Tue Sep 9 14:38:38 UTC 2025 I: starting to build samtools/forky/arm64 on jenkins on '2025-09-09 14:38' Tue Sep 9 14:38:38 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/95816/console.log Tue Sep 9 14:38:38 UTC 2025 I: Downloading source for forky/samtools=1.22.1-1 --2025-09-09 14:38:38-- http://deb.debian.org/debian/pool/main/s/samtools/samtools_1.22.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2266 (2.2K) [text/prs.lines.tag] Saving to: ‘samtools_1.22.1-1.dsc’ 0K .. 100% 257M=0s 2025-09-09 14:38:38 (257 MB/s) - ‘samtools_1.22.1-1.dsc’ saved [2266/2266] Tue Sep 9 14:38:38 UTC 2025 I: samtools_1.22.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.22.1-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://www.htslib.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/samtools Vcs-Git: https://salsa.debian.org/med-team/samtools.git Testsuite: autopkgtest Testsuite-Triggers: tabix Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl , libncurses-dev, libhts-dev (>= 1.22~), 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: 0709b89fe86790635f2ee3b96d2c69613127abd6 5742289 samtools_1.22.1.orig.tar.gz 5b0cf4c258c2541fa4a26b8e0ec9a7a2722a4733 22116 samtools_1.22.1-1.debian.tar.xz Checksums-Sha256: 55d233093fb831ea8b95b538de907f37be78862163029e7e91ab713e4744a208 5742289 samtools_1.22.1.orig.tar.gz b978ee6553de42b277b35e5e7254d795429422dc02daf608c6e0dcf7cd945071 22116 samtools_1.22.1-1.debian.tar.xz Files: c6140e6437d2cdea09b0e8dc195103c5 5742289 samtools_1.22.1.orig.tar.gz 2dcee5acb7ac69bf04c39008cc3c3875 22116 samtools_1.22.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEE3z4uQkp+J5wuSwI6ucKa7rL0UKcFAmiiQC8ACgkQucKa7rL0 UKd6MBAAhhACt4mdHsyiMGXbAInHdFNVLLmemPqteu2ZMCFEDHorn0ltC+l77Azb 5ITIfQjAiViQEOl+EE5KOVtTd09S7dJHEdhGW9byXAUpD40yROU3hATPyguVEMWi xbTjZoBkcgj3KZ5CCrU48W3yURVLN1wp3jZ4TwxFx5rV4soo2DQU75B3PxPt/Fae suWAUDCxFoVxczYDgtI1WkjA1q66TMOJJQIATKQO3UPV99rqxAIR5tOD8M9GM32p R/kaReKIGTk54srkGveg1HU3tjfrQm3NBDiFzJt7m2kLQXWje7cU7UXJ4WKVhdmE cj5Rnuk/JAr3e+bD/XQ+RUwcDXyH5jfRp341RPLJS/7v9muJnjmDrDEnD948gEcz Zguq0wA7ZclqIrAsGNjGGSTFC3nYZgrtj5AJJeOSPVk+J7pJBh/fr2XVkwEeIhGR eSLqhevS/5LFoz6lP1VPC45p2hidCIEamome+ZkNNjrxhOINsktLaiclI85gg3hT 7t3vzAk3Ek5ToETBeR1IV+9JbwDXLotW6vh+27bLFh9Bfh6xAs814nG0fCmm65Zx eh9kRbJCCc6OzCkiuHhO19x5uClSxRJUB2ZH5zKVWbQdPoLrzoN3p09gPKUK1reB hM3lsjzWxCDcYGozFD+JLilm9YA90MaZFk6nG7k3SezqBd6yzSQ= =urW3 -----END PGP SIGNATURE----- Tue Sep 9 14:38:38 UTC 2025 I: Checking whether the package is not for us Tue Sep 9 14:38:38 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Tue Sep 9 14:38:38 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Tue Sep 9 14:46:22 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 9 02:38:41 -12 2025 I: pbuilder-time-stamp: 1757428721 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_1.22.1-1.dsc] I: copying [./samtools_1.22.1.orig.tar.gz] I: copying [./samtools_1.22.1-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./samtools_1.22.1-1.dsc: no acceptable signature found dpkg-source: info: extracting samtools in samtools-1.22.1 dpkg-source: info: unpacking samtools_1.22.1.orig.tar.gz dpkg-source: info: unpacking samtools_1.22.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2637509/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='9cf5e3691cbe448397686291b088f373' 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='2637509' 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.TiC0FOk1/pbuilderrc_46Q2 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TiC0FOk1/b1 --logfile b1/build.log samtools_1.22.1-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2637509/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.22~), 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 ... 20012 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 (>= 1.22~); 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} comerr-dev{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} krb5-multidev{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} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libio-pty-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{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} libp11-kit0{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{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{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, 99 newly installed, 0 to remove and 0 not upgraded. Need to get 32.8 MB of archives. After unpacking 129 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 bash-completion all 1:2.16.0-7 [319 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.1-2 [93.9 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-1 [316 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 comerr-dev arm64 2.1-1.47.2-3+b3 [56.9 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.26 [91.8 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.14.2-1 [19.8 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.14.2-1 [8768 B] Get: 26 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.2 [582 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 debhelper all 13.26 [939 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 37 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.9-3 [1375 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.11.0-1 [121 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.11.0-1 [28.2 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.15.0-1 [355 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libunbound8 arm64 1.23.1-1 [561 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libgnutls-dane0t64 arm64 3.8.9-3 [453 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libgnutls-openssl27t64 arm64 3.8.9-3 [453 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libidn2-dev arm64 2.3.8-4 [102 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5 [329 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5 [621 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 libgnutls28-dev arm64 3.8.9-3 [1416 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 libldap-dev arm64 2.6.10+dfsg-1 [305 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libnghttp2-dev arm64 1.64.0-1.1+b1 [112 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 libnghttp3-dev arm64 1.8.0-1 [89.4 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.11.0-1 [33.9 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 libngtcp2-dev arm64 1.11.0-1 [174 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-3 [173 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 libssl-dev arm64 3.5.2-1 [3386 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libzstd-dev arm64 1.5.7+dfsg-1.1 [335 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 libcurl4-gnutls-dev arm64 8.15.0-1 [490 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libdeflate-dev arm64 1.23-2 [51.3 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 liblzma-dev arm64 5.8.1-1.1 [344 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 libhts-dev arm64 1.22.1+ds2-1 [1684 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 libio-pty-perl arm64 1:1.20-1+b3 [34.0 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libncurses-dev arm64 6.5+20250216-2 [340 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 tabix arm64 1.22.1+ds2-1 [469 kB] Fetched 32.8 MB in 1s (52.2 MB/s) Preconfiguring packages ... 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 ... 