Fri Oct 25 23:47:47 UTC 2024 I: starting to build samtools/trixie/amd64 on jenkins on '2024-10-25 23:47' Fri Oct 25 23:47:47 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_22/24777/console.log Fri Oct 25 23:47:47 UTC 2024 I: Downloading source for trixie/samtools=1.20-3 --2024-10-25 23:47:47-- http://deb.debian.org/debian/pool/main/s/samtools/samtools_1.20-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2281 (2.2K) [text/prs.lines.tag] Saving to: ‘samtools_1.20-3.dsc’ 0K .. 100% 251M=0s 2024-10-25 23:47:47 (251 MB/s) - ‘samtools_1.20-3.dsc’ saved [2281/2281] Fri Oct 25 23:47:47 UTC 2024 I: samtools_1.20-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.20-3 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://www.htslib.org/ Standards-Version: 4.7.0 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 (>= 1.20~), 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: 2b83ecc36ffcd39871749e840930c4eb0cdb70cf 5682525 samtools_1.20.orig.tar.gz e539b922b2610d9838682a4aa015bf2e72bbf3ae 22020 samtools_1.20-3.debian.tar.xz Checksums-Sha256: d0ca264732c2897ba85839e65e19cef0c5e1c19f54f4cd8e4ee10c07e3e1d20a 5682525 samtools_1.20.orig.tar.gz 4e6bb7814b0a360dac463c2e80868f1797158465d9c42bcb52580ef118c64641 22020 samtools_1.20-3.debian.tar.xz Files: 2c4b7e07bd7c1fce1e060a9039b27818 5682525 samtools_1.20.orig.tar.gz 5bf195cc49a1de89b804d215113d9158 22020 samtools_1.20-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZYzCAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdo0ww/+N1jO38yIrIbXlXhBJmCL+Le8GkR/ btt6j3rQ88rEAFmBxzsFri0LJ0hzcXnZtOJhSN8FN7ftmiWDbIUq+792odmlJCxV vmXlb9UzFW4+wdiuGEXvYjyz/vPkmxbXV2/e5EvdeBP0+A/ecVWmZlYS6itw74Xu wzKoabm1ztsvmnl3rLQ8doLCu0s8GuICQfN7EOTtEoqlwUiuzjguYRwZX1Qb6SaB 31fQ4dnvjRNC6j+e3z4Jk1kTASDqi9OCp+cVmUu1bOQBD0VcAiQ5CFJPRnEjuCJs D7Bka5HHtG5urgoOv0vdGEuYk7mlk4LUOnSybHjphhNvc3VVi3JWnf80zr5RLWuO NfdewfrspyaL3ouBz76TQDvrrHoEY81nEM3pfu41otUiH2RnUQQ1nOP2Qn+AFxvP dINeX0VAwtPmHqyuwsExULwWc73j+j4AITpYALtB+X8R/bfdhtkRB7GNaYcvsvE4 feWgHwn77+YvCHjwRgmI6d/8vW1f9tEvjXrl6uqtwrTrmr4gcTfAyU603/ape7nG r8csaO7hTCE5vL737iBUuPoKjSUipEgK//vXdTxXjCG0MHCUfdWPMBtH7x9r9yGU cWhy+EzCHrlwB7fS2oN+acl30aC1ALgGU1B2jtHI7wpW4bEsDlzxVWT+WA2MUjOo jSw/5L4Fp6A3lho= =eAPr -----END PGP SIGNATURE----- Fri Oct 25 23:47:47 UTC 2024 I: Checking whether the package is not for us Fri Oct 25 23:47:47 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Fri Oct 25 23:47:47 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Fri Oct 25 23:49:59 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 27 18:10:46 -12 2025 I: pbuilder-time-stamp: 1764310246 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_1.20-3.dsc] I: copying [./samtools_1.20.orig.tar.gz] I: copying [./samtools_1.20-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu May 30 18:57:36 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_1.20-3.dsc: no acceptable signature found dpkg-source: info: extracting samtools in samtools-1.20 dpkg-source: info: unpacking samtools_1.20.orig.tar.gz dpkg-source: info: unpacking samtools_1.20-3.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/777351/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='45a5b0451d2c46369016f1f42b132f0b' 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='777351' 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.dxCKbPu2/pbuilderrc_VLpx --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.dxCKbPu2/b1 --logfile b1/build.log samtools_1.20-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/777351/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: amd64 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 (>= 1.20~), 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 ... 21880 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 (>= 1.20~); 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} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 38.3 MB of archives. After unpacking 144 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 bash-completion all 1:2.14.0-1 [305 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b4 [313 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 39 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.10.1-2 [360 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.6-2 [439 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2 [439 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2 [123 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-2 [208 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.19.0-3+b2 [98.0 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10-1 [1316 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.6-2 [1381 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.63.0-1 [115 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.4.0-1 [86.5 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1 [77.4 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b4 [67.7 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.3.2-1 [2742 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [368 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.10.1-2 [471 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.2-2 [299 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5-2 [349 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 tabix amd64 1.20+ds-1 [483 kB] Fetched 38.3 MB in 1s (34.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21880 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_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package bash-completion. 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Setting up libp11-kit-dev:amd64 (0.25.5-2) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... 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 (1.14.0-1) ... Setting up libncurses-dev:amd64 (6.5-2) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up nettle-dev:amd64 (3.10-1) ... Setting up libtool (2.4.7-7) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.6-2) ... Setting up libnghttp2-dev:amd64 (1.63.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up debhelper (13.20) ... Setting up libcurl4-gnutls-dev:amd64 (8.10.1-2) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... Processing triggers for libc-bin (2.40-3) ... 