Thu Apr 25 14:03:01 UTC 2024 I: starting to build samtools/trixie/armhf on jenkins on '2024-04-25 14:02' Thu Apr 25 14:03:01 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_6/3879/console.log Thu Apr 25 14:03:02 UTC 2024 I: Downloading source for trixie/samtools=1.19.2-1 --2024-04-25 14:03:02-- http://deb.debian.org/debian/pool/main/s/samtools/samtools_1.19.2-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2295 (2.2K) [text/prs.lines.tag] Saving to: ‘samtools_1.19.2-1.dsc’ 0K .. 100% 263M=0s 2024-04-25 14:03:02 (263 MB/s) - ‘samtools_1.19.2-1.dsc’ saved [2295/2295] Thu Apr 25 14:03:02 UTC 2024 I: samtools_1.19.2-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.19.2-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://www.htslib.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/samtools Vcs-Git: https://salsa.debian.org/med-team/samtools.git Testsuite: autopkgtest Testsuite-Triggers: tabix Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl , libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev Package-List: samtools deb science optional arch=any samtools-test deb science optional arch=all Checksums-Sha1: 8dff98a03e9295730b24e26cb1447b41887af669 5666279 samtools_1.19.2.orig.tar.gz ac8048d48e8883df9b4700dd4a26bccd6542cfc8 21752 samtools_1.19.2-1.debian.tar.xz Checksums-Sha256: 93b4ee042003d536a2f822a17dd5e65439f724214d5d2b5becc8a9f190ef2efd 5666279 samtools_1.19.2.orig.tar.gz ab11a07d6e8e80fadb62672ec5974867a0328f31d5b6faa7c2d8e5b7de9936a1 21752 samtools_1.19.2-1.debian.tar.xz Files: dc7d1649a27689287499876dc05785c4 5666279 samtools_1.19.2.orig.tar.gz 3eea35b7ce97c48454c4f5b378ab722a 21752 samtools_1.19.2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmXQ7ZEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqg/A//dxkPboHt/1/2CjEvRG51q7sEcs/F hBDxKGyMoAIcfHT74AYrr64GfWace3+uhytp/gq1VAhzJPXe+DZTbDry90JJ54oG ci5GjfN/JErckvf0sjp1OfdyWWfcpgQEmyTnOGj+mgZpkk4LLM5wcoGPwjQdRYlo auT+QDx1hMFqqogwEcLk49L04sFh6ECbgeEQxmUrfCiwqmodEQzppQURJ6U47LrV ht/DcOEHpwHqkVc+a4RYbzvMkGquRY+LP5W+J/iNjOo8Z212RaLK031MxqKhmQL2 6jFR4/cKB7wOqU8IA5tTHrjLqrgWCSrZRFuipMtsLZNg2qKEqS9hc+BsCNP4owkY qKZAdtko2LF8v68BqN/fgj3CGQCamH8d+tEjN9uyqYsyIdwPlvaHKgBCr3W44khX ZiWt3kRKxz0zg8f13e2aEv2G2DkHHemkUmNjbyY2JME8FKX+eu6vpPJxSVnrgTTO Y8g7vEHefMZKwIJeR6TGp9SLRYxxcN5oyhaflIRn5ASYsL5I4HJY3k5Dha4xUTX8 qfzR/04OEbWHPLa+VQy06sqiP8z34nkWIbhtNpjeg+gA9P7pIrNWNME1Hj84/r6O WlkFwUsiGfYog+9YKyXcvQNPpbu4DkvW3Ox+5tzhDTQau7YBBHa94rIYL+tsMWqu F3rea22F/v/AQOY= =ODlH -----END PGP SIGNATURE----- Thu Apr 25 14:03:02 UTC 2024 I: Checking whether the package is not for us Thu Apr 25 14:03:02 UTC 2024 I: Starting 1st build on remote node virt64b-armhf-rb.debian.net. Thu Apr 25 14:03:02 UTC 2024 I: Preparing to do remote build '1' on virt64b-armhf-rb.debian.net. Thu Apr 25 14:13:56 UTC 2024 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 25 02:03:12 -12 2024 I: pbuilder-time-stamp: 1714053792 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [samtools_1.19.2-1.dsc] I: copying [./samtools_1.19.2.orig.tar.gz] I: copying [./samtools_1.19.2-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Feb 17 17:32:01 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./samtools_1.19.2-1.dsc: no acceptable signature found dpkg-source: info: extracting samtools in samtools-1.19.2 dpkg-source: info: unpacking samtools_1.19.2.orig.tar.gz dpkg-source: info: unpacking samtools_1.19.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/32695/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='033eeb130bdc4d44ba353c8fc2ca393b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='32695' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/pbuilderrc_ykEy --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/b1 --logfile b1/build.log samtools_1.19.2-1.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64b 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 23 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/32695/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19638 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.17~); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on automake; however: Package automake is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB of archives. After unpacking 91.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf bash-completion all 1:2.11-8 [224 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 25 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-5.1 [28.3 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libcurl3-gnutls armhf 8.5.0-2 [378 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.5.0-2 [490 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libhts3 armhf 1.19+ds-1 [394 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1 [1598 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libio-pty-perl armhf 1:1.20-1 [33.7 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.4+20240414-1 [81.8 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libncurses-dev armhf 6.4+20240414-1 [309 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-1+b2 [31.9 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf tabix armhf 1.19+ds-1 [409 kB] Fetched 25.4 MB in 1s (37.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19638 files and directories currently installed.) Preparing to unpack .../00-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package bash-completion. Preparing to unpack .../02-bash-completion_1%3a2.11-8_all.deb ... Unpacking bash-completion (1:2.11-8) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../04-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../24-libelf1_0.190-1+b1_armhf.deb ... Unpacking libelf1:armhf (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../26-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../32-libbrotli1_1.1.0-2+b3_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b3) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../33-libbz2-dev_1.0.8-5.1_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-5.1) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../34-libsasl2-modules-db_2.1.28+dfsg1-4+b1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../35-libsasl2-2_2.1.28+dfsg1-4+b1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../36-libldap-2.5-0_2.5.13+dfsg-5+b3_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../37-libnghttp2-14_1.59.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.59.