp/mFb3u6qHYf/auto_indexed.csi .. ok test_index: /<>/samtools view -@ 2 /tmp/mFb3u6qHYf/large_chrom.bam ref2 .. ok test_index: /<>/samtools view -@ 2 /tmp/mFb3u6qHYf/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/mFb3u6qHYf/test_input_1_b.bam.bai ref2 .. 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/mFb3u6qHYf/test_input_1_b.bam.bai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.bam /tmp/mFb3u6qHYf/auto_indexed.csi && cat /tmp/mFb3u6qHYf/auto_indexed.csi .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/auto_indexed.tmp.cram /tmp/mFb3u6qHYf/auto_indexed.crai && cat /tmp/mFb3u6qHYf/auto_indexed.crai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.sam /tmp/mFb3u6qHYf/auto_indexed.csi && cat /tmp/mFb3u6qHYf/auto_indexed.csi .. ok test_mpileup: /<>/samtools mpileup -b /tmp/mFb3u6qHYf/mpileup.bam.list -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/mFb3u6qHYf/mpileup.cram.list -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/mFb3u6qHYf/mpileup.bam.urllist -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/mFb3u6qHYf/mpileup.cram.urllist -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/mFb3u6qHYf/mpileup.bam.list -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/mFb3u6qHYf/mpileup.cram.list -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/mFb3u6qHYf/mpileup.cram.list -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/mFb3u6qHYf/mpileup.cram.list -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mFb3u6qHYf/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/mFb3u6qHYf/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mFb3u6qHYf/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, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, tview, view, depad .. 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 Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure 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 bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth Usage on stderr rather than stdout .. expected failure 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 Usage on stderr rather than stdout .. expected failure 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_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/mFb3u6qHYf/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/mFb3u6qHYf/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/mFb3u6qHYf/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/mFb3u6qHYf/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/mFb3u6qHYf/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/mFb3u6qHYf/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/mFb3u6qHYf/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/mFb3u6qHYf/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/mFb3u6qHYf/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/mFb3u6qHYf/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/mFb3u6qHYf/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/mFb3u6qHYf/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/mFb3u6qHYf/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/mFb3u6qHYf/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/mFb3u6qHYf/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/mFb3u6qHYf/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/mFb3u6qHYf/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/mFb3u6qHYf/view.001.fogn (CRAM input).. ok 67: Filter -d BC:TGCA (SAM input) .. ok 68: Count -d BC:TGCA (SAM input) .. ok 69: Filter -d BC:TGCA (BAM input) .. ok 70: Count -d BC:TGCA (BAM input) .. ok 71: Filter -d BC:TGCA (CRAM input) .. ok 72: Count -d BC:TGCA (CRAM input) .. ok 73: Filter -D BC:/tmp/mFb3u6qHYf/view.001.fobc (SAM input) .. ok 74: Count -D BC:/tmp/mFb3u6qHYf/view.001.fobc (SAM input) .. ok 75: Filter -D BC:/tmp/mFb3u6qHYf/view.001.fobc (BAM input) .. ok 76: Count -D BC:/tmp/mFb3u6qHYf/view.001.fobc (BAM input) .. ok 77: Filter -D BC:/tmp/mFb3u6qHYf/view.001.fobc (CRAM input) .. ok 78: Count -D BC:/tmp/mFb3u6qHYf/view.001.fobc (CRAM input) .. ok 79: Filter -D BC:/tmp/mFb3u6qHYf/view.001.fobc -d BC:TGCA (SAM input).. ok 80: Count -D BC:/tmp/mFb3u6qHYf/view.001.fobc -d BC:TGCA (SAM input).. ok 81: Filter -D BC:/tmp/mFb3u6qHYf/view.001.fobc -d BC:TGCA (BAM input).. ok 82: Count -D BC:/tmp/mFb3u6qHYf/view.001.fobc -d BC:TGCA (BAM input).. ok 83: Filter -D BC:/tmp/mFb3u6qHYf/view.001.fobc -d BC:TGCA (CRAM input).. ok 84: Count -D BC:/tmp/mFb3u6qHYf/view.001.fobc -d BC:TGCA (CRAM input).. ok 85: Filter -d BC:TGCA -D BC:/tmp/mFb3u6qHYf/view.001.fobc (SAM input).. ok 86: Count -d BC:TGCA -D BC:/tmp/mFb3u6qHYf/view.001.fobc (SAM input).. ok 87: Filter -d BC:TGCA -D BC:/tmp/mFb3u6qHYf/view.001.fobc (BAM input).. ok 88: Count -d BC:TGCA -D BC:/tmp/mFb3u6qHYf/view.001.fobc (BAM input).. ok 89: Filter -d BC:TGCA -D BC:/tmp/mFb3u6qHYf/view.001.fobc (CRAM input).. ok 90: Count -d BC:TGCA -D BC:/tmp/mFb3u6qHYf/view.001.fobc (CRAM input).. ok 91: Filter -D RG:/tmp/mFb3u6qHYf/view.001.fogn (SAM input) .. ok 92: Count -D RG:/tmp/mFb3u6qHYf/view.001.fogn (SAM input) .. ok 93: Filter -D