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-1.20/ && 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_1.20-3_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.20-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from samtools-1.20/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-1.20' rm -f config.mk touch config.mk dh_auto_clean -- make -j42 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.20' 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-1.20' make[1]: Leaving directory '/build/reproducible-path/samtools-1.20' 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-1.20' 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=x86_64-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/x86_64-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 gcc option to enable large file support... none needed 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-1.20' 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-1.20' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j42 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.20' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 echo '#define SAMTOOLS_VERSION "1.20"' > version.h cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c echo '#define SAMTOOLS_CC "gcc"' >> version.h cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection"' >> version.h cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 echo '#define SAMTOOLS_HTSDIR ""' >> version.h cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c echo '#define SAMTOOLS_LIBS ""' >> version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 sed -i -e 's@/build/reproducible-path/samtools-1.20@«BUILDPATH»@g' version.h cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C 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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option '-frelease' is valid for D but not for C 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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -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 test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz 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 misc/wgsim misc/wgsim.o -lm -lhts -lz ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o 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/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_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-1.20' make[1]: Leaving directory '/build/reproducible-path/samtools-1.20' 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-1.20' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.20' 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-1.20/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.20/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.20/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.20/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.20/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.20/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.20/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.20/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/5Bd_3TQ5So/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/5Bd_3TQ5So/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/5Bd_3TQ5So/bgzip.dat.gz .. ok /build/reproducible-path/samtools-1.20/samtools faidx /tmp/5Bd_3TQ5So/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.20/samtools faidx /tmp/5Bd_3TQ5So/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.20/samtools faidx /tmp/5Bd_3TQ5So/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.20/samtools faidx /tmp/5Bd_3TQ5So/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.20/samtools faidx /tmp/5Bd_3TQ5So/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.20/samtools faidx /tmp/5Bd_3TQ5So/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.20/samtools faidx /tmp/5Bd_3TQ5So/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.20/samtools faidx /tmp/5Bd_3TQ5So/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5Bd_3TQ5So/fqidx.fq 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5Bd_3TQ5So/fqidx.fq.gz 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5Bd_3TQ5So/fqidx.fq 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5Bd_3TQ5So/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5Bd_3TQ5So/fqidx.fq 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5Bd_3TQ5So/fqidx.fq.gz 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5Bd_3TQ5So/fqidx.fq 1:99998-100007 .. ok .. ok /build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5Bd_3TQ5So/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/reproducible-path/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/reproducible-path/samtools-1.20/test/dat/dict.fa .. ok test_dict: /build/reproducible-path/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/5Bd_3TQ5So/dict.fa.gz .. ok test_dict: cat /build/reproducible-path/samtools-1.20/test/dat/dict.fa | /build/reproducible-path/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/reproducible-path/samtools-1.20/samtools dict -AH < /build/reproducible-path/samtools-1.20/test/dat/dict.alias.fa .. ok test_dict: /build/reproducible-path/samtools-1.20/samtools dict -H -l /build/reproducible-path/samtools-1.20/test/dat/dict.alt < /build/reproducible-path/samtools-1.20/test/dat/dict.alias.fa .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view /tmp/5Bd_3TQ5So/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view /tmp/5Bd_3TQ5So/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/5Bd_3TQ5So/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/5Bd_3TQ5So/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai /tmp/5Bd_3TQ5So/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/5Bd_3TQ5So/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam /tmp/5Bd_3TQ5So/auto_indexed.csi && cat /tmp/5Bd_3TQ5So/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/5Bd_3TQ5So/auto_indexed.crai && cat /tmp/5Bd_3TQ5So/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.sam /tmp/5Bd_3TQ5So/auto_indexed.csi && cat /tmp/5Bd_3TQ5So/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/5Bd_3TQ5So/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/5Bd_3TQ5So/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -@ 2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/5Bd_3TQ5So/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/5Bd_3TQ5So/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai /tmp/5Bd_3TQ5So/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/5Bd_3TQ5So/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -@ 2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -@ 2 -M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -@ 2 -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam /tmp/5Bd_3TQ5So/auto_indexed.csi && cat /tmp/5Bd_3TQ5So/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -@ 2 /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/5Bd_3TQ5So/auto_indexed.crai && cat /tmp/5Bd_3TQ5So/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.20/samtools index -@ 2 -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.sam /tmp/5Bd_3TQ5So/auto_indexed.csi && cat /tmp/5Bd_3TQ5So/auto_indexed.csi .. ok test_mpileup: /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/5Bd_3TQ5So/mpileup.bam.list -f /tmp/5Bd_3TQ5So/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/5Bd_3TQ5So/mpileup.cram.list -f /tmp/5Bd_3TQ5So/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/5Bd_3TQ5So/mpileup.bam.urllist -f /tmp/5Bd_3TQ5So/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/5Bd_3TQ5So/mpileup.cram.urllist -f /tmp/5Bd_3TQ5So/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/5Bd_3TQ5So/mpileup.ref.fa.gz -r17:1050-1060 /tmp/5Bd_3TQ5So/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/5Bd_3TQ5So/mpileup.ref.fa.gz -r17:1050-1060 /tmp/5Bd_3TQ5So/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.20/samtools mpileup /build/reproducible-path/samtools-1.20/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/5Bd_3TQ5So/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/5Bd_3TQ5So/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/5Bd_3TQ5So/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/5Bd_3TQ5So/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/5Bd_3TQ5So/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/5Bd_3TQ5So/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/5Bd_3TQ5So/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/5Bd_3TQ5So/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/5Bd_3TQ5So/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/5Bd_3TQ5So/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/5Bd_3TQ5So/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/5Bd_3TQ5So/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/5Bd_3TQ5So/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/5Bd_3TQ5So/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/5Bd_3TQ5So/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/5Bd_3TQ5So/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/5Bd_3TQ5So/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/5Bd_3TQ5So/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/5Bd_3TQ5So/view.001.forn (SAM input) .. ok 68: Count -N /tmp/5Bd_3TQ5So/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/5Bd_3TQ5So/view.001.forn (BAM input) .. ok 70: Count -N /tmp/5Bd_3TQ5So/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/5Bd_3TQ5So/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/5Bd_3TQ5So/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/5Bd_3TQ5So/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/5Bd_3TQ5So/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/5Bd_3TQ5So/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/5Bd_3TQ5So/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/5Bd_3TQ5So/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/5Bd_3TQ5So/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/5Bd_3TQ5So/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/5Bd_3TQ5So/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/5Bd_3TQ5So/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/5Bd_3TQ5So/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/5Bd_3TQ5So/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/5Bd_3TQ5So/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/5Bd_3TQ5So/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/5Bd_3TQ5So/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-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test115.sam -h -d TGCA /tmp/5Bd_3TQ5So/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-1.20/samtools view -c -d TGCA /tmp/5Bd_3TQ5So/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-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test117.sam -h -d TGCA /tmp/5Bd_3TQ5So/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-1.20/samtools view -c -d TGCA /tmp/5Bd_3TQ5So/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-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test119.sam -h -d TGCA /tmp/5Bd_3TQ5So/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-1.20/samtools view -c -d TGCA /tmp/5Bd_3TQ5So/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5Bd_3TQ5So/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test121.sam -h -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc /tmp/5Bd_3TQ5So/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5Bd_3TQ5So/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc /tmp/5Bd_3TQ5So/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5Bd_3TQ5So/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test123.sam -h -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc /tmp/5Bd_3TQ5So/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5Bd_3TQ5So/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc /tmp/5Bd_3TQ5So/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5Bd_3TQ5So/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test125.sam -h -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc /tmp/5Bd_3TQ5So/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5Bd_3TQ5So/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/5Bd_3TQ5So/view.001.fobc /tmp/5Bd_3TQ5So/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-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/5Bd_3TQ5So/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-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/5Bd_3TQ5So/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-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/5Bd_3TQ5So/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-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/5Bd_3TQ5So/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-1.20/samtools view -o /tmp/5Bd_3TQ5So/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/5Bd_3TQ5So/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-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/5Bd_3TQ5So/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-1.20/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /build/reproducible-path/samtools-1.20/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /build/reproducible-path/samtools-1.20/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-1.20/samtools head /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -h 0 /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -h 1 /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -h 5 /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -h 29 /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -h 30 /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -n 0 /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -n 1 /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -n 5 /build/reproducible-path/samtools-1.20/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.20/samtools head -h 5 -n 5 < /build/reproducible-path/samtools-1.20/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-1.20/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq -0 /build/reproducible-path/samtools-1.20/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq -0 /build/reproducible-path/samtools-1.20/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq -s /build/reproducible-path/samtools-1.20/test/s.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq -N -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq -N -T RG,BC,QT -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/reproducible-path/samtools-1.20/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /build/reproducible-path/samtools-1.20/samtools import --no-PG --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-1.20/samtools import --no-PG --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-1.20/samtools fastq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.20/test/bc.