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../38-libpsl5_0.21.2-1+b1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../39-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../40-libssh2-1_1.11.0-4_armhf.deb ... Unpacking libssh2-1:armhf (1.11.0-4) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../41-libcurl3-gnutls_8.5.0-2_armhf.deb ... Unpacking libcurl3-gnutls:armhf (8.5.0-2) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../42-libcurl4-gnutls-dev_8.5.0-2_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (8.5.0-2) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../43-libdeflate0_1.20-1_armhf.deb ... Unpacking libdeflate0:armhf (1.20-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../44-libdeflate-dev_1.20-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.20-1) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../45-libhtscodecs2_1.6.0-1+b1_armhf.deb ... Unpacking libhtscodecs2:armhf (1.6.0-1+b1) ... Selecting previously unselected package libhts3:armhf. Preparing to unpack .../46-libhts3_1.19+ds-1_armhf.deb ... Unpacking libhts3:armhf (1.19+ds-1) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../47-liblzma-dev_5.6.1+really5.4.5-1_armhf.deb ... Unpacking liblzma-dev:armhf (5.6.1+really5.4.5-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../48-zlib1g-dev_1%3a1.3.dfsg-3+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../49-libhts-dev_1.19+ds-1_armhf.deb ... Unpacking libhts-dev:armhf (1.19+ds-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../50-libio-pty-perl_1%3a1.20-1_armhf.deb ... Unpacking libio-pty-perl (1:1.20-1) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../51-libncurses6_6.4+20240414-1_armhf.deb ... Unpacking libncurses6:armhf (6.4+20240414-1) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../52-libncurses-dev_6.4+20240414-1_armhf.deb ... Unpacking libncurses-dev:armhf (6.4+20240414-1) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../53-libpkgconf3_1.8.1-1+b2_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-1+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../54-pkgconf-bin_1.8.1-1+b2_armhf.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../55-pkgconf_1.8.1-1+b2_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-1+b2) ... Selecting previously unselected package tabix. Preparing to unpack .../56-tabix_1.19+ds-1_armhf.deb ... Unpacking tabix (1.19+ds-1) ... Setting up libhtscodecs2:armhf (1.6.0-1+b1) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libpsl5:armhf (0.21.2-1+b1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libio-pty-perl (1:1.20-1) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libnghttp2-14:armhf (1.59.0-1) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up autoconf-archive (20220903-3) ... Setting up file (1:5.45-2+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-1+b2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up bash-completion (1:2.11-8) ... Setting up libncurses6:armhf (6.4+20240414-1) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:armhf (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1:armhf (1.11.0-4) ... Setting up libdeflate-dev:armhf (1.20-1) ... Setting up tabix (1.19+ds-1) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up libbz2-dev:armhf (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libncurses-dev:armhf (6.4+20240414-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Setting up pkgconf:armhf (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:armhf (8.5.0-2) ... Setting up libcurl4-gnutls-dev:armhf (8.5.0-2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:armhf (1.19+ds-1) ... Setting up libhts-dev:armhf (1.19+ds-1) ... Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-18) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/samtools-1.19.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../samtools_1.19.2-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.19.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' rm -f config.mk touch config.mk dh_auto_clean -- make -j3 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* cd test/reference && rm -f mpileup.*.fai rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS rm -rf autom4te.cache make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.19.2"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/reproducible-path/samtools-1.19.2@«BUILDPATH»@g' version.h cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -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,-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,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-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,-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,-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,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -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 make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j3 test "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} test_reference: /build/reproducible-path/samtools-1.19.2/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.19.2/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.19.2/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.19.2/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.19.2/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.19.2/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.19.2/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.19.2/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/XT5zqzfyuV/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/XT5zqzfyuV/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/XT5zqzfyuV/bgzip.dat.gz .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/XT5zqzfyuV/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq.gz 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq.gz 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq 1:99998-100007 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/XT5zqzfyuV/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/reproducible-path/samtools-1.19.2/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/reproducible-path/samtools-1.19.2/test/dat/dict.fa .. ok test_dict: /build/reproducible-path/samtools-1.19.2/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/XT5zqzfyuV/dict.fa.gz .. ok test_dict: cat /build/reproducible-path/samtools-1.19.2/test/dat/dict.fa | /build/reproducible-path/samtools-1.19.2/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/reproducible-path/samtools-1.19.2/samtools dict -AH < /build/reproducible-path/samtools-1.19.2/test/dat/dict.alias.fa .. ok test_dict: /build/reproducible-path/samtools-1.19.2/samtools dict -H -l /build/reproducible-path/samtools-1.19.2/test/dat/dict.alt < /build/reproducible-path/samtools-1.19.2/test/dat/dict.alias.fa .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view /tmp/XT5zqzfyuV/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view /tmp/XT5zqzfyuV/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/XT5zqzfyuV/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/XT5zqzfyuV/auto_indexed.csi && cat /tmp/XT5zqzfyuV/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/XT5zqzfyuV/auto_indexed.crai && cat /tmp/XT5zqzfyuV/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/XT5zqzfyuV/auto_indexed.csi && cat /tmp/XT5zqzfyuV/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/XT5zqzfyuV/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/XT5zqzfyuV/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/XT5zqzfyuV/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/XT5zqzfyuV/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/XT5zqzfyuV/auto_indexed.csi && cat /tmp/XT5zqzfyuV/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/XT5zqzfyuV/auto_indexed.crai && cat /tmp/XT5zqzfyuV/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/XT5zqzfyuV/auto_indexed.csi && cat /tmp/XT5zqzfyuV/auto_indexed.csi .