RG:/tmp/mFb3u6qHYf/view.001.fogn (BAM input) .. ok 94: Count -D RG:/tmp/mFb3u6qHYf/view.001.fogn (BAM input) .. ok 95: Filter -D RG:/tmp/mFb3u6qHYf/view.001.fogn (CRAM input) .. ok 96: Count -D RG:/tmp/mFb3u6qHYf/view.001.fogn (CRAM input) .. ok 97: Filter -d NE:TGCA (SAM input) .. ok 98: Count -d NE:TGCA (SAM input) .. ok 99: Filter -d NE:TGCA (BAM input) .. ok 100: Count -d NE:TGCA (BAM input) .. ok 101: Filter -d NE:TGCA (CRAM input) .. ok 102: Count -d NE:TGCA (CRAM input) .. ok 103: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/mFb3u6qHYf/view.test103.sam -h -d TGCA /tmp/mFb3u6qHYf/view.001.sam --no-PG .. expected failure 104: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/mFb3u6qHYf/view.001.sam --no-PG .. expected failure 105: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/mFb3u6qHYf/view.test105.sam -h -d TGCA /tmp/mFb3u6qHYf/view.test001.bam --no-PG .. expected failure 106: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/mFb3u6qHYf/view.test001.bam --no-PG .. expected failure 107: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/mFb3u6qHYf/view.test107.sam -h -d TGCA /tmp/mFb3u6qHYf/view.test006.cram --no-PG .. expected failure 108: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/mFb3u6qHYf/view.test006.cram --no-PG .. expected failure 109: Filter -D BClong:/tmp/mFb3u6qHYf/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mFb3u6qHYf/view.001.fobc" Failed command: /<>/samtools view -o /tmp/mFb3u6qHYf/view.test109.sam -h -D BClong:/tmp/mFb3u6qHYf/view.001.fobc /tmp/mFb3u6qHYf/view.001.sam --no-PG .. expected failure 110: Count -D BClong:/tmp/mFb3u6qHYf/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mFb3u6qHYf/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/mFb3u6qHYf/view.001.fobc /tmp/mFb3u6qHYf/view.001.sam --no-PG .. expected failure 111: Filter -D BClong:/tmp/mFb3u6qHYf/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mFb3u6qHYf/view.001.fobc" Failed command: /<>/samtools view -o /tmp/mFb3u6qHYf/view.test111.sam -h -D BClong:/tmp/mFb3u6qHYf/view.001.fobc /tmp/mFb3u6qHYf/view.test001.bam --no-PG .. expected failure 112: Count -D BClong:/tmp/mFb3u6qHYf/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mFb3u6qHYf/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/mFb3u6qHYf/view.001.fobc /tmp/mFb3u6qHYf/view.test001.bam --no-PG .. expected failure 113: Filter -D BClong:/tmp/mFb3u6qHYf/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mFb3u6qHYf/view.001.fobc" Failed command: /<>/samtools view -o /tmp/mFb3u6qHYf/view.test113.sam -h -D BClong:/tmp/mFb3u6qHYf/view.001.fobc /tmp/mFb3u6qHYf/view.test006.cram --no-PG .. expected failure 114: Count -D BClong:/tmp/mFb3u6qHYf/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mFb3u6qHYf/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/mFb3u6qHYf/view.001.fobc /tmp/mFb3u6qHYf/view.test006.cram --no-PG .. expected failure 115: 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/mFb3u6qHYf/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/mFb3u6qHYf/view.001.sam --no-PG .. expected failure 116: 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/mFb3u6qHYf/view.001.sam --no-PG .. expected failure 117: 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/mFb3u6qHYf/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/mFb3u6qHYf/view.test001.bam --no-PG .. expected failure 118: 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/mFb3u6qHYf/view.test001.bam --no-PG .. expected failure 119: 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/mFb3u6qHYf/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/mFb3u6qHYf/view.test006.cram --no-PG .. expected failure 120: 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/mFb3u6qHYf/view.test006.cram --no-PG .. expected failure 121: Filter -l Library 2 (SAM input) .. ok 122: Count -l Library 2 (SAM input) .. ok 123: Filter -l Library 2 (BAM input) .. ok 124: Count -l Library 2 (BAM input) .. ok 125: Filter -l Library 2 (CRAM input) .. ok 126: Count -l Library 2 (CRAM input) .. ok 127: Filter -l Library 3 (SAM input) .. ok 128: Count -l Library 3 (SAM input) .. ok 129: Filter -l Library 3 (BAM input) .. ok 130: Count -l Library 3 (BAM input) .. ok 131: Filter -l Library 3 (CRAM input) .. ok 132: Count -l Library 3 (CRAM input) .. ok 133: Filter -q 50 (SAM input) .. ok 134: Count -q 50 (SAM input) .. ok 135: Filter -q 50 (BAM input) .. ok 136: Count -q 50 (BAM input) .. ok 137: Filter -q 50 (CRAM input) .. ok 138: Count -q 50 (CRAM input) .. ok 139: Filter -q 99 (SAM input) .. ok 140: Count -q 99 (SAM input) .. ok 141: Filter -q 99 (BAM input) .. ok 142: Count -q 99 (BAM input) .. ok 143: Filter -q 99 (CRAM input) .. ok 144: Count -q 99 (CRAM input) .. ok 145: Filter -q 100 (SAM input) .. ok 146: Count -q 100 (SAM input) .. ok 147: Filter -q 100 (BAM input) .. ok 148: Count -q 100 (BAM input) .. ok 149: Filter -q 100 (CRAM input) .. ok 150: Count -q 100 (CRAM input) .. ok 151: Filter -x fa (SAM input) .. ok 152: Count -x fa (SAM input) .. ok 153: Filter -x fa (BAM input) .. ok 154: Count -x fa (BAM input) .. ok 155: Filter -x fa (CRAM input) .. ok 156: Count -x fa (CRAM input) .. ok 157: Filter -x fa -x ha (SAM input) .. ok 158: Count -x fa -x ha (SAM input) .. ok 159: Filter -x fa -x ha (BAM input) .. ok 160: Count -x fa -x ha (BAM input) .. ok 161: Filter -x fa -x ha (CRAM input) .. ok 162: Count -x fa -x ha (CRAM input) .. ok 163: Filter -x fa -r grp2 (SAM input) .. ok 164: Count -x fa -r grp2 (SAM input) .. ok 165: Filter -x fa -r grp2 (BAM input) .. ok 166: Count -x fa -r grp2 (BAM input) .. ok 167: Filter -x fa -r grp2 (CRAM input) .. ok 168: Count -x fa -r grp2 (CRAM input) .. ok 169: Filter -x RG -r grp2 (SAM input) .. ok 170: Count -x RG -r grp2 (SAM input) .. ok 171: Filter -x RG -r grp2 (BAM input) .. ok 172: Count -x RG -r grp2 (BAM input) .. ok 173: Filter -x RG -r grp2 (CRAM input) .. ok 174: Count -x RG -r grp2 (CRAM input) .. ok 175: Filter -m 10 (SAM input) .. ok 176: Count -m 10 (SAM input) .. ok 177: Filter -m 10 (BAM input) .. ok 178: Count -m 10 (BAM input) .. ok 179: Filter -m 10 (CRAM input) .. ok 180: Count -m 10 (CRAM input) .. ok 181: Filter -m 11 (SAM input) .. ok 182: Count -m 11 (SAM input) .. ok 183: Filter -m 11 (BAM input) .. ok 184: Count -m 11 (BAM input) .. ok 185: Filter -m 11 (CRAM input) .. ok 186: Count -m 11 (CRAM input) .. ok 187: Filter -m 15 (SAM input) .. ok 188: Count -m 15 (SAM input) .. ok 189: Filter -m 15 (BAM input) .. ok 190: Count -m 15 (BAM input) .. ok 191: Filter -m 15 (CRAM input) .. ok 192: Count -m 15 (CRAM input) .. ok 193: Filter -m 16 (SAM input) .. ok 194: Count -m 16 (SAM input) .. ok 195: Filter -m 16 (BAM input) .. ok 196: Count -m 16 (BAM input) .. ok 197: Filter -m 16 (CRAM input) .. ok 198: Count -m 16 (CRAM input) .. ok 199: 1bp reads file SAM -> BAM -> SAM .. ok 200: 1bp reads file SAM -> CRAM -> SAM .. ok 200: Region Z (BAM input) .. ok 201: Count Z (BAM input) .. ok 202: Region Z (CRAM input) .. ok 203: Count Z (CRAM input) .. ok 204: Region Z:30 (BAM input) .. ok 205: Count Z:30 (BAM input) .. ok 206: Region Z:30 (CRAM input) .. ok 207: Count Z:30 (CRAM input) .. ok 208: Region Z:20-40 (BAM input) .. ok 209: Count Z:20-40 (BAM input) .. ok 210: Region Z:20-40 (CRAM input) .. ok 211: Count Z:20-40 (CRAM input) .. ok 212: Region ref1 (BAM input) .. ok 213: Count ref1 (BAM input) .. ok 214: Region ref1 (CRAM input) .. ok 215: Count ref1 (CRAM input) .. ok 216: Region ref1:15 (BAM input) .. ok 217: Count ref1:15 (BAM input) .. ok 218: Region ref1:15 (CRAM input) .. ok 219: Count ref1:15 (CRAM input) .. ok 220: Region ref1:15-45 (BAM input) .. ok 221: Count ref1:15-45 (BAM input) .. ok 222: Region ref1:15-45 (CRAM input) .. ok 223: Count ref1:15-45 (CRAM input) .. ok 224: Region ref1:15-45 ref2 (BAM input) .. ok 225: Count ref1:15-45 ref2 (BAM input) .. ok 226: Region ref1:15-45 ref2 (CRAM input) .. ok 227: Count ref1:15-45 ref2 (CRAM input) .. ok 228: Region ref1:15-45 ref2:16 (BAM input) .. ok 229: Count ref1:15-45 ref2:16 (BAM input) .. ok 230: Region ref1:15-45 ref2:16 (CRAM input) .. ok 231: Count ref1:15-45 ref2:16 (CRAM input) .. ok 232: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 233: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 234: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 235: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 236: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 237: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 238: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 239: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 240: Region -f 128 ref1 (BAM input) .. ok 241: Count -f 128 ref1 (BAM input) .. ok 242: Region -f 128 ref1 (CRAM input) .. ok 243: Count -f 128 ref1 (CRAM input) .. ok 244: Region -q 50 ref1:15-45 (BAM input) .. ok 245: Count -q 50 ref1:15-45 (BAM input) .. ok 246: Region -q 50 ref1:15-45 (CRAM input) .. ok 247: Count -q 50 ref1:15-45 (CRAM input) .. ok 248: Region -r grp2 ref1:15-45 (BAM input) .. ok 249: Count -r grp2 ref1:15-45 (BAM input) .. ok 250: Region -r grp2 ref1:15-45 (CRAM input) .. ok 251: Count -r grp2 ref1:15-45 (CRAM input) .. ok 252: Region * (BAM input) .. ok 253: Count * (BAM input) .. ok 254: Region * (CRAM input) .. ok 255: Count * (CRAM input) .. ok 256: Region -L /<>/test/dat/view.002.01.bed (BAM input).. ok 257: Count -L /<>/test/dat/view.002.01.bed (BAM input).. ok 258: Region -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 259: Count -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 260: Region -L /<>/test/dat/view.002.02.bed (BAM input).. ok 261: Count -L /<>/test/dat/view.002.02.bed (BAM input).. ok 262: Region -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 263: Count -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 264: Region -L /<>/test/dat/view.001.01.bed (BAM input).. ok 265: Count -L /<>/test/dat/view.001.01.bed (BAM input).. ok 266: Region -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 267: Count -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 268: Region -L /<>/test/dat/view.001.02.bed (BAM input).. ok 269: Count -L /<>/test/dat/view.001.02.bed (BAM