Sat Apr 27 12:21:39 UTC 2024 I: starting to build samtools/trixie/arm64 on jenkins on '2024-04-27 12:21' Sat Apr 27 12:21:39 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/39951/console.log Sat Apr 27 12:21:39 UTC 2024 I: Downloading source for trixie/samtools=1.19.2-1 --2024-04-27 12:21:40-- 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% 232M=0s 2024-04-27 12:21:40 (232 MB/s) - ‘samtools_1.19.2-1.dsc’ saved [2295/2295] Sat Apr 27 12:21:40 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----- Sat Apr 27 12:21:40 UTC 2024 I: Checking whether the package is not for us Sat Apr 27 12:21:40 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Sat Apr 27 12:21:40 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Sat Apr 27 12:23:30 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 30 06:44:41 -12 2025 I: pbuilder-time-stamp: 1748630681 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/3442223/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='bc4fe93317e04fabae42d4c474e4c750' 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='3442223' 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.BrPP9j4n/pbuilderrc_tW4x --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.BrPP9j4n/b1 --logfile b1/build.log samtools_1.19.2-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3442223/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: arm64 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 ... 19937 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} libbz2-dev{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libpipeline1{a} libpkgconf3{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 curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 22.0 MB of archives. After unpacking 91.9 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libhts-dev (>= 1.17~) but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libssl3 [3.1.5-1 (now)] Install the following packages: 2) libbrotli1 [1.1.0-2+b3 (testing)] 3) libcurl3t64-gnutls [8.7.1-3 (testing)] 4) libcurl4-gnutls-dev [8.7.1-3 (testing)] 5) libdeflate-dev [1.20-1 (testing)] 6) libhts-dev [1.19+ds-1 (testing)] 7) libhts3 [1.19+ds-1 (testing)] 8) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 9) libnghttp2-14 [1.59.0-1 (testing)] 10) libpsl5t64 [0.21.2-1.1 (testing)] 11) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 12) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 13) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 14) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 15) libssl3t64 [3.2.1-3 (testing)] 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} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{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} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssl3t64{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 will be REMOVED: libssl3{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, 58 newly installed, 1 to remove and 0 not upgraded. Need to get 28.5 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 autoconf-archive all 20220903-3 [775 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 bash-completion all 1:2.11-8 [224 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 26 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-5.1 [31.8 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-3 [523 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libhts3 arm64 1.19+ds-1 [412 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.19+ds-1 [1603 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1 [33.8 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.4+20240414-1 [95.6 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libncurses-dev arm64 6.4+20240414-1 [336 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 tabix arm64 1.19+ds-1 [445 kB] Fetched 28.5 MB in 0s (136 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19937 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:arm64. (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 ... 19924 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... 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 ... 19939 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_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../04-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_arm64.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 libelf1t64:arm64. Preparing to unpack .../24-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../26-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.3+b2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-14+b1_arm64.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:arm64. Preparing to unpack .../32-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../33-libbz2-dev_1.0.8-5.1_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-5.1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../34-libsasl2-modules-db_2.1.28+dfsg1-4+b1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../35-libsasl2-2_2.1.28+dfsg1-4+b1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../36-libldap-2.5-0_2.5.13+dfsg-5+b3_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../37-libnghttp2-14_1.59.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.59.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../38-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../39-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../40-libssh2-1t64_1.11.0-4.1+b2_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../41-libcurl3t64-gnutls_8.7.1-3_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.7.1-3) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../42-libcurl4-gnutls-dev_8.7.1-3_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (8.7.1-3) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../43-libdeflate0_1.20-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.20-1) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../44-libdeflate-dev_1.20-1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.20-1) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../45-libhtscodecs2_1.6.0-1+b1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3:arm64. Preparing to unpack .../46-libhts3_1.19+ds-1_arm64.deb ... Unpacking libhts3:arm64 (1.19+ds-1) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../47-liblzma-dev_5.6.1+really5.4.5-1_arm64.deb ... Unpacking liblzma-dev:arm64 (5.6.1+really5.4.5-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../48-zlib1g-dev_1%3a1.3.dfsg-3.1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../49-libhts-dev_1.19+ds-1_arm64.deb ... Unpacking libhts-dev:arm64 (1.19+ds-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../50-libio-pty-perl_1%3a1.20-1_arm64.deb ... Unpacking libio-pty-perl (1:1.20-1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../51-libncurses6_6.4+20240414-1_arm64.deb ... Unpacking libncurses6:arm64 (6.4+20240414-1) ... Selecting previously unselected package libncurses-dev:arm64. Preparing to unpack .../52-libncurses-dev_6.4+20240414-1_arm64.deb ... Unpacking libncurses-dev:arm64 (6.4+20240414-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../53-libpkgconf3_1.8.1-1+b2_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-1+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../54-pkgconf-bin_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../55-pkgconf_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-1+b2) ... Selecting previously unselected package tabix. Preparing to unpack .../56-tabix_1.19+ds-1_arm64.deb ... Unpacking tabix (1.19+ds-1) ... Setting up libhtscodecs2:arm64 (1.6.0-1+b1) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (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:arm64 (1.1.0-2+b3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.59.0-1) ... Setting up libmagic1:arm64 (1:5.45-2+b1) ... Setting up libdeflate0:arm64 (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 libelf1t64:arm64 (0.191-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-4+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up bash-completion (1:2.11-8) ... Setting up libncurses6:arm64 (6.4+20240414-1) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:arm64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libdeflate-dev:arm64 (1.20-1) ... Setting up tabix (1.19+ds-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Setting up libbz2-dev:arm64 (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:arm64 (6.4+20240414-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Setting up pkgconf:arm64 (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 groff-base (1.23.0-3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up libcurl4-gnutls-dev:arm64 (8.7.1-3) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:arm64 (1.19+ds-1) ... Setting up libhts-dev:arm64 (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 arm64 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 -j12 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=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/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 -j12 "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 -mbranch-protection=standard" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -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 -mbranch-protection=standard"' >> 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 echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/reproducible-path/samtools-1.19.2@«BUILDPATH»@g' 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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -mbranch-protection=standard -DMAQ_LONGREADS -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread 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 -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 misc/wgsim misc/wgsim.o -lm -lhts -lz 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 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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.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 -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.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 -mbranch-protection=standard -I. -I./lz4 -frelease -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 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 -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/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/merge/test_bam_translate test/merge/test_bam_translate.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 -j12 test "TESTSUITEFLAGS=-j12 --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/Cme7lyWau_/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/Cme7lyWau_/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/Cme7lyWau_/bgzip.dat.gz .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/Cme7lyWau_/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/Cme7lyWau_/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/Cme7lyWau_/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/Cme7lyWau_/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/Cme7lyWau_/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/Cme7lyWau_/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/Cme7lyWau_/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/Cme7lyWau_/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/Cme7lyWau_/fqidx.fq 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/Cme7lyWau_/fqidx.fq.gz 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/Cme7lyWau_/fqidx.fq 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/Cme7lyWau_/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/Cme7lyWau_/fqidx.fq 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/Cme7lyWau_/fqidx.fq.gz 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/Cme7lyWau_/fqidx.fq 1:99998-100007 .. ok .. ok /build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/auto_indexed.csi && cat /tmp/Cme7lyWau_/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/Cme7lyWau_/auto_indexed.crai && cat /tmp/Cme7lyWau_/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/Cme7lyWau_/auto_indexed.csi && cat /tmp/Cme7lyWau_/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/Cme7lyWau_/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/auto_indexed.csi && cat /tmp/Cme7lyWau_/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/Cme7lyWau_/auto_indexed.crai && cat /tmp/Cme7lyWau_/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/Cme7lyWau_/auto_indexed.csi && cat /tmp/Cme7lyWau_/auto_indexed.csi .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/Cme7lyWau_/mpileup.bam.list -f /tmp/Cme7lyWau_/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/Cme7lyWau_/mpileup.cram.list -f /tmp/Cme7lyWau_/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/Cme7lyWau_/mpileup.bam.urllist -f /tmp/Cme7lyWau_/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/Cme7lyWau_/mpileup.cram.urllist -f /tmp/Cme7lyWau_/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/Cme7lyWau_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Cme7lyWau_/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/Cme7lyWau_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Cme7lyWau_/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/Cme7lyWau_/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/Cme7lyWau_/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/Cme7lyWau_/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/Cme7lyWau_/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/Cme7lyWau_/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/Cme7lyWau_/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/Cme7lyWau_/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/Cme7lyWau_/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/Cme7lyWau_/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/Cme7lyWau_/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/Cme7lyWau_/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/Cme7lyWau_/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/Cme7lyWau_/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/Cme7lyWau_/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/Cme7lyWau_/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/Cme7lyWau_/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/Cme7lyWau_/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/Cme7lyWau_/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/Cme7lyWau_/view.001.forn (SAM input) .. ok 68: Count -N /tmp/Cme7lyWau_/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/Cme7lyWau_/view.001.forn (BAM input) .. ok 70: Count -N /tmp/Cme7lyWau_/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/Cme7lyWau_/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/Cme7lyWau_/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/Cme7lyWau_/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/Cme7lyWau_/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/Cme7lyWau_/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/Cme7lyWau_/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/Cme7lyWau_/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/Cme7lyWau_/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/Cme7lyWau_/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/Cme7lyWau_/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/Cme7lyWau_/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/Cme7lyWau_/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/Cme7lyWau_/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/Cme7lyWau_/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/Cme7lyWau_/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/Cme7lyWau_/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/Cme7lyWau_/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/Cme7lyWau_/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/Cme7lyWau_/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/Cme7lyWau_/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/Cme7lyWau_/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/Cme7lyWau_/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/Cme7lyWau_/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/Cme7lyWau_/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/Cme7lyWau_/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/Cme7lyWau_/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/Cme7lyWau_/view.test115.sam -h -d TGCA /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/view.test117.sam -h -d TGCA /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/view.test119.sam -h -d TGCA /tmp/Cme7lyWau_/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/Cme7lyWau_/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/Cme7lyWau_/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Cme7lyWau_/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/Cme7lyWau_/view.test121.sam -h -D BClong:/tmp/Cme7lyWau_/view.001.fobc /tmp/Cme7lyWau_/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/Cme7lyWau_/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Cme7lyWau_/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/Cme7lyWau_/view.001.fobc /tmp/Cme7lyWau_/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/Cme7lyWau_/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Cme7lyWau_/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/Cme7lyWau_/view.test123.sam -h -D BClong:/tmp/Cme7lyWau_/view.001.fobc /tmp/Cme7lyWau_/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/Cme7lyWau_/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Cme7lyWau_/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/Cme7lyWau_/view.001.fobc /tmp/Cme7lyWau_/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/Cme7lyWau_/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Cme7lyWau_/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/Cme7lyWau_/view.test125.sam -h -D BClong:/tmp/Cme7lyWau_/view.001.fobc /tmp/Cme7lyWau_/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/Cme7lyWau_/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Cme7lyWau_/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/Cme7lyWau_/view.001.fobc /tmp/Cme7lyWau_/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/Cme7lyWau_/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/bam2fq.discard.s.fq -0 /tmp/Cme7lyWau_/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/Cme7lyWau_/bam2fq.discard.s.fq -0 /tmp/Cme7lyWau_/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/y9U3tBAYpC - /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/Cme7lyWau_/merge.tag.1.bam /tmp/Cme7lyWau_/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/Cme7lyWau_/merge.tag.3.bam /tmp/Cme7lyWau_/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/Cme7lyWau_/merge.bed.1.bam /tmp/Cme7lyWau_/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/Z8lOjgHSWU - /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/Cme7lyWau_/merge.tag.1.bam /tmp/Cme7lyWau_/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/Cme7lyWau_/merge.tag.3.bam /tmp/Cme7lyWau_/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/Cme7lyWau_/merge.bed.1.bam /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/Cme7lyWau_/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/Cme7lyWau_/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/Cme7lyWau_/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-r_hoAtPX 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 -j12 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 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 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 chmod 0644 -- 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 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-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 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 chmod 0644 -- 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 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 chmod 0644 -- 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 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.