20012 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_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package bash-completion. Preparing to unpack .../02-bash-completion_1%3a2.16.0-7_all.deb ... Unpacking bash-completion (1:2.16.0-7) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../04-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.41.1-2_arm64.deb ... Unpacking bsdextrautils (2.41.1-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.20-1_arm64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../17-libcom-err2_1.47.2-3+b3_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../18-comerr-dev_2.1-1.47.2-3+b3_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../19-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../20-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../21-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../22-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../23-libfile-stripnondeterminism-perl_1.14.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../24-dh-strip-nondeterminism_1.14.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.2-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../25-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../26-dwz_0.16-2_arm64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../27-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../28-libxml2-16_2.14.5+dfsg-0.2_arm64.deb ... Unpacking libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../33-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../34-libk5crypto3_1.21.3-5_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../35-libkeyutils1_1.6.3-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../36-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../37-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../38-libgssrpc4t64_1.21.3-5_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../39-libkadm5clnt-mit12_1.21.3-5_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../40-libkdb5-10t64_1.21.3-5_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../41-libkadm5srv-mit12_1.21.3-5_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../42-krb5-multidev_1.21.3-5_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-5) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../43-libbrotli1_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../44-libbrotli-dev_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../45-libbz2-dev_1.0.8-6_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-6) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../46-libidn2-0_2.3.8-4_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-4) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../47-libffi8_3.4.8-2_arm64.deb ... Unpacking libffi8:arm64 (3.4.8-2) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../48-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../49-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../50-libgnutls30t64_3.8.9-3_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../51-libsasl2-modules-db_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../52-libsasl2-2_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../53-libldap2_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../54-libnghttp2-14_1.64.0-1.1+b1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../55-libnghttp3-9_1.8.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.8.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../56-libngtcp2-16_1.11.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../57-libngtcp2-crypto-gnutls8_1.11.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../58-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../59-librtmp1_2.4+20151223.gitfa8646d.1-3_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../60-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../61-libcurl3t64-gnutls_8.15.0-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.15.0-1) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../62-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:arm64. Preparing to unpack .../63-libunbound8_1.23.1-1_arm64.deb ... Unpacking libunbound8:arm64 (1.23.1-1) ... Selecting previously unselected package libgnutls-dane0t64:arm64. Preparing to unpack .../64-libgnutls-dane0t64_3.8.9-3_arm64.deb ... Unpacking libgnutls-dane0t64:arm64 (3.8.9-3) ... Selecting previously unselected package libgnutls-openssl27t64:arm64. Preparing to unpack .../65-libgnutls-openssl27t64_3.8.9-3_arm64.deb ... Unpacking libgnutls-openssl27t64:arm64 (3.8.9-3) ... Selecting previously unselected package libidn2-dev:arm64. Preparing to unpack .../66-libidn2-dev_2.3.8-4_arm64.deb ... Unpacking libidn2-dev:arm64 (2.3.8-4) ... Selecting previously unselected package libp11-kit-dev:arm64. Preparing to unpack .../67-libp11-kit-dev_0.25.5-3_arm64.deb ... Unpacking libp11-kit-dev:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6-dev:arm64. Preparing to unpack .../68-libtasn1-6-dev_4.20.0-2_arm64.deb ... Unpacking libtasn1-6-dev:arm64 (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../69-libgmpxx4ldbl_2%3a6.3.0+dfsg-5_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../70-libgmp-dev_2%3a6.3.0+dfsg-5_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package nettle-dev:arm64. Preparing to unpack .../71-nettle-dev_3.10.1-1_arm64.deb ... Unpacking nettle-dev:arm64 (3.10.1-1) ... Selecting previously unselected package libgnutls28-dev:arm64. Preparing to unpack .../72-libgnutls28-dev_3.8.9-3_arm64.deb ... Unpacking libgnutls28-dev:arm64 (3.8.9-3) ... Selecting previously unselected package libkrb5-dev:arm64. Preparing to unpack .../73-libkrb5-dev_1.21.3-5_arm64.deb ... Unpacking libkrb5-dev:arm64 (1.21.3-5) ... Selecting previously unselected package libldap-dev:arm64. Preparing to unpack .../74-libldap-dev_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap-dev:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../75-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../76-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../77-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:arm64. Preparing to unpack .../78-libnghttp2-dev_1.64.0-1.1+b1_arm64.deb ... Unpacking libnghttp2-dev:arm64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-dev:arm64. Preparing to unpack .../79-libnghttp3-dev_1.8.0-1_arm64.deb ... Unpacking libnghttp3-dev:arm64 (1.8.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:arm64. Preparing to unpack .../80-libngtcp2-crypto-gnutls-dev_1.11.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:arm64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-dev:arm64. Preparing to unpack .../81-libngtcp2-dev_1.11.0-1_arm64.deb ... Unpacking libngtcp2-dev:arm64 (1.11.0-1) ... Selecting previously unselected package libpsl-dev:arm64. Preparing to unpack .../82-libpsl-dev_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl-dev:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../83-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:arm64. Preparing to unpack .../84-librtmp-dev_2.4+20151223.gitfa8646d.1-3_arm64.deb ... Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssl-dev:arm64. Preparing to unpack .../85-libssl-dev_3.5.2-1_arm64.deb ... Unpacking libssl-dev:arm64 (3.5.2-1) ... Selecting previously unselected package libssh2-1-dev:arm64. Preparing to unpack .../86-libssh2-1-dev_1.11.1-1_arm64.deb ... Unpacking libssh2-1-dev:arm64 (1.11.1-1) ... Selecting previously unselected package libzstd-dev:arm64. Preparing to unpack .../87-libzstd-dev_1.5.7+dfsg-1.1_arm64.deb ... Unpacking libzstd-dev:arm64 (1.5.7+dfsg-1.1) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../88-libcurl4-gnutls-dev_8.15.0-1_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (8.15.0-1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../89-libdeflate0_1.23-2_arm64.deb ... Unpacking libdeflate0:arm64 (1.23-2) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../90-libdeflate-dev_1.23-2_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.23-2) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../91-libhtscodecs2_1.6.1-2_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.1-2) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../92-libhts3t64_1.22.1+ds2-1_arm64.deb ... Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../93-liblzma-dev_5.8.1-1.1_arm64.deb ... Unpacking liblzma-dev:arm64 (5.8.1-1.1) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../94-libhts-dev_1.22.1+ds2-1_arm64.deb ... Unpacking libhts-dev:arm64 (1.22.1+ds2-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../95-libio-pty-perl_1%3a1.20-1+b3_arm64.deb ... Unpacking libio-pty-perl (1:1.20-1+b3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../96-libncurses6_6.5+20250216-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5+20250216-2) ... Selecting previously unselected package libncurses-dev:arm64. Preparing to unpack .../97-libncurses-dev_6.5+20250216-2_arm64.deb ... Unpacking libncurses-dev:arm64 (6.5+20250216-2) ... Selecting previously unselected package tabix. Preparing to unpack .../98-tabix_1.22.1+ds2-1_arm64.deb ... Unpacking tabix (1.22.1+ds2-1) ... Setting up libhtscodecs2:arm64 (1.6.1-2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libzstd-dev:arm64 (1.5.7+dfsg-1.1) ... Setting up bsdextrautils (2.41.1-2) ... Setting up libio-pty-perl (1:1.20-1+b3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Setting up libdeflate0:arm64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:arm64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up autotools-dev (20240727.1) ... Setting up libunbound8:arm64 (1.23.1-1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5) ... Setting up bash-completion (1:2.16.0-7) ... Setting up libncurses6:arm64 (6.5+20250216-2) ... Setting up comerr-dev:arm64 (2.1-1.47.2-3+b3) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up libssl-dev:arm64 (3.5.2-1) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up libnghttp3-dev:arm64 (1.8.0-1) ... Setting up liblzma-dev:arm64 (5.8.1-1.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up libngtcp2-16:arm64 (1.11.0-1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up libdeflate-dev:arm64 (1.23-2) ... Setting up tabix (1.22.1+ds2-1) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b7) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.2-1) ... Setting up libncurses-dev:arm64 (6.5+20250216-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:arm64 (3.10.1-1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:arm64 (2.3.8-4) ... Setting up libngtcp2-dev:arm64 (1.11.0-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:arm64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.8-4) ... Setting up dh-strip-nondeterminism (1.14.2-1) ... Setting up groff-base (1.23.0-9) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libgnutls30t64:arm64 (3.8.9-3) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-3) ... Setting up libnghttp2-dev:arm64 (1.64.0-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-3) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:arm64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-5) ... Setting up libgnutls28-dev:arm64 (3.8.9-3) ... Setting up libkdb5-10t64:arm64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:arm64 (8.15.0-1) ... Setting up debhelper (13.26) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.11.0-1) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-5) ... Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... Setting up krb5-multidev:arm64 (1.21.3-5) ... Setting up libkrb5-dev:arm64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:arm64 (8.15.0-1) ... Setting up libhts-dev:arm64 (1.22.1+ds2-1) ... Processing triggers for libc-bin (2.41-12) ... 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-1.22.1/ && 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_1.22.1-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.22.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from samtools-1.22.1/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-1.22.1' rm -f config.mk touch config.mk dh_auto_clean -- make -j12 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/consensus && rm -f *.bam *.bam.csi cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.fa.fai 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-1.22.1' make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' 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-1.22.1' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... 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-1.22.1' 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-1.22.1' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j12 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.22.1"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/reproducible-path/samtools-1.22.1@«BUILDPATH»@g' version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_checksum.o bam_checksum.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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c 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-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o 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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o bam_checksum.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.22.1' make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' 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-1.22.1' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j12 test "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' 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-1.22.1/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.22.1/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.22.1/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.22.1/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.22.1/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.22.1/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.22.1/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.22.1/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/VYCxrIX1OA/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/VYCxrIX1OA/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/VYCxrIX1OA/bgzip.dat.gz .. ok /build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/VYCxrIX1OA/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/VYCxrIX1OA/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/VYCxrIX1OA/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/VYCxrIX1OA/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/VYCxrIX1OA/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/VYCxrIX1OA/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/VYCxrIX1OA/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/VYCxrIX1OA/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/VYCxrIX1OA/fqidx.fq 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/VYCxrIX1OA/fqidx.fq.gz 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/VYCxrIX1OA/fqidx.fq 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/VYCxrIX1OA/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/VYCxrIX1OA/fqidx.fq 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/VYCxrIX1OA/fqidx.fq.gz 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/VYCxrIX1OA/fqidx.fq 1:99998-100007 .. ok .. ok /build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/VYCxrIX1OA/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/reproducible-path/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/reproducible-path/samtools-1.22.1/test/dat/dict.fa .. ok test_dict: /build/reproducible-path/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/VYCxrIX1OA/dict.fa.gz .. ok test_dict: cat /build/reproducible-path/samtools-1.22.1/test/dat/dict.fa | /build/reproducible-path/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/reproducible-path/samtools-1.22.1/samtools dict -AH < /build/reproducible-path/samtools-1.22.1/test/dat/dict.alias.fa .. ok test_dict: /build/reproducible-path/samtools-1.22.1/samtools dict -H -l /build/reproducible-path/samtools-1.22.1/test/dat/dict.alt < /build/reproducible-path/samtools-1.22.1/test/dat/dict.alias.fa .