input).. ok 270: Region -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 271: Count -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 272: Region -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 273: Count -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 274: Region -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 275: Count -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 276: Region -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 277: Count -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 278: Region -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 279: Count -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 280: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 281: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 282: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 283: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 284: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 285: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 286: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 287: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 288: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 289: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 290: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 291: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 292: Region -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 293: Count -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 294: Region -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 295: Count -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 296: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 297: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 298: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 299: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 300: Region -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 301: Count -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 302: Region -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 303: Count -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 304: Region -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 305: Count -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 306: Region -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 307: Count -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 308: Region -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 309: Count -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 310: Region -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 311: Count -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 312: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 313: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 314: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 315: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 316: Make BAM with no M5/UR tags .. ok 317: Add @SQ with -t (SAM -> SAM) .. ok 318: Add @SQ with -T (SAM -> SAM) .. ok 319: Add @SQ with -t (BAM -> SAM) .. ok 320: Add @SQ with -T (BAM -> SAM) .. ok 321: Add @SQ with -t (SAM -> BAM) .. ok 322: Add @SQ with -T (SAM -> BAM) .. ok 323: Add @SQ with -t (BAM -> BAM) .. ok 324: Add @SQ with -T (BAM -> BAM) .. ok 325: Add @SQ with -t (SAM -> CRAM) .. ok 326: Add @SQ with -T (SAM -> CRAM) .. ok 327: Add @SQ with -t (BAM -> CRAM) .. ok 328: Add @SQ with -T (BAM -> CRAM) .. ok 329: Make CRAM with no UR field .. ok 330: Decoding CRAM with no UR field via -T .. ok 331: CIGAR B-operator removal .. ok 332: Big SAM -> BAM .. ok 333: Big SAM -> BAM (2 threads) .. ok 334: Big SAM -> BAM (4 threads) .. ok 335: Big SAM -> CRAM .. ok 336: Big SAM -> CRAM (2 threads) .. ok 337: Big SAM -> CRAM (4 threads) .. ok 338: Subsample 0.2 (SAM input) ............ ok 339: Subsample 0.5 (SAM input) ............ ok 340: Subsample 0.8 (SAM input) ............ ok 341: Subsample 0.2 (BAM input) ............ ok 342: Subsample 0.5 (BAM input) ............ ok 343: Subsample 0.8 (BAM input) ............ ok 344: Subsample 0.2 (CRAM input) ............ ok 345: Subsample 0.5 (CRAM input) ............ ok 346: Subsample 0.8 (CRAM input) ............ ok 347: SAM add PG .. 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_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 fastq -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -s /tmp/mFb3u6qHYf/bam2fq.discard.s.fq -0 /tmp/mFb3u6qHYf/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: 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 fastq -@ 2 -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -s /tmp/mFb3u6qHYf/bam2fq.discard.s.fq -0 /tmp/mFb3u6qHYf/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_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_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/Ywk_WXb1dD - /<>/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 -s 1 -p -c -t PG -O SAM - /tmp/mFb3u6qHYf/merge.tag.1.bam /tmp/mFb3u6qHYf/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/mFb3u6qHYf/merge.tag.3.bam /tmp/mFb3u6qHYf/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/mFb3u6qHYf/merge.bed.1.bam /tmp/mFb3u6qHYf/merge.bed.2.bam .. 