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.20/test/bc.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.20/test/bc.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.20/test/bc_split.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -t -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -t -T MD,ia -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.20/test/i.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.20/test/i.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -1 /build/reproducible-path/samtools-1.20/test/o.fq -2 /build/reproducible-path/samtools-1.20/test/o.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fasta -N -1 /build/reproducible-path/samtools-1.20/test/o.fa -2 /build/reproducible-path/samtools-1.20/test/o.fa /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -o /build/reproducible-path/samtools-1.20/test/o.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -s /tmp/5Bd_3TQ5So/bam2fq.discard.s.fq -0 /tmp/5Bd_3TQ5So/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.20/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.20/test/i1.fq --i2 /build/reproducible-path/samtools-1.20/test/i2.fq -0 /build/reproducible-path/samtools-1.20/test/0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -T '' /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -t -T '*' /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -N -T '*' -d ia /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.20/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-1.20/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.20/test/bc.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.20/test/bc.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.20/test/bc.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.20/test/bc_split.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -t -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -t -T MD,ia -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.20/test/i.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.20/test/i.fq -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.20/test/s.fq -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.20/test/1.fq -2 /build/reproducible-path/samtools-1.20/test/2.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -1 /build/reproducible-path/samtools-1.20/test/o.fq -2 /build/reproducible-path/samtools-1.20/test/o.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fasta -@ 2 -N -1 /build/reproducible-path/samtools-1.20/test/o.fa -2 /build/reproducible-path/samtools-1.20/test/o.fa /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -o /build/reproducible-path/samtools-1.20/test/o.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -s /tmp/5Bd_3TQ5So/bam2fq.discard.s.fq -0 /tmp/5Bd_3TQ5So/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.20/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.20/test/i1.fq --i2 /build/reproducible-path/samtools-1.20/test/i2.fq -0 /build/reproducible-path/samtools-1.20/test/0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -T '' /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -t -T '*' /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -T '*' -d ia /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.20/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-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/stat/test.fa -i 0 /build/reproducible-path/samtools-1.20/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -S RG -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -S RG -r /build/reproducible-path/samtools-1.20/test/stat/test.fa /build/reproducible-path/samtools-1.20/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -t /build/reproducible-path/samtools-1.20/test/stat/11.stats.targets /build/reproducible-path/samtools-1.20/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -g 4 -t /build/reproducible-path/samtools-1.20/test/stat/11.stats.targets /build/reproducible-path/samtools-1.20/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -g 4 /build/reproducible-path/samtools-1.20/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.20/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.20/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.20/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.20/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/reproducible-path/samtools-1.20/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/reproducible-path/samtools-1.20/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.20/samtools stats /build/reproducible-path/samtools-1.20/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/reproducible-path/samtools-1.20/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.20/samtools stats -I s1 /build/reproducible-path/samtools-1.20/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -I grp2 /build/reproducible-path/samtools-1.20/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -I grp3 /build/reproducible-path/samtools-1.20/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -I Sample /build/reproducible-path/samtools-1.20/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.20/samtools stats -r /build/reproducible-path/samtools-1.20/test/mpileup/ce.fa /build/reproducible-path/samtools-1.20/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -s 1 -O sam -b /tmp/M7W_2q25vG - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -r -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -cp -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -o - -s 1 -O sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/5Bd_3TQ5So/merge.tag.1.bam /tmp/5Bd_3TQ5So/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/5Bd_3TQ5So/merge.tag.3.bam /tmp/5Bd_3TQ5So/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge --no-PG -O SAM - /build/reproducible-path/samtools-1.20/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.20/test/merge/merge.bed - /tmp/5Bd_3TQ5So/merge.bed.1.bam /tmp/5Bd_3TQ5So/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge --no-PG -r -O SAM - /build/reproducible-path/samtools-1.20/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -O sam -b /tmp/OSgKTUg4ZL - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -r -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -cp -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -o - -s 1 -O sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/5Bd_3TQ5So/merge.tag.1.bam /tmp/5Bd_3TQ5So/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/5Bd_3TQ5So/merge.tag.3.bam /tmp/5Bd_3TQ5So/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 --no-PG -O SAM - /build/reproducible-path/samtools-1.20/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.20/test/merge/merge.bed - /tmp/5Bd_3TQ5So/merge.bed.1.bam /tmp/5Bd_3TQ5So/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.20/samtools merge -@ 2 --no-PG -r -O SAM - /build/reproducible-path/samtools-1.20/test/merge/test_no_pg_rg_co.sam .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5Bd_3TQ5So/sortout .