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-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 chmod 0644 -- 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 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 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 chmod 0644 -- 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 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 chmod 0644 -- 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 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-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/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/aarch64-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 800309 new size 821501 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/49 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/49/705e910ac6e905fd4d4185896f284598fe42f4.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/49/705e910ac6e905fd4d4185896f284598fe42f4.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/49/705e910ac6e905fd4d4185896f284598fe42f4.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a7 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a7/ccf9c3fe812fb4b9e2139efbf4f5875d9a748a.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a7/ccf9c3fe812fb4b9e2139efbf4f5875d9a748a.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/a7/ccf9c3fe812fb4b9e2139efbf4f5875d9a748a.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a7 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a7/7c09efc1b22c85a8f2d7072176736ced22bd58.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a7/7c09efc1b22c85a8f2d7072176736ced22bd58.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/a7/7c09efc1b22c85a8f2d7072176736ced22bd58.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/7f7c4c087d5f0babbd185c8502884acb178e22.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/7f7c4c087d5f0babbd185c8502884acb178e22.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/bd/7f7c4c087d5f0babbd185c8502884acb178e22.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9d/f0b6bf1d7cfdfad125dcb438e4e3861e6bf071.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9d/f0b6bf1d7cfdfad125dcb438e4e3861e6bf071.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/9d/f0b6bf1d7cfdfad125dcb438e4e3861e6bf071.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/9deb8d645c27b2d6ee824a77e6051226d52523.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/9deb8d645c27b2d6ee824a77e6051226d52523.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/46/9deb8d645c27b2d6ee824a77e6051226d52523.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/60 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/60/1e87b382af1f67ddf57978300ba7a34562a444.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/60/1e87b382af1f67ddf57978300ba7a34562a444.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/60/1e87b382af1f67ddf57978300ba7a34562a444.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools 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=469deb8d645c27b2d6ee824a77e6051226d52523 49705e910ac6e905fd4d4185896f284598fe42f4 601e87b382af1f67ddf57978300ba7a34562a444 9df0b6bf1d7cfdfad125dcb438e4e3861e6bf071 a77c09efc1b22c85a8f2d7072176736ced22bd58 a7ccf9c3fe812fb4b9e2139efbf4f5875d9a748a bd7f7c4c087d5f0babbd185c8502884acb178e22" -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 ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools-test/DEBIAN install -m0755 -d debian/samtools/DEBIAN cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools' in '../samtools_1.19.2-1_arm64.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.19.2-1_arm64.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.19.2-1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.19.2-1_arm64.buildinfo dpkg-genchanges --build=binary -O../samtools_1.19.2-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ 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/3442223 and its subdirectories I: Current time: Fri May 30 06:46:27 -12 2025 I: pbuilder-time-stamp: 1748630787 Sat Apr 27 12:23:30 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sat Apr 27 12:23:30 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sat Apr 27 12:25:21 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sat Apr 27 12:25:21 UTC 2024 I: samtools_1.19.2-1_arm64.changes: Format: 1.8 Date: Sat, 17 Feb 2024 18:22:41 +0100 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: arm64 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: 5fa7d7eb4d7e6db80137795eb88428269007c180 944380 samtools-dbgsym_1.19.2-1_arm64.deb a4f85f744a45b8c71bcfc5ed3971fc0ff69d1f4c 2359180 samtools-test_1.19.2-1_all.deb 9178f3b0628ee6ad66a68e742cf8a9bd9247a74e 6652 samtools_1.19.2-1_arm64.buildinfo 2c60712f8af9157ff47dba4f62388818a09853cc 617116 samtools_1.19.2-1_arm64.deb Checksums-Sha256: d310102fc05958dcbb0e44186ee2b646e3ef598e93f1ff661706410a7b25534d 944380 samtools-dbgsym_1.19.2-1_arm64.deb 0740b2f73b47a437baeaa03d4def4cc252a70055ee0bf5634a3853c4c0bae472 2359180 samtools-test_1.19.2-1_all.deb 8f519d7ae94f9166bd6577cfd221d78dcc48e7af3728f4dfdf919bc05adbb7cd 6652 samtools_1.19.2-1_arm64.buildinfo fde5b67f8e07a07a9c5a43cd3560b034792153abcb0e40c7e504331ab5efba47 617116 samtools_1.19.2-1_arm64.deb Files: b807a9aac144e93b9ca545ccff85286c 944380 debug optional samtools-dbgsym_1.19.2-1_arm64.deb ca61d2bb3972d5452f58da73d8210c7f 2359180 science optional samtools-test_1.19.2-1_all.deb 0ff57947273ac1d327426fc4cae55650 6652 science optional samtools_1.19.2-1_arm64.buildinfo c2d7b90a8eca51a5fda89c04a19803dc 617116 science optional samtools_1.19.2-1_arm64.deb Sat Apr 27 12:25:22 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_15-39951.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.BrPP9j4n/samtools_1.19.2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.BrPP9j4n/samtools_1.19.2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.BrPP9j4n/samtools_1.19.2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.BrPP9j4n/b1/samtools_1.19.2-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.BrPP9j4n/b2/samtools_1.19.2-1_arm64.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: 0.442s) 0.442s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.069s) 0.069s 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: 826ms CPU time consumed: 826ms Sat Apr 27 12:25:24 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sat Apr 27 12:25:24 UTC 2024 I: samtools from trixie built successfully and reproducibly on arm64. Sat Apr 27 12:25:26 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Apr 27 12:25:26 UTC 2024 I: Submitting 8.0K b1/samtools_1.19.2-1_arm64.buildinfo.asc Sat Apr 27 12:25:30 UTC 2024 I: Submitting 8.0K b2/samtools_1.19.2-1_arm64.buildinfo.asc Sat Apr 27 12:25:31 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Apr 27 12:25:31 UTC 2024 I: Done submitting .buildinfo files. Sat Apr 27 12:25:31 UTC 2024 I: Removing signed samtools_1.19.2-1_arm64.buildinfo.asc files: removed './b1/samtools_1.19.2-1_arm64.buildinfo.asc' removed './b2/samtools_1.19.2-1_arm64.buildinfo.asc'