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view /tmp/VYCxrIX1OA/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view /tmp/VYCxrIX1OA/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/VYCxrIX1OA/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/VYCxrIX1OA/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai /tmp/VYCxrIX1OA/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/VYCxrIX1OA/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -c /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam /tmp/VYCxrIX1OA/auto_indexed.csi && cat /tmp/VYCxrIX1OA/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.cram /tmp/VYCxrIX1OA/auto_indexed.crai && cat /tmp/VYCxrIX1OA/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -c /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.sam /tmp/VYCxrIX1OA/auto_indexed.csi && cat /tmp/VYCxrIX1OA/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 /tmp/VYCxrIX1OA/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 /tmp/VYCxrIX1OA/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/VYCxrIX1OA/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/VYCxrIX1OA/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai /tmp/VYCxrIX1OA/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/VYCxrIX1OA/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 -M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 -c /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam /tmp/VYCxrIX1OA/auto_indexed.csi && cat /tmp/VYCxrIX1OA/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.cram /tmp/VYCxrIX1OA/auto_indexed.crai && cat /tmp/VYCxrIX1OA/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 -c /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.sam /tmp/VYCxrIX1OA/auto_indexed.csi && cat /tmp/VYCxrIX1OA/auto_indexed.csi .. ok test_mpileup: /build/reproducible-path/samtools-1.22.1/samtools mpileup -b /tmp/VYCxrIX1OA/mpileup.bam.list -f /tmp/VYCxrIX1OA/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.22.1/samtools mpileup -b /tmp/VYCxrIX1OA/mpileup.cram.list -f /tmp/VYCxrIX1OA/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.22.1/samtools mpileup -b /tmp/VYCxrIX1OA/mpileup.bam.urllist -f /tmp/VYCxrIX1OA/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.22.1/samtools mpileup -b /tmp/VYCxrIX1OA/mpileup.cram.urllist -f /tmp/VYCxrIX1OA/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.22.1/samtools mpileup -B --ff 0x14 -f /tmp/VYCxrIX1OA/mpileup.ref.fa.gz -r17:1050-1060 /tmp/VYCxrIX1OA/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.22.1/samtools mpileup -B --ff 0x14 -f /tmp/VYCxrIX1OA/mpileup.ref.fa.gz -r17:1050-1060 /tmp/VYCxrIX1OA/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.22.1/samtools mpileup /build/reproducible-path/samtools-1.22.1/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, checksum, 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 checksum Usage on stderr rather than stdout .. expected failure 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/VYCxrIX1OA/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/VYCxrIX1OA/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/VYCxrIX1OA/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/VYCxrIX1OA/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/VYCxrIX1OA/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/VYCxrIX1OA/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/VYCxrIX1OA/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/VYCxrIX1OA/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/VYCxrIX1OA/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/VYCxrIX1OA/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/VYCxrIX1OA/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/VYCxrIX1OA/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/VYCxrIX1OA/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/VYCxrIX1OA/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/VYCxrIX1OA/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/VYCxrIX1OA/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/VYCxrIX1OA/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/VYCxrIX1OA/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/VYCxrIX1OA/view.001.forn (SAM input) .. ok 68: Count -N /tmp/VYCxrIX1OA/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/VYCxrIX1OA/view.001.forn (BAM input) .. ok 70: Count -N /tmp/VYCxrIX1OA/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/VYCxrIX1OA/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/VYCxrIX1OA/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/VYCxrIX1OA/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/VYCxrIX1OA/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/VYCxrIX1OA/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/VYCxrIX1OA/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/VYCxrIX1OA/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/VYCxrIX1OA/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/VYCxrIX1OA/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/VYCxrIX1OA/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/VYCxrIX1OA/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/VYCxrIX1OA/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/VYCxrIX1OA/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/VYCxrIX1OA/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/VYCxrIX1OA/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/VYCxrIX1OA/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/VYCxrIX1OA/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/VYCxrIX1OA/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/VYCxrIX1OA/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/VYCxrIX1OA/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/VYCxrIX1OA/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/VYCxrIX1OA/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/VYCxrIX1OA/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/VYCxrIX1OA/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/VYCxrIX1OA/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/VYCxrIX1OA/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-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test115.sam -h -d TGCA /tmp/VYCxrIX1OA/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-1.22.1/samtools view -c -d TGCA /tmp/VYCxrIX1OA/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-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test117.sam -h -d TGCA /tmp/VYCxrIX1OA/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-1.22.1/samtools view -c -d TGCA /tmp/VYCxrIX1OA/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-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test119.sam -h -d TGCA /tmp/VYCxrIX1OA/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-1.22.1/samtools view -c -d TGCA /tmp/VYCxrIX1OA/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/VYCxrIX1OA/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VYCxrIX1OA/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test121.sam -h -D BClong:/tmp/VYCxrIX1OA/view.001.fobc /tmp/VYCxrIX1OA/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/VYCxrIX1OA/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VYCxrIX1OA/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.22.1/samtools view -c -D BClong:/tmp/VYCxrIX1OA/view.001.fobc /tmp/VYCxrIX1OA/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/VYCxrIX1OA/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VYCxrIX1OA/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test123.sam -h -D BClong:/tmp/VYCxrIX1OA/view.001.fobc /tmp/VYCxrIX1OA/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/VYCxrIX1OA/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VYCxrIX1OA/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.22.1/samtools view -c -D BClong:/tmp/VYCxrIX1OA/view.001.fobc /tmp/VYCxrIX1OA/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/VYCxrIX1OA/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VYCxrIX1OA/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test125.sam -h -D BClong:/tmp/VYCxrIX1OA/view.001.fobc /tmp/VYCxrIX1OA/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/VYCxrIX1OA/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VYCxrIX1OA/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.22.1/samtools view -c -D BClong:/tmp/VYCxrIX1OA/view.001.fobc /tmp/VYCxrIX1OA/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-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/VYCxrIX1OA/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-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/VYCxrIX1OA/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-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/VYCxrIX1OA/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-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/VYCxrIX1OA/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-1.22.1/samtools view -o /tmp/VYCxrIX1OA/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/VYCxrIX1OA/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-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/VYCxrIX1OA/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-1.22.1/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 406: -L with nested regions .. ok 407: Make BAM with no M5/UR tags .. ok 408: Add @SQ with -t (SAM -> SAM) .. ok 409: Add @SQ with -T (SAM -> SAM) .. ok 410: Add @SQ with -t (BAM -> SAM) .. ok 411: Add @SQ with -T (BAM -> SAM) .. ok 412: Add @SQ with -t (SAM -> BAM) .. ok 413: Add @SQ with -T (SAM -> BAM) .. ok 414: Add @SQ with -t (BAM -> BAM) .. ok 415: Add @SQ with -T (BAM -> BAM) .. ok 416: Add @SQ with -t (SAM -> CRAM) .. ok 417: Add @SQ with -T (SAM -> CRAM) .. ok 418: Add @SQ with -t (BAM -> CRAM) .. ok 419: Add @SQ with -T (BAM -> CRAM) .. ok 420: Make CRAM with no UR field .. ok 421: Decoding CRAM with no UR field via -T .. ok 422: CIGAR B-operator removal .. ok 423: Big SAM -> BAM .. ok 424: Big SAM -> BAM (2 threads) .. ok 425: Big SAM -> BAM (4 threads) .. ok 426: Big SAM -> CRAM .. ok 427: Big SAM -> CRAM (2 threads) .. ok 428: Big SAM -> CRAM (4 threads) .. ok 429: Subsample 0.2 (SAM input) ............ ok 430: Subsample 0.5 (SAM input) ............ ok 431: Subsample 0.8 (SAM input) ............ ok 432: Subsample 0.2 (BAM input) ............ ok 433: Subsample 0.5 (BAM input) ............ ok 434: Subsample 0.8 (BAM input) ............ ok 435: Subsample 0.2 (CRAM input) ............ ok 436: Subsample 0.5 (CRAM input) ............ ok 437: Subsample 0.8 (CRAM input) ............ ok 438: SAM add PG .. ok 439: Unset dup flag, remove dt and do tags .. ok 440: Unmap dup flagged reads. .. ok 441: Unmap dup flagged reads. .. ok 442: fetch pairs .. ok 443: fetch pairs .. ok 444: fetch pairs .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -h 0 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -h 1 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -h 5 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -h 29 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -h 30 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -n 0 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -n 1 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -n 5 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.22.1/samtools head -h 5 -n 5 < /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate BAM region file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate BAM region file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate BAM region file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate BAM region 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 CRAM subregion files .. ok 5: cat BAM files to stdout .. ok 6: cat recompressed BAM files to stdout .. ok 7: cat CRAM files to stdout .. ok 8: cat CRAM subregion files to stdout .. ok 9: cat CRAM part 1/2 .. ok 9: cat CRAM part 2/2 .. ok 9: cat CRAM parts 1/2 + 2/2 .. ok 10: cat BAM files with new header .. ok 11: cat recompressed BAM files with new header .. ok 12: cat CRAM files with new header .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -0 /build/reproducible-path/samtools-1.22.1/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -0 /build/reproducible-path/samtools-1.22.1/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -s /build/reproducible-path/samtools-1.22.1/test/s.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -N -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T RG,BC,QT -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.22.1/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-1.22.1/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-1.22.1/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-1.22.1/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /build/reproducible-path/samtools-1.22.1/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-1.22.1/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-1.22.1/samtools fastq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.22.1/test/bc_split.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -t -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -t -T MD,ia -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/i.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.22.1/test/i.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -1 /build/reproducible-path/samtools-1.22.1/test/o.fq -2 /build/reproducible-path/samtools-1.22.1/test/o.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fasta -N -1 /build/reproducible-path/samtools-1.22.1/test/o.fa -2 /build/reproducible-path/samtools-1.22.1/test/o.fa /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -o /build/reproducible-path/samtools-1.22.1/test/o.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -s /tmp/VYCxrIX1OA/bam2fq.discard.s.fq -0 /tmp/VYCxrIX1OA/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.22.1/test/i1.fq --i2 /build/reproducible-path/samtools-1.22.1/test/i2.fq -0 /build/reproducible-path/samtools-1.22.1/test/0.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T '' /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -t -T '*' /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T '*' -d ia /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.22.1/test/bc_split.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -t -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -t -T MD,ia -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/i.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.22.1/test/i.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -1 /build/reproducible-path/samtools-1.22.1/test/o.fq -2 /build/reproducible-path/samtools-1.22.1/test/o.