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -f /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5Bd_3TQ5So/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -o /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5Bd_3TQ5So/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -n -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -N -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -n -m 10M /build/reproducible-path/samtools-1.20/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -t RG -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -n -t RG -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -t AS -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -t FI -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort --template-coordinate -m 10M /build/reproducible-path/samtools-1.20/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools reset /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.20/samtools sort -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools reset /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.20/samtools sort -M -K10 -I /build/reproducible-path/samtools-1.20/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools reset /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.20/samtools sort -MH -K10 -I /build/reproducible-path/samtools-1.20/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5Bd_3TQ5So/sortout .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5Bd_3TQ5So/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5Bd_3TQ5So/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -N -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.20/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -t RG -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -n -t RG -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -t AS -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -t FI -m 10M /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools sort -@ 2 --template-coordinate -m 10M /build/reproducible-path/samtools-1.20/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools reset /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools reset /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -M -K10 -I /build/reproducible-path/samtools-1.20/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.20/samtools reset /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -MH -K10 -I /build/reproducible-path/samtools-1.20/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate --output-fmt=sam -O /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate -o /build/reproducible-path/samtools-1.20/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate -o /build/reproducible-path/samtools-1.20/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.20/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate --output-fmt=sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.20/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate --output-fmt=sam -f /build/reproducible-path/samtools-1.20/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.20/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.20/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.20/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate -@ 2 --output-fmt=sam -O /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.20/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.20/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.20/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate -@ 2 --output-fmt=sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.20/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate -@ 2 --output-fmt=sam -f /build/reproducible-path/samtools-1.20/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.20/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.20/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.20/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.20/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -O sam /build/reproducible-path/samtools-1.20/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-1.20/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -O sam /build/reproducible-path/samtools-1.20/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -O sam /build/reproducible-path/samtools-1.20/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -cO sam /build/reproducible-path/samtools-1.20/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -cO sam /build/reproducible-path/samtools-1.20/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -O sam /build/reproducible-path/samtools-1.20/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.20/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-1.20/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.20/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.20/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.20/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.20/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.20/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.20/test/fixmate/mod_bounds.sam - .. ok /build/reproducible-path/samtools-1.20/samtools calmd -uAr /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.20/test/dat/mpileup.ref.fa .. ok /build/reproducible-path/samtools-1.20/samtools calmd -@ 2 -uAr /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.20/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/reproducible-path/samtools-1.20/samtools idxstats /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/reproducible-path/samtools-1.20/samtools idxstats /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/reproducible-path/samtools-1.20/samtools idxstats /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck /build/reproducible-path/samtools-1.20/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck -v /build/reproducible-path/samtools-1.20/test/quickcheck/1.quickcheck.badeof.bam /build/reproducible-path/samtools-1.20/test/quickcheck/2.quickcheck.badheader.bam /build/reproducible-path/samtools-1.20/test/quickcheck/3.quickcheck.ok.bam /build/reproducible-path/samtools-1.20/test/quickcheck/4.quickcheck.ok.bam /build/reproducible-path/samtools-1.20/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/reproducible-path/samtools-1.20/test/quickcheck/6.quickcheck.cram21.ok.cram /build/reproducible-path/samtools-1.20/test/quickcheck/7.quickcheck.cram30.ok.cram /build/reproducible-path/samtools-1.20/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/reproducible-path/samtools-1.20/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/reproducible-path/samtools-1.20/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/reproducible-path/samtools-1.20/samtools quickcheck -uv /build/reproducible-path/samtools-1.20/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/reproducible-path/samtools-1.20/samtools reheader /build/reproducible-path/samtools-1.20/test/reheader/hdr.sam /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.20/samtools reheader /build/reproducible-path/samtools-1.20/test/reheader/hdr.sam /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.v21.cram | /build/reproducible-path/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.20/samtools reheader /build/reproducible-path/samtools-1.20/test/reheader/hdr.sam /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.20/samtools reheader --in-place /build/reproducible-path/samtools-1.20/test/reheader/hdr.sam /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.v21.cram && /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.20/samtools reheader --in-place /build/reproducible-path/samtools-1.20/test/reheader/hdr.sam /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.v30.cram && /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.20/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.20/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.20/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -O sam -m overwrite_all /build/reproducible-path/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -O sam -m orphan_only /build/reproducible-path/samtools-1.20/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -O sam -R '1#9' /build/reproducible-path/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.20/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.20/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/reproducible-path/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/reproducible-path/samtools-1.20/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/reproducible-path/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.20/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.20/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.20/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.20/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-1.20/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.20/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-1.20/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.20/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-1.20/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -O sam -r --no-PG /build/reproducible-path/samtools-1.20/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -S -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.20/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.20/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/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-1.20/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/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-1.20/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.20/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/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-1.20/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/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-1.20/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.20/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.20/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-1.20/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.20/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-1.20/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.20/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-1.20/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -O sam -r --no-PG /build/reproducible-path/samtools-1.20/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -S -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.20/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.20/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/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-1.20/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/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-1.20/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.20/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/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-1.20/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/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-1.20/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.20/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.20/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.20/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /build/reproducible-path/samtools-1.20/samtools bedcov /build/reproducible-path/samtools-1.20/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.20/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.20/samtools bedcov -j /build/reproducible-path/samtools-1.20/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.20/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.20/samtools bedcov -g512 -G2048 /build/reproducible-path/samtools-1.20/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.20/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.20/samtools bedcov -c /build/reproducible-path/samtools-1.20/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.20/test/bedcov/bedcov.bam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split --output-fmt sam -d an -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.20/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.20/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split -@ 2 --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split -@ 2 --output-fmt sam -d an -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.20/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.20/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.20/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.20/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.20/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.20/test/split/split_d_nn.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/5Bd_3TQ5So/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/5Bd_3TQ5So/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.20/test/large_pos/test.bed /tmp/5Bd_3TQ5So/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools sort -O sam --no-PG -m 10M /build/reproducible-path/samtools-1.20/test/large_pos/longref_name.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools merge -O sam --no-PG - /build/reproducible-path/samtools-1.20/test/large_pos/longref.sam /build/reproducible-path/samtools-1.20/test/large_pos/longref2.