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/T9W1INFpAe - /<>/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 -s 1 -p -c -t PG -O SAM - /tmp/mFb3u6qHYf/merge.tag.1.bam /tmp/mFb3u6qHYf/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/mFb3u6qHYf/merge.tag.3.bam /tmp/mFb3u6qHYf/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/mFb3u6qHYf/merge.bed.1.bam /tmp/mFb3u6qHYf/merge.bed.2.bam .. ok test_sort: /<>/samtools sort /<>/test/dat/test_input_1_a.bam /tmp/mFb3u6qHYf/sortout .. ok test_sort: /<>/samtools sort -f /<>/test/dat/test_input_1_a.bam /tmp/mFb3u6qHYf/sortout.bam .. ok test_sort: /<>/samtools sort -o /<>/test/dat/test_input_1_a.bam /tmp/mFb3u6qHYf/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 -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 -@ 2 /<>/test/dat/test_input_1_a.bam /tmp/mFb3u6qHYf/sortout .. ok test_sort: /<>/samtools sort -@ 2 -f /<>/test/dat/test_input_1_a.bam /tmp/mFb3u6qHYf/sortout.bam .. ok test_sort: /<>/samtools sort -@ 2 -o /<>/test/dat/test_input_1_a.bam /tmp/mFb3u6qHYf/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 -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_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 -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 -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/8_isize_overflow_64bit.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 -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 -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/8_isize_overflow_64bit.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 -@ 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_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: [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: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [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: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [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 -@ 2 -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: [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: [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: [markdup] error: no MC tag. Please run samtools fixmate on file first. [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: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [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_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_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 -@ 2 --output-fmt sam -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/mFb3u6qHYf/longref.sam.gz .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/mFb3u6qHYf/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /<>/samtools view -h --no-PG -L /<>/test/large_pos/test.bed /tmp/mFb3u6qHYf/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/mFb3u6qHYf/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 -@ 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_ampliconstats: /<>/samtools ampliconstats -@ 2 -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 | egrep -v 'Samtools version|Command line' | tee /tmp/out.txt .. ok Number of tests: total .. 700 passed .. 654 failed .. 0 expected failure .. 46 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 === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 163 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: 47 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS make[2]: Leaving directory '/<>' rm -fr -- /tmp/dh-xdg-rundir-duEmFYcV make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a 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 -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/interpolate_sam.pl misc/novo2sam.pl 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 misc/plot-ampliconstats /<>/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 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* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a 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 -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -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// cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ install -d debian/.debhelper/generated/samtools install -d debian/.debhelper/generated/samtools-test # 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 make[1]: Leaving directory '/<>' dh_installdocs -a install -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 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 install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/<>' dh_installexamples -a install -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 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/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-coverage.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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.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-reheader.