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/XT5zqzfyuV/mpileup.bam.list -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/XT5zqzfyuV/mpileup.cram.list -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/XT5zqzfyuV/mpileup.bam.urllist -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/XT5zqzfyuV/mpileup.cram.urllist -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:1050-1060 /tmp/XT5zqzfyuV/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/XT5zqzfyuV/mpileup.ref.fa.gz -r17:1050-1060 /tmp/XT5zqzfyuV/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup /build/reproducible-path/samtools-1.19.2/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate .. ok test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools consensus .. ok test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools import .. ok test_usage_subcommand: samtools reference .. ok test_usage_subcommand: samtools reset .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth .. ok test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags .. ok test_usage_subcommand: samtools head .. ok test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools samples Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/XT5zqzfyuV/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/XT5zqzfyuV/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/XT5zqzfyuV/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/XT5zqzfyuV/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/XT5zqzfyuV/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/XT5zqzfyuV/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/XT5zqzfyuV/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/XT5zqzfyuV/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/XT5zqzfyuV/view.001.forn (SAM input) .. ok 68: Count -N /tmp/XT5zqzfyuV/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/XT5zqzfyuV/view.001.forn (BAM input) .. ok 70: Count -N /tmp/XT5zqzfyuV/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/XT5zqzfyuV/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/XT5zqzfyuV/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/XT5zqzfyuV/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/XT5zqzfyuV/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/XT5zqzfyuV/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/XT5zqzfyuV/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/XT5zqzfyuV/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/XT5zqzfyuV/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/XT5zqzfyuV/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test115.sam -h -d TGCA /tmp/XT5zqzfyuV/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/XT5zqzfyuV/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test117.sam -h -d TGCA /tmp/XT5zqzfyuV/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/XT5zqzfyuV/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test119.sam -h -d TGCA /tmp/XT5zqzfyuV/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/XT5zqzfyuV/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test121.sam -h -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test123.sam -h -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test125.sam -h -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/XT5zqzfyuV/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/XT5zqzfyuV/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/XT5zqzfyuV/view.001.fobc /tmp/XT5zqzfyuV/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/XT5zqzfyuV/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/XT5zqzfyuV/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa,ha (SAM input) .. ok 188: Count -x fa,ha (SAM input) .. ok 189: Filter -x fa,ha (BAM input) .. ok 190: Count -x fa,ha (BAM input) .. ok 191: Filter -x fa,ha (CRAM input) .. ok 192: Count -x fa,ha (CRAM input) .. ok 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 205: Filter -x fa -r grp2 (SAM input) .. ok 206: Count -x fa -r grp2 (SAM input) .. ok 207: Filter -x fa -r grp2 (BAM input) .. ok 208: Count -x fa -r grp2 (BAM input) .. ok 209: Filter -x fa -r grp2 (CRAM input) .. ok 210: Count -x fa -r grp2 (CRAM input) .. ok 211: Filter -x RG -r grp2 (SAM input) .. ok 212: Count -x RG -r grp2 (SAM input) .. ok 213: Filter -x RG -r grp2 (BAM input) .. ok 214: Count -x RG -r grp2 (BAM input) .. ok 215: Filter -x RG -r grp2 (CRAM input) .. ok 216: Count -x RG -r grp2 (CRAM input) .. ok 217: Filter -m 10 (SAM input) .. ok 218: Count -m 10 (SAM input) .. ok 219: Filter -m 10 (BAM input) .. ok 220: Count -m 10 (BAM input) .. ok 221: Filter -m 10 (CRAM input) .. ok 222: Count -m 10 (CRAM input) .. ok 223: Filter -m 11 (SAM input) .. ok 224: Count -m 11 (SAM input) .. ok 225: Filter -m 11 (BAM input) .. ok 226: Count -m 11 (BAM input) .. ok 227: Filter -m 11 (CRAM input) .. ok 228: Count -m 11 (CRAM input) .. ok 229: Filter -m 15 (SAM input) .. ok 230: Count -m 15 (SAM input) .. ok 231: Filter -m 15 (BAM input) .. ok 232: Count -m 15 (BAM input) .. ok 233: Filter -m 15 (CRAM input) .. ok 234: Count -m 15 (CRAM input) .. ok 235: Filter -m 16 (SAM input) .. ok 236: Count -m 16 (SAM input) .. ok 237: Filter -m 16 (BAM input) .. ok 238: Count -m 16 (BAM input) .. ok 239: Filter -m 16 (CRAM input) .. ok 240: Count -m 16 (CRAM input) .. ok 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247: Filter -e [BC] (SAM input) .. ok 248: Count -e [BC] (SAM input) .. ok 249: Filter -e [BC] (BAM input) .. ok 250: Count -e [BC] (BAM input) .. ok 251: Filter -e [BC] (CRAM input) .. ok 252: Count -e [BC] (CRAM input) .. ok 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 259: Filter -e mapq >= 50 (SAM input) .. ok 260: Count -e mapq >= 50 (SAM input) .. ok 261: Filter -e mapq >= 50 (BAM input) .. ok 262: Count -e mapq >= 50 (BAM input) .. ok 263: Filter -e mapq >= 50 (CRAM input) .. ok 264: Count -e mapq >= 50 (CRAM input) .. ok 265: Filter -e mapq >= 99 (SAM input) .. ok 266: Count -e mapq >= 99 (SAM input) .. ok 267: Filter -e mapq >= 99 (BAM input) .. ok 268: Count -e mapq >= 99 (BAM input) .. ok 269: Filter -e mapq >= 99 (CRAM input) .. ok 270: Count -e mapq >= 99 (CRAM input) .. ok 271: Filter -e mapq >= 100 (SAM input) .. ok 272: Count -e mapq >= 100 (SAM input) .. ok 273: Filter -e mapq >= 100 (BAM input) .. ok 274: Count -e mapq >= 100 (BAM input) .. ok 275: Filter -e mapq >= 100 (CRAM input) .. ok 276: Count -e mapq >= 100 (CRAM input) .. ok 277: 1bp reads file SAM -> BAM -> SAM .. ok 278: 1bp reads file SAM -> CRAM -> SAM .. ok 278: Region Z (BAM input) .. ok 279: Count Z (BAM input) .. ok 280: Region Z (CRAM input) .. ok 281: Count Z (CRAM input) .. ok 282: Region Z:30 (BAM input) .. ok 283: Count Z:30 (BAM input) .. ok 284: Region Z:30 (CRAM input) .. ok 285: Count Z:30 (CRAM input) .. ok 286: Region Z:20-40 (BAM input) .. ok 287: Count Z:20-40 (BAM input) .. ok 288: Region Z:20-40 (CRAM input) .. ok 289: Count Z:20-40 (CRAM input) .. ok 290: Region ref1 (BAM input) .. ok 291: Count ref1 (BAM input) .. ok 292: Region ref1 (CRAM input) .. ok 293: Count ref1 (CRAM input) .. ok 294: Region ref1:15 (BAM input) .. ok 295: Count ref1:15 (BAM input) .. ok 296: Region ref1:15 (CRAM input) .. ok 297: Count ref1:15 (CRAM input) .. ok 