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools depth /build/reproducible-path/samtools-1.20/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools depth -b /build/reproducible-path/samtools-1.20/test/large_pos/test.bed /build/reproducible-path/samtools-1.20/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/5Bd_3TQ5So/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.20/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/reproducible-path/samtools-1.20/samtools fixmate -O sam --no-PG - - | /build/reproducible-path/samtools-1.20/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /build/reproducible-path/samtools-1.20/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconclip/1_hard_clipped.expected.sam /build/reproducible-path/samtools-1.20/test/ampliconclip/1_soft_clipped.expected.sam /build/reproducible-path/samtools-1.20/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/reproducible-path/samtools-1.20/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.20/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.20/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.20/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.20/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.20/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.20/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.20/samtools reset | /build/reproducible-path/samtools-1.20/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset < /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.20/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.20/samtools view .. ok test_reset: cat /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.20/samtools reset -o /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset -o /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset -o /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.cram .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa_index /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG sam_to_fixed_bam /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa_index --no-PG /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.20/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam --no-RG -o /build/reproducible-path/samtools-1.20/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/reproducible-path/samtools-1.20/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/reproducible-path/samtools-1.20/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/reproducible-path/samtools-1.20/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/reproducible-path/samtools-1.20/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/reproducible-path/samtools-1.20/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset --reject-PG bwa /build/reproducible-path/samtools-1.20/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/reproducible-path/samtools-1.20/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.20/samtools reset /build/reproducible-path/samtools-1.20/test/reset/seq.sam -o /build/reproducible-path/samtools-1.20/test/reset/output .. ok Number of tests: total .. 973 passed .. 929 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: 120 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/mpileup && AWK="mawk" ../regression.sh cram-size.reg === Testing cram-size.reg regressions === Expected passes: 5 Unexpected passes: 0 Expected failures: 0 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-1.20' rm -fr -- /tmp/dh-xdg-rundir-WcRmzq3O make[1]: Leaving directory '/build/reproducible-path/samtools-1.20' 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-1.20' dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.20/debian/tmp make -j42 install DESTDIR=/build/reproducible-path/samtools-1.20/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.20' mkdir -p -m 755 /build/reproducible-path/samtools-1.20/debian/tmp/usr/bin /build/reproducible-path/samtools-1.20/debian/tmp/usr/bin /build/reproducible-path/samtools-1.20/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.20/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-1.20/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-1.20/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/reproducible-path/samtools-1.20/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/samtools-1.20' make clean make[2]: Entering directory '/build/reproducible-path/samtools-1.20' 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-1.20' make[1]: Leaving directory '/build/reproducible-path/samtools-1.20' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/samtools-1.20' 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-1.20' 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-1.20' 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-1.20' 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-1.20' # 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-1.20' 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 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 man-recode --to-code UTF-8 --suffix .dh-new 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.1 debian/samtools/usr/share/man/man1/samtools.pl.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/wgsim.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/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.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 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.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 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-bedcov.1 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-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.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-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.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/wgsim.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-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.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-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.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 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.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 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.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 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-markdup.1 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-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.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-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.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-tview.1 debian/samtools/usr/share/man/man1/samtools-view.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-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.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-sort.1 debian/samtools/usr/share/man/man1/samtools-split.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 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.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 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.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 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.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 1717095173 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1717095173 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/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 cd '/build/reproducible-path/samtools-1.20' cd '/build/reproducible-path/samtools-1.20' 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-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools -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 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 debian/rules execute_after_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/samtools-1.20' chmod -x /build/reproducible-path/samtools-1.20/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam make[1]: Leaving directory '/build/reproducible-path/samtools-1.20' dh_missing dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/x86_64-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 809747 new size 832143 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/f1ba36ea954b86053cb61d10c99d8686be87bb.