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-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/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-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.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-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.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-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.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-idxstats.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-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.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-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-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 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 dh_lintian -a install -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl -a (grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > debian/samtools.substvars.new 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 1601563342 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/NEWS.Debian 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-coverage.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-idxstats.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-reheader.1 usr/share/man/man1/samtools-rmdup.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/NEWS.Debian 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-coverage.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-idxstats.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-reheader.1 usr/share/man/man1/samtools-rmdup.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 -a install -d debian/samtools/usr/lib/debug/.dwz/powerpc64le-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/powerpc64le-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/powerpc64le-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 702745 new size 724889 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/powerpc64le-linux-gnu/samtools.debug dh_strip -a -a install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/b5fc412028de77a563437928e63b5904ea858b.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/b5fc412028de77a563437928e63b5904ea858b.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/da/b5fc412028de77a563437928e63b5904ea858b.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5c/ce8ce6e676ea4493caf184d6012361fb897cc0.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5c/ce8ce6e676ea4493caf184d6012361fb897cc0.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5c/ce8ce6e676ea4493caf184d6012361fb897cc0.debug debian/samtools/usr/bin/samtools install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7f objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7f/cc9d1b04af737fe823779a0cab203945f83fff.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7f/cc9d1b04af737fe823779a0cab203945f83fff.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7f/cc9d1b04af737fe823779a0cab203945f83fff.debug debian/samtools/usr/bin/md5fa install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/20 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/20/7b4f054a61653374e406446a1e18170711de71.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/20/7b4f054a61653374e406446a1e18170711de71.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/20/7b4f054a61653374e406446a1e18170711de71.debug debian/samtools/usr/bin/ace2sam install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29/d7401428939671218abf761eadd8f0f2695ff9.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29/d7401428939671218abf761eadd8f0f2695ff9.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29/d7401428939671218abf761eadd8f0f2695ff9.debug debian/samtools/usr/bin/maq2sam-long install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3b objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3b/86a69bbd0ae9f49c06d3688fc73efe0be85e1e.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3b/86a69bbd0ae9f49c06d3688fc73efe0be85e1e.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3b/86a69bbd0ae9f49c06d3688fc73efe0be85e1e.debug debian/samtools/usr/bin/wgsim install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63/608ef781f5cf327628fc0a90576c64535ca7ee.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63/608ef781f5cf327628fc0a90576c64535ca7ee.