298: Region ref1:15-45 (BAM input) .. ok 299: Count ref1:15-45 (BAM input) .. ok 300: Region ref1:15-45 (CRAM input) .. ok 301: Count ref1:15-45 (CRAM input) .. ok 302: Region ref1:15-45 ref2 (BAM input) .. ok 303: Count ref1:15-45 ref2 (BAM input) .. ok 304: Region ref1:15-45 ref2 (CRAM input) .. ok 305: Count ref1:15-45 ref2 (CRAM input) .. ok 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 318: Region -f 128 ref1 (BAM input) .. ok 319: Count -f 128 ref1 (BAM input) .. ok 320: Region -f 128 ref1 (CRAM input) .. ok 321: Count -f 128 ref1 (CRAM input) .. ok 322: Region -q 50 ref1:15-45 (BAM input) .. ok 323: Count -q 50 ref1:15-45 (BAM input) .. ok 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 330: Region * (BAM input) .. ok 331: Count * (BAM input) .. ok 332: Region * (CRAM input) .. ok 333: Count * (CRAM input) .. ok 334: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /build/reproducible-path/samtools-1.19.2/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 406: Make BAM with no M5/UR tags .. ok 407: Add @SQ with -t (SAM -> SAM) .. ok 408: Add @SQ with -T (SAM -> SAM) .. ok 409: Add @SQ with -t (BAM -> SAM) .. ok 410: Add @SQ with -T (BAM -> SAM) .. ok 411: Add @SQ with -t (SAM -> BAM) .. ok 412: Add @SQ with -T (SAM -> BAM) .. ok 413: Add @SQ with -t (BAM -> BAM) .. ok 414: Add @SQ with -T (BAM -> BAM) .. ok 415: Add @SQ with -t (SAM -> CRAM) .. ok 416: Add @SQ with -T (SAM -> CRAM) .. ok 417: Add @SQ with -t (BAM -> CRAM) .. ok 418: Add @SQ with -T (BAM -> CRAM) .. ok 419: Make CRAM with no UR field .. ok 420: Decoding CRAM with no UR field via -T .. ok 421: CIGAR B-operator removal .. ok 422: Big SAM -> BAM .. ok 423: Big SAM -> BAM (2 threads) .. ok 424: Big SAM -> BAM (4 threads) .. ok 425: Big SAM -> CRAM .. ok 426: Big SAM -> CRAM (2 threads) .. ok 427: Big SAM -> CRAM (4 threads) .. ok 428: Subsample 0.2 (SAM input) ............ ok 429: Subsample 0.5 (SAM input) ............ ok 430: Subsample 0.8 (SAM input) ............ ok 431: Subsample 0.2 (BAM input) ............ ok 432: Subsample 0.5 (BAM input) ............ ok 433: Subsample 0.8 (BAM input) ............ ok 434: Subsample 0.2 (CRAM input) ............ ok 435: Subsample 0.5 (CRAM input) ............ ok 436: Subsample 0.8 (CRAM input) ............ ok 437: SAM add PG .. ok 438: Unset dup flag, remove dt and do tags .. ok 439: Unmap dup flagged reads. .. ok 440: Unmap dup flagged reads. .. ok 441: fetch pairs .. ok 442: fetch pairs .. ok 443: fetch pairs .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -h 0 /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -h 1 /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -h 5 /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -h 29 /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -h 30 /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -n 0 /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -n 1 /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -n 5 /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.19.2/samtools head -h 5 -n 5 < /build/reproducible-path/samtools-1.19.2/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import -0 test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq -0 /build/reproducible-path/samtools-1.19.2/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import -s test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq -0 /build/reproducible-path/samtools-1.19.2/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import -s test/bam2fq/5.s.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq -s /build/reproducible-path/samtools-1.19.2/test/s.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq -N -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq -N -T RG,BC,QT -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/reproducible-path/samtools-1.19.2/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/import/2.interleaved.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/import/3.interleaved.fq -i .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/import/4.aux.fq -T "*" .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/import/4.aux.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /build/reproducible-path/samtools-1.19.2/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.19.2/test/bc.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.19.2/test/bc.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.19.2/test/bc.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.19.2/test/bc_split.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -t -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -t -T MD,ia -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.19.2/test/i.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.19.2/test/i.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -1 /build/reproducible-path/samtools-1.19.2/test/o.fq -2 /build/reproducible-path/samtools-1.19.2/test/o.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fasta -N -1 /build/reproducible-path/samtools-1.19.2/test/o.fa -2 /build/reproducible-path/samtools-1.19.2/test/o.fa /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -o /build/reproducible-path/samtools-1.19.2/test/o.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -s /tmp/XT5zqzfyuV/bam2fq.discard.s.fq -0 /tmp/XT5zqzfyuV/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.19.2/test/i1.fq --i2 /build/reproducible-path/samtools-1.19.2/test/i2.fq -0 /build/reproducible-path/samtools-1.19.2/test/0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -T '' /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -t -T '*' /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -N -T '*' -d ia /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.19.2/test/bc.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.19.2/test/bc.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.19.2/test/bc.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.19.2/test/bc_split.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -t -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -t -T MD,ia -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.19.2/test/i.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.19.2/test/i.fq -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.19.2/test/s.fq -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.19.2/test/1.fq -2 /build/reproducible-path/samtools-1.19.2/test/2.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -1 /build/reproducible-path/samtools-1.19.2/test/o.fq -2 /build/reproducible-path/samtools-1.19.2/test/o.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fasta -@ 2 -N -1 /build/reproducible-path/samtools-1.19.2/test/o.fa -2 /build/reproducible-path/samtools-1.19.2/test/o.fa /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -o /build/reproducible-path/samtools-1.19.2/test/o.