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fasta -@ 2 -N -1 /build/reproducible-path/samtools-1.22.1/test/o.fa -2 /build/reproducible-path/samtools-1.22.1/test/o.fa /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -o /build/reproducible-path/samtools-1.22.1/test/o.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -s /tmp/VYCxrIX1OA/bam2fq.discard.s.fq -0 /tmp/VYCxrIX1OA/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.22.1/test/i1.fq --i2 /build/reproducible-path/samtools-1.22.1/test/i2.fq -0 /build/reproducible-path/samtools-1.22.1/test/0.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -T '' /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -t -T '*' /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d ia /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa -i 0 /build/reproducible-path/samtools-1.22.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -S RG -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -S RG -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -t /build/reproducible-path/samtools-1.22.1/test/stat/11.stats.targets /build/reproducible-path/samtools-1.22.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -g 4 -t /build/reproducible-path/samtools-1.22.1/test/stat/11.stats.targets /build/reproducible-path/samtools-1.22.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -g 4 /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.22.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.22.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.22.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.22.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/reproducible-path/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/reproducible-path/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/reproducible-path/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -I s1 /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -I grp2 /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -I grp3 /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -I Sample /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/mpileup/ce.fa /build/reproducible-path/samtools-1.22.1/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam -b /tmp/QG5doVCp5f - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -r -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -cp -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -o - -s 1 -O sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/VYCxrIX1OA/merge.tag.1.bam /tmp/VYCxrIX1OA/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/VYCxrIX1OA/merge.tag.3.bam /tmp/VYCxrIX1OA/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge --no-PG -O SAM - /build/reproducible-path/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.22.1/test/merge/merge.bed - /tmp/VYCxrIX1OA/merge.bed.1.bam /tmp/VYCxrIX1OA/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge --no-PG -r -O SAM - /build/reproducible-path/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.22.1/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.22.1/test/merge/test_template_coordinate.2.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/yG72GUzobI - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -r -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -cp -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -o - -s 1 -O sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/VYCxrIX1OA/merge.tag.1.bam /tmp/VYCxrIX1OA/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/VYCxrIX1OA/merge.tag.3.bam /tmp/VYCxrIX1OA/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM - /build/reproducible-path/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.22.1/test/merge/merge.bed - /tmp/VYCxrIX1OA/merge.bed.1.bam /tmp/VYCxrIX1OA/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 --no-PG -r -O SAM - /build/reproducible-path/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.22.1/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.22.1/test/merge/test_template_coordinate.2.sam .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/VYCxrIX1OA/sortout .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -f /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/VYCxrIX1OA/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -o /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/VYCxrIX1OA/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -n -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -N -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -n -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -t RG -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -n -t RG -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -t AS -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -t FI -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort --template-coordinate -m 10M /build/reproducible-path/samtools-1.22.1/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -m 10M -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -m 10M -M -K10 -I /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -m 10M -MH -K10 -I /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/VYCxrIX1OA/sortout .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/VYCxrIX1OA/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/VYCxrIX1OA/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -N -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -t RG -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -n -t RG -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -t AS -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -t FI -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 --template-coordinate -m 10M /build/reproducible-path/samtools-1.22.1/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -m 10M -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -m 10M -M -K10 -I /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -m 10M -MH -K10 -I /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate --output-fmt=sam -O /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate -o /build/reproducible-path/samtools-1.22.1/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate -o /build/reproducible-path/samtools-1.22.1/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.22.1/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate --output-fmt=sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.22.1/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate --output-fmt=sam -f /build/reproducible-path/samtools-1.22.1/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.22.1/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.22.1/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.22.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -O /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.22.1/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.22.1/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.22.1/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.22.1/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -f /build/reproducible-path/samtools-1.22.1/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.22.1/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.22.1/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.22.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -cO sam /build/reproducible-path/samtools-1.22.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -cO sam /build/reproducible-path/samtools-1.22.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.22.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.22.