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63/608ef781f5cf327628fc0a90576c64535ca7ee.debug debian/samtools/usr/bin/maq2sam-short install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/powerpc64le-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 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym dh_makeshlibs -a -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a -a install -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -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 -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=207b4f054a61653374e406446a1e18170711de71 29d7401428939671218abf761eadd8f0f2695ff9 3b86a69bbd0ae9f49c06d3688fc73efe0be85e1e 5cce8ce6e676ea4493caf184d6012361fb897cc0 63608ef781f5cf327628fc0a90576c64535ca7ee 7fcc9d1b04af737fe823779a0cab203945f83fff dab5fc412028de77a563437928e63b5904ea858b" -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 cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums 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 .. install -d debian/.debhelper/scratch-space/build-samtools dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root debian/.debhelper/scratch-space/build-samtools INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 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/.debhelper/samtools/dbgsym-root/DEBIAN/control, package samtools-dbgsym, directory debian/.debhelper/samtools/dbgsym-root dpkg-deb: building package 'samtools-dbgsym' in 'debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.11-1_ppc64el.deb'. pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools .. removing usr/share/doc/samtools/changelog.gz pkgstripfiles: Truncating usr/share/doc/samtools/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'samtools' in '../samtools_1.11-1_ppc64el.deb'. Renaming samtools-dbgsym_1.11-1_ppc64el.deb to samtools-dbgsym_1.11-1_ppc64el.ddeb mv debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.11-1_ppc64el.deb ../samtools-dbgsym_1.11-1_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../samtools_1.11-1_ppc64el.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-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-10-29T14:59:30Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools_1.11-1_ppc64el.changes: -------------------------------- Format: 1.8 Date: Thu, 01 Oct 2020 16:42:22 +0200 Source: samtools Binary: samtools Architecture: ppc64el Version: 1.11-1 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats Changes: samtools (1.11-1) unstable; urgency=medium . * New upstream version * Versioned Build-Depends: libhts-dev (>= 1.11) Checksums-Sha1: b5202b4a386ba54adbcfa650564c27b4b0ba586f 948332 samtools-dbgsym_1.11-1_ppc64el.ddeb 8845ca41260565ee9e38292ffa6273b4b33e10bb 7005 samtools_1.11-1_ppc64el.buildinfo e72b09def45029813147f072535f31d891190431 589628 samtools_1.11-1_ppc64el.deb Checksums-Sha256: 229aa692158656a5d7aa44fb442affea9e23da58298342d994cefef6c0f0a8a8 948332 samtools-dbgsym_1.11-1_ppc64el.ddeb a18bdf68c061481b777f3db1e34264ddd591c1977959a03e2ea0f1c05de1c3a6 7005 samtools_1.11-1_ppc64el.buildinfo f64d6f4c9cf748ee7a55aebfd9eb093c2b9613ade4ba9c3d98ed0e4036d49bce 589628 samtools_1.11-1_ppc64el.deb Files: 0b276fe4b33907576562c38b84a0d79a 948332 debug optional samtools-dbgsym_1.11-1_ppc64el.ddeb b41998a2e3db0dc29ec2a526443786fe 7005 science optional samtools_1.11-1_ppc64el.buildinfo 6a44fc05f76b0e48799625e2ff2cd8a4 589628 science optional samtools_1.11-1_ppc64el.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: samtools Binary: samtools samtools-dbgsym Architecture: ppc64el Version: 1.11-1 Checksums-Md5: 0b276fe4b33907576562c38b84a0d79a 948332 samtools-dbgsym_1.11-1_ppc64el.ddeb 6a44fc05f76b0e48799625e2ff2cd8a4 589628 samtools_1.11-1_ppc64el.deb Checksums-Sha1: b5202b4a386ba54adbcfa650564c27b4b0ba586f 948332 samtools-dbgsym_1.11-1_ppc64el.ddeb e72b09def45029813147f072535f31d891190431 589628 samtools_1.11-1_ppc64el.deb Checksums-Sha256: 229aa692158656a5d7aa44fb442affea9e23da58298342d994cefef6c0f0a8a8 948332 samtools-dbgsym_1.11-1_ppc64el.ddeb f64d6f4c9cf748ee7a55aebfd9eb093c2b9613ade4ba9c3d98ed0e4036d49bce 589628 samtools_1.11-1_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Thu, 29 Oct 2020 14:59:30 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-11.1), autoconf-archive (= 20190106-2.1ubuntu1), automake (= 1:1.16.2-4ubuntu1), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.0-6ubuntu2), bash-completion (= 1:2.11-2ubuntu1), binutils (= 2.35.1-2ubuntu1), binutils-common (= 2.35.1-2ubuntu1), binutils-powerpc64le-linux-gnu (= 2.35.1-2ubuntu1), bsdextrautils (= 2.36-3ubuntu1), bsdutils (= 1:2.36-3ubuntu1), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), coreutils (= 8.32-3ubuntu1), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.0-15ubuntu1), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2.1ubuntu1), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.5ubuntu2), dpkg-dev (= 1.20.5ubuntu2), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1ubuntu2), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.0-15ubuntu1), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.0-15ubuntu1), gcc-10-base (= 10.2.0-15ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), hostname (= 3.23), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libasan6 (= 10.2.0-15ubuntu1), libasn1-8-heimdal (= 7.7.0+dfsg-2), libatomic1 (= 10.2.0-15ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3ubuntu2), libaudit1 (= 1:2.8.5-3ubuntu2), libbinutils (= 2.35.1-2ubuntu1), libblkid1 (= 2.36-3ubuntu1), libbrotli1 (= 1.0.9-2build1), libbz2-1.0 (= 1.0.8-4ubuntu2), libbz2-dev (= 1.0.8-4ubuntu2), libc-bin (= 2.32-0ubuntu3), libc-dev-bin (= 2.32-0ubuntu3), libc6 (= 2.32-0ubuntu3), libc6-dev (= 2.32-0ubuntu3), libcap-ng0 (= 0.7.9-2.2), libcc1-0 (= 