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -s /tmp/XT5zqzfyuV/bam2fq.discard.s.fq -0 /tmp/XT5zqzfyuV/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.19.2/test/i1.fq --i2 /build/reproducible-path/samtools-1.19.2/test/i2.fq -0 /build/reproducible-path/samtools-1.19.2/test/0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -T '' /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -t -T '*' /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -T '*' -d ia /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa -i 0 /build/reproducible-path/samtools-1.19.2/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -S RG -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -S RG -r /build/reproducible-path/samtools-1.19.2/test/stat/test.fa /build/reproducible-path/samtools-1.19.2/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -t /build/reproducible-path/samtools-1.19.2/test/stat/11.stats.targets /build/reproducible-path/samtools-1.19.2/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -g 4 -t /build/reproducible-path/samtools-1.19.2/test/stat/11.stats.targets /build/reproducible-path/samtools-1.19.2/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -g 4 /build/reproducible-path/samtools-1.19.2/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.19.2/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.19.2/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.19.2/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.19.2/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/reproducible-path/samtools-1.19.2/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/reproducible-path/samtools-1.19.2/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats /build/reproducible-path/samtools-1.19.2/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/reproducible-path/samtools-1.19.2/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -I s1 /build/reproducible-path/samtools-1.19.2/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -I grp2 /build/reproducible-path/samtools-1.19.2/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -I grp3 /build/reproducible-path/samtools-1.19.2/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -I Sample /build/reproducible-path/samtools-1.19.2/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.19.2/samtools stats -r /build/reproducible-path/samtools-1.19.2/test/mpileup/ce.fa /build/reproducible-path/samtools-1.19.2/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam -b /tmp/EscCUgVokG - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -r -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -cp -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -o - -s 1 -O sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/XT5zqzfyuV/merge.tag.1.bam /tmp/XT5zqzfyuV/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/XT5zqzfyuV/merge.tag.3.bam /tmp/XT5zqzfyuV/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge --no-PG -O SAM - /build/reproducible-path/samtools-1.19.2/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/XT5zqzfyuV/merge.bed.1.bam /tmp/XT5zqzfyuV/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge --no-PG -r -O SAM - /build/reproducible-path/samtools-1.19.2/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam -b /tmp/g6yeMwTvYd - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -r -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -cp -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -o - -s 1 -O sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/XT5zqzfyuV/merge.tag.1.bam /tmp/XT5zqzfyuV/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/XT5zqzfyuV/merge.tag.3.bam /tmp/XT5zqzfyuV/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 --no-PG -O SAM - /build/reproducible-path/samtools-1.19.2/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/XT5zqzfyuV/merge.bed.1.bam /tmp/XT5zqzfyuV/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 --no-PG -r -O SAM - /build/reproducible-path/samtools-1.19.2/test/merge/test_no_pg_rg_co.sam .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sortout .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -n -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -N -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -t RG -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -n -t RG -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -t AS -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -t FI -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort --template-coordinate -m 10M /build/reproducible-path/samtools-1.19.2/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools reset /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.19.2/samtools sort -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools reset /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.19.2/samtools sort -M -K10 -I /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools reset /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.19.2/samtools sort -MH -K10 -I /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sortout .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/XT5zqzfyuV/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -N -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -t RG -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -n -t RG -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -t AS -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -t FI -m 10M /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 --template-coordinate -m 10M /build/reproducible-path/samtools-1.19.2/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools reset /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools reset /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -M -K10 -I /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.19.2/samtools reset /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -MH -K10 -I /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate --output-fmt=sam -O /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate -o /build/reproducible-path/samtools-1.19.2/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate -o /build/reproducible-path/samtools-1.19.2/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.19.2/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate --output-fmt=sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.19.2/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate --output-fmt=sam -f /build/reproducible-path/samtools-1.19.2/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.19.2/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.19.2/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.19.2/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate -@ 2 --output-fmt=sam -O /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.19.2/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.19.2/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.19.2/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate -@ 2 --output-fmt=sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.19.2/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate -@ 2 --output-fmt=sam -f /build/reproducible-path/samtools-1.19.2/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.19.2/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.19.2/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.19.2/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.19.2/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -cO sam /build/reproducible-path/samtools-1.19.2/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -cO