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/f1ba36ea954b86053cb61d10c99d8686be87bb.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/28/f1ba36ea954b86053cb61d10c99d8686be87bb.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2e objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2e/25390d6bec714c340169fa6947f9da2fb85375.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2e/25390d6bec714c340169fa6947f9da2fb85375.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2e/25390d6bec714c340169fa6947f9da2fb85375.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/11 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/11/1a331ffa581ec536de6de7022a565af2bad9a9.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/11/1a331ffa581ec536de6de7022a565af2bad9a9.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/11/1a331ffa581ec536de6de7022a565af2bad9a9.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee/7ed89f52cae5bef8c1645f4b3639552f79cd33.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee/7ed89f52cae5bef8c1645f4b3639552f79cd33.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/ee/7ed89f52cae5bef8c1645f4b3639552f79cd33.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c5 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c5/f6874db199cd8644972405eab656249717c0ca.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c5/f6874db199cd8644972405eab656249717c0ca.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/c5/f6874db199cd8644972405eab656249717c0ca.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/567ff40e0de960071152a4f2fcaa061c6cd227.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/567ff40e0de960071152a4f2fcaa061c6cd227.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/35/567ff40e0de960071152a4f2fcaa061c6cd227.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af/06752cb21e7506be1b412999e92e22a16222f0.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af/06752cb21e7506be1b412999e92e22a16222f0.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/af/06752cb21e7506be1b412999e92e22a16222f0.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short dh_installdeb install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN dh_gencontrol 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=111a331ffa581ec536de6de7022a565af2bad9a9 28f1ba36ea954b86053cb61d10c99d8686be87bb 2e25390d6bec714c340169fa6947f9da2fb85375 35567ff40e0de960071152a4f2fcaa061c6cd227 af06752cb21e7506be1b412999e92e22a16222f0 c5f6874db199cd8644972405eab656249717c0ca ee7ed89f52cae5bef8c1645f4b3639552f79cd33" -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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 dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools' in '../samtools_1.20-3_amd64.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.20-3_all.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.20-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.20-3_amd64.buildinfo dpkg-genchanges --build=binary -O../samtools_1.20-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.20/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original 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/777351 and its subdirectories I: Current time: Thu Nov 27 18:12:55 -12 2025 I: pbuilder-time-stamp: 1764310375 Fri Oct 25 23:50:00 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Fri Oct 25 23:50:00 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Fri Oct 25 23:53:56 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Fri Oct 25 23:53:57 UTC 2024 I: samtools_1.20-3_amd64.changes: Format: 1.8 Date: Thu, 30 May 2024 20:52:53 +0200 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: amd64 all Version: 1.20-3 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 (1.20-3) unstable; urgency=medium . * [56a4a28] d/rules: fix no-arch-all builds. The initial issue flown below radar due to leftover htslib version discrepancy, triggering the build failure too early. Checksums-Sha1: db23698b3889b77047add55b4bb7fa8b463ca87c 991432 samtools-dbgsym_1.20-3_amd64.deb 16035b5c40a5945e72a35fcc47a467464eb3b171 2364248 samtools-test_1.20-3_all.deb 8acaee040aa98b9a0f1ae6a231e8c992fb929cb1 7123 samtools_1.20-3_amd64.buildinfo 1554fefc8cbdf56c99477f088a870bc286311200 657732 samtools_1.20-3_amd64.deb Checksums-Sha256: fde54bc296401e71678822c39004d7f9ad02f6175c1ab360e0ed01f1075fb1ea 991432 samtools-dbgsym_1.20-3_amd64.deb 8c9c5ddf0aa46dc2e7b99f0eb12e659297bc90dd665156356b434b3637234ff4 2364248 samtools-test_1.20-3_all.deb 1a30d4c5b63da14da2b276c9230ff66b495c596935ea1f8c509f0213b8dc9ca9 7123 samtools_1.20-3_amd64.buildinfo d3146e2ba4deb7fa49815c8ec232436d6a6ff002786b5040960d0e57b36bcbd9 657732 samtools_1.20-3_amd64.deb Files: b5c37d9af4f8f3e329dd90d3d24cf682 991432 debug optional samtools-dbgsym_1.20-3_amd64.deb 828d763364c1eeb129440bdf139ba5f1 2364248 science optional samtools-test_1.20-3_all.deb a1df8d2326472662d9ac854488732da2 7123 science optional samtools_1.20-3_amd64.buildinfo f5bcb932a515db4bad3fc38ab50e25e2 657732 science optional samtools_1.20-3_amd64.deb Fri Oct 25 23:53:58 UTC 2024 I: diffoscope 281 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_22-24777.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dxCKbPu2/samtools_1.20-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dxCKbPu2/samtools_1.20-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dxCKbPu2/samtools_1.20-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dxCKbPu2/b1/samtools_1.20-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dxCKbPu2/b2/samtools_1.20-3_amd64.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: 0.428s) 0.428s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.062s) 0.062s 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: 787ms CPU time consumed: 766ms Fri Oct 25 23:53:59 UTC 2024 I: diffoscope 281 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 25 23:53:59 UTC 2024 I: samtools from trixie built successfully and reproducibly on amd64. Fri Oct 25 23:54:01 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Oct 25 23:54:01 UTC 2024 I: Submitting 8.0K b1/samtools_1.20-3_amd64.buildinfo.asc Fri Oct 25 23:54:02 UTC 2024 I: Submitting 8.0K b2/samtools_1.20-3_amd64.buildinfo.asc Fri Oct 25 23:54:03 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Oct 25 23:54:03 UTC 2024 I: Done submitting .buildinfo files. Fri Oct 25 23:54:03 UTC 2024 I: Removing signed samtools_1.20-3_amd64.buildinfo.asc files: removed './b1/samtools_1.20-3_amd64.buildinfo.asc' removed './b2/samtools_1.20-3_amd64.buildinfo.asc'