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_bounds.sam - .. ok /build/reproducible-path/samtools-1.22.1/samtools calmd -uAr /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa .. ok /build/reproducible-path/samtools-1.22.1/samtools calmd -@ 2 -uAr /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/reproducible-path/samtools-1.22.1/samtools idxstats /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/reproducible-path/samtools-1.22.1/samtools idxstats /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/reproducible-path/samtools-1.22.1/samtools idxstats /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck -v /build/reproducible-path/samtools-1.22.1/test/quickcheck/1.quickcheck.badeof.bam /build/reproducible-path/samtools-1.22.1/test/quickcheck/2.quickcheck.badheader.bam /build/reproducible-path/samtools-1.22.1/test/quickcheck/3.quickcheck.ok.bam /build/reproducible-path/samtools-1.22.1/test/quickcheck/4.quickcheck.ok.bam /build/reproducible-path/samtools-1.22.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/6.quickcheck.cram21.ok.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/7.quickcheck.cram30.ok.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/reproducible-path/samtools-1.22.1/samtools quickcheck -uv /build/reproducible-path/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/reproducible-path/samtools-1.22.1/samtools reheader /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.22.1/samtools reheader /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v21.cram | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.22.1/samtools reheader /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.22.1/samtools reheader --in-place /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v21.cram && /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.22.1/samtools reheader --in-place /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v30.cram && /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.22.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.22.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -m overwrite_all /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -m orphan_only /build/reproducible-path/samtools-1.22.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -R '1#9' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.22.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.22.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/reproducible-path/samtools-1.22.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.22.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.22.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam -r --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -S -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.22.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.22.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/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-1.22.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/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-1.22.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/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-1.22.1/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/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-1.22.1/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.22.1/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/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-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam -r --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.22.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.22.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/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-1.22.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/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-1.22.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/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-1.22.1/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/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-1.22.1/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.22.1/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /build/reproducible-path/samtools-1.22.1/samtools bedcov /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.22.1/samtools bedcov -j /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.22.1/samtools bedcov -g512 -G2048 /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.22.1/samtools bedcov -c /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bam .. ok .. ok .. ok .. ok .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -d an -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.22.1/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.22.1/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d an -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.22.1/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.22.1/test/split/split_d_nn.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG /tmp/VYCxrIX1OA/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG /tmp/VYCxrIX1OA/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.22.1/test/large_pos/test.bed /tmp/VYCxrIX1OA/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools sort -O sam --no-PG -m 10M /build/reproducible-path/samtools-1.22.1/test/large_pos/longref_name.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools merge -O sam --no-PG - /build/reproducible-path/samtools-1.22.1/test/large_pos/longref.sam /build/reproducible-path/samtools-1.22.1/test/large_pos/longref2.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools depth /build/reproducible-path/samtools-1.22.1/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools depth -b /build/reproducible-path/samtools-1.22.1/test/large_pos/test.bed /build/reproducible-path/samtools-1.22.1/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/VYCxrIX1OA/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.22.1/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam --no-PG - - | /build/reproducible-path/samtools-1.22.1/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /build/reproducible-path/samtools-1.22.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_hard_clipped.expected.sam /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_soft_clipped.expected.sam /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/reproducible-path/samtools-1.22.1/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.22.1/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.22.1/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.22.1/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag | /build/reproducible-path/samtools-1.22.1/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag < /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.22.1/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.22.1/samtools view .. ok test_reset: cat /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.cram .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG sam_to_fixed_bam /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index --no-PG /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/reset/seq.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.22.1/samtools reset /build/reproducible-path/samtools-1.22.1/test/reset/seq.