sam /build/reproducible-path/samtools-1.19.2/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.19.2/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.19.2/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.19.2/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.19.2/test/fixmate/sanitize.sam - .. ok /build/reproducible-path/samtools-1.19.2/samtools calmd -uAr /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.ref.fa .. ok /build/reproducible-path/samtools-1.19.2/samtools calmd -@ 2 -uAr /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/reproducible-path/samtools-1.19.2/samtools idxstats /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/reproducible-path/samtools-1.19.2/samtools idxstats /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/reproducible-path/samtools-1.19.2/samtools idxstats /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck /build/reproducible-path/samtools-1.19.2/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck -v /build/reproducible-path/samtools-1.19.2/test/quickcheck/1.quickcheck.badeof.bam /build/reproducible-path/samtools-1.19.2/test/quickcheck/2.quickcheck.badheader.bam /build/reproducible-path/samtools-1.19.2/test/quickcheck/3.quickcheck.ok.bam /build/reproducible-path/samtools-1.19.2/test/quickcheck/4.quickcheck.ok.bam /build/reproducible-path/samtools-1.19.2/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/reproducible-path/samtools-1.19.2/test/quickcheck/6.quickcheck.cram21.ok.cram /build/reproducible-path/samtools-1.19.2/test/quickcheck/7.quickcheck.cram30.ok.cram /build/reproducible-path/samtools-1.19.2/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/reproducible-path/samtools-1.19.2/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/reproducible-path/samtools-1.19.2/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/reproducible-path/samtools-1.19.2/samtools quickcheck -uv /build/reproducible-path/samtools-1.19.2/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/reproducible-path/samtools-1.19.2/samtools reheader /build/reproducible-path/samtools-1.19.2/test/reheader/hdr.sam /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.19.2/samtools reheader /build/reproducible-path/samtools-1.19.2/test/reheader/hdr.sam /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.v21.cram | /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.19.2/samtools reheader /build/reproducible-path/samtools-1.19.2/test/reheader/hdr.sam /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.19.2/samtools reheader --in-place /build/reproducible-path/samtools-1.19.2/test/reheader/hdr.sam /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.v21.cram && /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.19.2/samtools reheader --in-place /build/reproducible-path/samtools-1.19.2/test/reheader/hdr.sam /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.v30.cram && /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.19.2/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.19.2/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.19.2/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -O sam -m overwrite_all /build/reproducible-path/samtools-1.19.2/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -O sam -m orphan_only /build/reproducible-path/samtools-1.19.2/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -O sam -R '1#9' /build/reproducible-path/samtools-1.19.2/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.19.2/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.19.2/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.19.2/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.19.2/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/reproducible-path/samtools-1.19.2/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/reproducible-path/samtools-1.19.2/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/reproducible-path/samtools-1.19.2/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.19.2/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.19.2/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.19.2/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.19.2/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.19.2/test/addrprg/1_fixup.sam .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -O sam -r --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.19.2/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.19.2/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.19.2/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -O sam -r --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.19.2/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.19.2/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.19.2/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.19.2/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.19.2/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /build/reproducible-path/samtools-1.19.2/samtools bedcov /build/reproducible-path/samtools-1.19.2/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.19.2/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.19.2/samtools bedcov -j /build/reproducible-path/samtools-1.19.2/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.19.2/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.19.2/samtools bedcov -g512 -G2048 /build/reproducible-path/samtools-1.19.2/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.19.2/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.19.2/samtools bedcov -c /build/reproducible-path/samtools-1.19.2/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.19.2/test/bedcov/bedcov.bam .. ok test_split: /build/reproducible-path/samtools-1.19.2/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.19.2/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.19.2/samtools split --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.19.2/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.19.2/samtools split --output-fmt sam -d an -u /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.19.2/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.19.2/samtools split --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.19.2/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.19.2/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.19.2/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.19.2/samtools split -@ 2 --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.19.2/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.19.2/samtools split -@ 2 --output-fmt sam -d an -u /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.19.2/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.19.2/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.19.2/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.19.2/test/split/split.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/XT5zqzfyuV/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/XT5zqzfyuV/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.19.2/test/large_pos/test.bed /tmp/XT5zqzfyuV/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools sort -O sam --no-PG -m 10M /build/reproducible-path/samtools-1.19.2/test/large_pos/longref_name.