10.2.0-15ubuntu1), libcom-err2 (= 1.45.6-1ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.17-1ubuntu1), libcrypt1 (= 1:4.4.17-1ubuntu1), libctf-nobfd0 (= 2.35.1-2ubuntu1), libctf0 (= 2.35.1-2ubuntu1), libcurl3-gnutls (= 7.68.0-1ubuntu4), libcurl4-gnutls-dev (= 7.68.0-1ubuntu4), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu3), libdebconfclient0 (= 0.254ubuntu1), libdebhelper-perl (= 13.2.1ubuntu1), libdeflate-dev (= 1.6-1), libdeflate0 (= 1.6-1), libdpkg-perl (= 1.20.5ubuntu2), libelf1 (= 0.181-1), libffi8ubuntu1 (= 3.4~20200819gead65ca871-0ubuntu3), libfile-stripnondeterminism-perl (= 1.9.0-1), libgcc-10-dev (= 10.2.0-15ubuntu1), libgcc-s1 (= 10.2.0-15ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu2), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libglib2.0-0 (= 2.66.1-2), libgmp10 (= 2:6.2.0+dfsg-6ubuntu1), libgnutls30 (= 3.6.15-4ubuntu2), libgomp1 (= 10.2.0-15ubuntu1), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10), libgssapi3-heimdal (= 7.7.0+dfsg-2), libhcrypto4-heimdal (= 7.7.0+dfsg-2), libheimbase1-heimdal (= 7.7.0+dfsg-2), libheimntlm0-heimdal (= 7.7.0+dfsg-2), libhogweed6 (= 3.6-2), libhts-dev (= 1.11-2), libhts3 (= 1.11-2), libhx509-5-heimdal (= 7.7.0+dfsg-2), libicu67 (= 67.1-4), libidn2-0 (= 2.3.0-1), libio-pty-perl (= 1:1.12-1), libisl22 (= 0.22.1-1), libitm1 (= 10.2.0-15ubuntu1), libk5crypto3 (= 1.17-10), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-2), libkrb5-3 (= 1.17-10), libkrb5support0 (= 1.17-10), libldap-2.4-2 (= 2.4.53+dfsg-1ubuntu1), liblsan0 (= 10.2.0-15ubuntu1), liblz4-1 (= 1.9.2-2), liblzma-dev (= 5.2.4-1ubuntu1), liblzma5 (= 5.2.4-1ubuntu1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.36-3ubuntu1), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libncurses-dev (= 6.2+20200918-1), libncurses5-dev (= 6.2+20200918-1), libncurses6 (= 6.2+20200918-1), libncursesw6 (= 6.2+20200918-1), libnettle8 (= 3.6-2), libnghttp2-14 (= 1.41.0-3), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), libnss-nis (= 3.1-0ubuntu4), libnss-nisplus (= 1.3-0ubuntu4), libp11-kit0 (= 0.23.21-2build1), libpam-modules (= 1.3.1-5ubuntu6), libpam-modules-bin (= 1.3.1-5ubuntu6), libpam-runtime (= 1.3.1-5ubuntu6), libpam0g (= 1.3.1-5ubuntu6), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.30 (= 5.30.3-4), libpipeline1 (= 1.5.3-1), libpsl5 (= 0.21.0-1.1ubuntu1), libquadmath0 (= 10.2.0-15ubuntu1), libroken18-heimdal (= 7.7.0+dfsg-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build2), libsasl2-2 (= 2.1.27+dfsg-2ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg-2ubuntu1), libseccomp2 (= 2.4.3-1ubuntu5), libselinux1 (= 3.1-2build1), libsigsegv2 (= 2.12-2build1), libsmartcols1 (= 2.36-3ubuntu1), libsqlite3-0 (= 3.33.0-1), libssh-4 (= 0.9.4-1ubuntu3), libssl1.1 (= 1.1.1f-1ubuntu4), libstdc++-10-dev (= 10.2.0-15ubuntu1), libstdc++6 (= 10.2.0-15ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 246.6-1ubuntu1), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2+20200918-1), libtirpc-common (= 1.2.6-3), libtirpc-dev (= 1.2.6-3), libtirpc3 (= 1.2.6-3), libtool (= 2.4.6-14), libtsan0 (= 10.2.0-15ubuntu1), libubsan1 (= 10.2.0-15ubuntu1), libuchardet0 (= 0.0.7-1), libudev1 (= 246.6-1ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36-3ubuntu1), libwind0-heimdal (= 7.7.0+dfsg-2), libxml2 (= 2.9.10+dfsg-6.1), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.0-26.27), login (= 1:4.8.1-1ubuntu6), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2+20200918-1), ncurses-bin (= 6.2+20200918-1), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), pkg-config (= 0.29.2-1ubuntu1), po-debconf (= 1.0.21), rpcsvc-proto (= 1.4.2-0ubuntu4), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.13), sysvinit-utils (= 2.96-5ubuntu1), tabix (= 1.11-2), tar (= 1.30+dfsg-7), util-linux (= 2.36-3ubuntu1), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1601563342" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ samtools_1.11-1_ppc64el.deb --------------------------- new Debian package, version 2.0. size 589628 bytes: control archive=2800 bytes. 970 bytes, 19 lines control 5020 bytes, 74 lines md5sums Package: samtools Version: 1.11-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1797 Depends: libc6 (>= 2.29), libhts3 (>= 1.11), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.1.4) Suggests: cwltool Breaks: bio-tradis (<= 1.4.5+dfsg-1), iva (<= 1.0.9+ds-6) Section: science Priority: optional Homepage: http://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. 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: n/a Build-Time: 104 Distribution: hirsute-proposed Host Architecture: ppc64el Install-Time: 19 Job: samtools_1.11-1.dsc Machine Architecture: ppc64el Package: samtools Package-Time: 125 Source-Version: 1.11-1 Space: n/a Status: successful Version: 1.11-1 -------------------------------------------------------------------------------- Finished at 2020-10-29T14:59:30Z Build needed 00:02:05, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20209978 Scanning for processes to kill in build PACKAGEBUILD-20209978