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools merge -O sam --no-PG - /build/reproducible-path/samtools-1.19.2/test/large_pos/longref.sam /build/reproducible-path/samtools-1.19.2/test/large_pos/longref2.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools depth /build/reproducible-path/samtools-1.19.2/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools depth -b /build/reproducible-path/samtools-1.19.2/test/large_pos/test.bed /build/reproducible-path/samtools-1.19.2/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/XT5zqzfyuV/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/reproducible-path/samtools-1.19.2/samtools fixmate -O sam --no-PG - - | /build/reproducible-path/samtools-1.19.2/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.19.2/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /build/reproducible-path/samtools-1.19.2/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_hard_clipped.expected.sam /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_soft_clipped.expected.sam /build/reproducible-path/samtools-1.19.2/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/reproducible-path/samtools-1.19.2/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.19.2/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.19.2/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.19.2/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.19.2/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.19.2/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.19.2/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.19.2/samtools reset | /build/reproducible-path/samtools-1.19.2/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset < /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.19.2/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.19.2/samtools view .. ok test_reset: cat /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.19.2/samtools reset -o /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset -o /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset -o /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.cram .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa_index /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG sam_to_fixed_bam /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa_index --no-PG /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.19.2/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam --no-RG -o /build/reproducible-path/samtools-1.19.2/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/reproducible-path/samtools-1.19.2/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/reproducible-path/samtools-1.19.2/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/reproducible-path/samtools-1.19.2/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/reproducible-path/samtools-1.19.2/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/reproducible-path/samtools-1.19.2/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.19.2/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/reproducible-path/samtools-1.19.2/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.19.2/samtools reset /build/reproducible-path/samtools-1.19.2/test/reset/seq.sam -o /build/reproducible-path/samtools-1.19.2/test/reset/output .. ok Number of tests: total .. 933 passed .. 889 failed .. 0 expected failure .. 44 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 118 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 53 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 65 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' rm -fr -- /tmp/dh-xdg-rundir-twqXnAxc make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/samtools.substvars debian/samtools-test.substvars rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/ debian/.debhelper/generated/samtools-test/ debian/samtools-test/ rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.19.2/debian/tmp make -j3 install DESTDIR=/build/reproducible-path/samtools-1.19.2/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' mkdir -p -m 755 /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' make clean make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* cd test/reference && rm -f mpileup.*.fai rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' dh_install install -m0755 -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -m0755 -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -m0755 -d debian/samtools/usr/share/commonwl/ cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl// install -m0755 -d debian/samtools/usr/share/man/man1 cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ install -m0755 -d debian/samtools-test/usr/share/doc/samtools cp --reflink=auto -a ./debian/tests/run-unit-test debian/samtools-test/usr/share/doc/samtools/ install -m0755 -d debian/samtools-test/usr/share/samtools cp --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/ # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done # Disable the executable bit on a dataset. if [ -d debian/samtools-test ] \ ; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \ ; fi make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' dh_installdocs install -m0755 -d debian/samtools/usr/share/doc/samtools install -m0755 -d debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./debian/README.test debian/samtools/usr/share/doc/samtools chmod -R u\+rw,go=rX debian/samtools/usr/share/doc install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test install -p -m0644 debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' dh_installchangelogs NEWS.md install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian install -p -m0644 NEWS.md debian/samtools-test/usr/share/doc/samtools-test/changelog install -m0755 -d debian/samtools/usr/share/doc/samtools install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' dh_installexamples install -m0755 -d debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules execute_before_dh_installman make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' # Fix whatis entries for subcommands; "samtools subcommand \- desc." # will confuse the lexer, but "samtools-subcommand \- desc." will work. sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \ debian/*/usr/share/man/man*/*.* # .EX expects a indentation width. sed -i 's/^.EX$/.EX 8/' debian/*/usr/share/man/man*/*.* make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' dh_installman 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-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 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 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 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 dh_lintian install -m0755 -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl mv debian/samtools.substvars.new debian/samtools.substvars mv debian/samtools-test.substvars.new debian/samtools-test.substvars dh_link 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 Using 1708190561 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1708190561 as canonical time Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/samtools cd debian/samtools-test chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian chmod a-x usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/reproducible-path/samtools-1.19.2' cd '/build/reproducible-path/samtools-1.19.2' 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 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-test ! -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-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/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-test -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 -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 dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/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 696973 new size 719280 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/c17f69af515d044389d55224240178adca8372.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/c17f69af515d044389d55224240178adca8372.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/27/c17f69af515d044389d55224240178adca8372.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5/da0f40f9ca98123002e817b9fb23512c465f63.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5/da0f40f9ca98123002e817b9fb23512c465f63.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/a5/da0f40f9ca98123002e817b9fb23512c465f63.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2e objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2e/dc4bebc01192dacffb25dcd542d6d58b990321.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2e/dc4bebc01192dacffb25dcd542d6d58b990321.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/2e/dc4bebc01192dacffb25dcd542d6d58b990321.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.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/f5/f0232c54a3841e3f0d4a336ab6487e7e7d8db1.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9/7959d416b8184687911ecc73aab26c0f5bc693.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9/7959d416b8184687911ecc73aab26c0f5bc693.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/d9/7959d416b8184687911ecc73aab26c0f5bc693.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7b objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7b/736da9116a0005ad855ada6fc58cd2cd3fb0e7.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7b/736da9116a0005ad855ada6fc58cd2cd3fb0e7.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/7b/736da9116a0005ad855ada6fc58cd2cd3fb0e7.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/050730da5a56161fc0875af0a7ee36066276a2.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/050730da5a56161fc0875af0a7ee36066276a2.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/7e/050730da5a56161fc0875af0a7ee36066276a2.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long dh_installdeb install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN dh_gencontrol install -m0755 -d debian/samtools-test/DEBIAN echo misc:Depends= >> debian/samtools-test.substvars echo misc:Pre-Depends= >> debian/samtools-test.substvars dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=27c17f69af515d044389d55224240178adca8372 2edc4bebc01192dacffb25dcd542d6d58b990321 7b736da9116a0005ad855ada6fc58cd2cd3fb0e7 7e050730da5a56161fc0875af0a7ee36066276a2 a5da0f40f9ca98123002e817b9fb23512c465f63 d97959d416b8184687911ecc73aab26c0f5bc693 f5f0232c54a3841e3f0d4a336ab6487e7e7d8db1" -DSection=debug -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 -cdebian/control -Pdebian/samtools dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb: building package 'samtools' in '../samtools_1.19.2-1_armhf.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.19.2-1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.19.2-1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.19.2-1_armhf.buildinfo dpkg-genchanges --build=binary -O../samtools_1.19.2-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/32695 and its subdirectories I: Current time: Thu Apr 25 02:13:28 -12 2024 I: pbuilder-time-stamp: 1714054408 Thu Apr 25 14:13:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32z-armhf-rb.debian.net. Thu Apr 25 14:13:59 UTC 2024 I: Preparing to do remote build '2' on virt32z-armhf-rb.debian.net. Thu Apr 25 14:25:33 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. Thu Apr 25 14:25:36 UTC 2024 I: samtools_1.19.2-1_armhf.changes: Format: 1.8 Date: Sat, 17 Feb 2024 18:22:41 +0100 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: armhf all Version: 1.19.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats samtools-test - test files for the samtools package Changes: samtools (1.19.2-1) unstable; urgency=medium . * [3f34445] New upstream version 1.19.2 * [e0d4f37] d/control: replace pkg-config by pkgconf. Checksums-Sha1: 071b9408d157e87c4c431dcd52d39c3769a5bc8a 948060 samtools-dbgsym_1.19.2-1_armhf.deb a4f85f744a45b8c71bcfc5ed3971fc0ff69d1f4c 2359180 samtools-test_1.19.2-1_all.deb 52a68a3dbd6cc0c7eaf2fa3b0401c082441b3ece 6491 samtools_1.19.2-1_armhf.buildinfo 039814107214db47b56e8897096941ab494ebcb6 613696 samtools_1.19.2-1_armhf.deb Checksums-Sha256: b6f83d56e61b3cf673c0950d5fcb55a4aa97b9840b7677c40c35ea4cd2334d91 948060 samtools-dbgsym_1.19.2-1_armhf.deb 0740b2f73b47a437baeaa03d4def4cc252a70055ee0bf5634a3853c4c0bae472 2359180 samtools-test_1.19.2-1_all.deb 2a3ae6a2a5266feb8067f06a8b353fa4135238c448276ba4c16f9c670e8d3573 6491 samtools_1.19.2-1_armhf.buildinfo 0f088d6be7606e5d97ec9e4f36eec822603b51adf1bf763a90db9d1da68b181a 613696 samtools_1.19.2-1_armhf.deb Files: cee715a980470700e7e008b84137bbb9 948060 debug optional samtools-dbgsym_1.19.2-1_armhf.deb ca61d2bb3972d5452f58da73d8210c7f 2359180 science optional samtools-test_1.19.2-1_all.deb a444cabba8ad56516ea1c5b591c773dd 6491 science optional samtools_1.19.2-1_armhf.buildinfo 57098bacf5532b109a85821d6662927d 613696 science optional samtools_1.19.2-1_armhf.deb Thu Apr 25 14:25:37 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_6-3879.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/samtools_1.19.2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/samtools_1.19.2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/samtools_1.19.2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/b1/samtools_1.19.2-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.G8G0lBNx/b2/samtools_1.19.2-1_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.390s) 0.390s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.061s) 0.061s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 703ms CPU time consumed: 690ms Thu Apr 25 14:25:38 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu Apr 25 14:25:38 UTC 2024 I: samtools from trixie built successfully and reproducibly on armhf. Thu Apr 25 14:25:40 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Apr 25 14:25:40 UTC 2024 I: Submitting 8.0K b1/samtools_1.19.2-1_armhf.buildinfo.asc Thu Apr 25 14:25:42 UTC 2024 I: Submitting 8.0K b2/samtools_1.19.2-1_armhf.buildinfo.asc Thu Apr 25 14:25:43 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Apr 25 14:25:43 UTC 2024 I: Done submitting .buildinfo files. Thu Apr 25 14:25:43 UTC 2024 I: Removing signed samtools_1.19.2-1_armhf.buildinfo.asc files: removed './b1/samtools_1.19.2-1_armhf.buildinfo.asc' removed './b2/samtools_1.19.2-1_armhf.buildinfo.asc'