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum /build/reproducible-path/samtools-1.22.1/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -a /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -qv /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -qv -a /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -m /build/reproducible-path/samtools-1.22.1/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -m /build/reproducible-path/samtools-1.22.1/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 /build/reproducible-path/samtools-1.22.1/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -a /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -qv /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -qv -a /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -m /build/reproducible-path/samtools-1.22.1/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -m /build/reproducible-path/samtools-1.22.1/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok Number of tests: total .. 1009 passed .. 964 failed .. 0 expected failure .. 45 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: 55 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: 77 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" PARAM="-@4 -Z4" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 77 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-1.22.1' rm -fr -- /tmp/dh-xdg-rundir-_yaNgekb make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' 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-1.22.1' dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.22.1/debian/tmp make -j12 install DESTDIR=/build/reproducible-path/samtools-1.22.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' mkdir -p -m 755 /build/reproducible-path/samtools-1.22.1/debian/tmp/usr/bin /build/reproducible-path/samtools-1.22.1/debian/tmp/usr/bin /build/reproducible-path/samtools-1.22.1/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.22.1/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-1.22.1/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-1.22.1/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/reproducible-path/samtools-1.22.1/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/samtools-1.22.1' make clean make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/consensus && rm -f *.bam *.bam.csi cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.fa.fai 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-1.22.1' make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/samtools-1.22.1' 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-1.22.1' 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-1.22.1' dh_installchangelogs NEWS.md install -m0755 -d debian/samtools/usr/share/doc/samtools install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog 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 make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' 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-1.22.1' # 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-1.22.1' dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-checksum.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-checksum.1.dh-new debian/samtools/usr/share/man/man1/samtools-checksum.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-checksum.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 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 1755458966 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1755458966 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-test cd debian/samtools chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian gzip -9nf 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-checksum.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/reproducible-path/samtools-1.22.1' 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-checksum.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/reproducible-path/samtools-1.22.1' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/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 debian/rules execute_after_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/samtools-1.22.1' chmod -x /build/reproducible-path/samtools-1.22.1/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' dh_missing dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 868896 new size 890669 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3/a76d6fa371b00bf6f5e9649926ddd5dc63d52f.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3/a76d6fa371b00bf6f5e9649926ddd5dc63d52f.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/a3/a76d6fa371b00bf6f5e9649926ddd5dc63d52f.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/24 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/24/45018a3e625f18c0280f463521e2d7bac62591.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/24/45018a3e625f18c0280f463521e2d7bac62591.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/24/45018a3e625f18c0280f463521e2d7bac62591.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2/a9efab1894ad9775b7f3f304d855a0c466932e.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2/a9efab1894ad9775b7f3f304d855a0c466932e.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/f2/a9efab1894ad9775b7f3f304d855a0c466932e.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/73 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/73/73bef9066328ade272e6b14dcfe269d8c32fba.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/73/73bef9066328ade272e6b14dcfe269d8c32fba.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/73/73bef9066328ade272e6b14dcfe269d8c32fba.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd/54a7f6c0f6108349d88170ce04c437b4d603ff.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd/54a7f6c0f6108349d88170ce04c437b4d603ff.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/fd/54a7f6c0f6108349d88170ce04c437b4d603ff.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b5 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b5/fa58b405bc497e420cb12b73dc2b1b67becad9.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b5/fa58b405bc497e420cb12b73dc2b1b67becad9.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/b5/fa58b405bc497e420cb12b73dc2b1b67becad9.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3/8e83537c33b4a1846fca52f358dbc25724d6d6.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3/8e83537c33b4a1846fca52f358dbc25724d6d6.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/a3/8e83537c33b4a1846fca52f358dbc25724d6d6.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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=2445018a3e625f18c0280f463521e2d7bac62591 7373bef9066328ade272e6b14dcfe269d8c32fba a38e83537c33b4a1846fca52f358dbc25724d6d6 a3a76d6fa371b00bf6f5e9649926ddd5dc63d52f b5fa58b405bc497e420cb12b73dc2b1b67becad9 f2a9efab1894ad9775b7f3f304d855a0c466932e fd54a7f6c0f6108349d88170ce04c437b4d603ff" -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 dpkg-gencontrol: warning: package samtools-test: 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 chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools-test/DEBIAN install -m0755 -d debian/samtools/DEBIAN cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.22.1-1_arm64.deb'. dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.22.1-1_all.deb'. dpkg-deb: building package 'samtools' in '../samtools_1.22.1-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.22.1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../samtools_1.22.1-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.22.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2637509 and its subdirectories I: Current time: Tue Sep 9 02:45:59 -12 2025 I: pbuilder-time-stamp: 1757429159 Tue Sep 9 14:46:24 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Tue Sep 9 14:46:24 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Tue Sep 9 14:48:34 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Tue Sep 9 14:48:35 UTC 2025 I: samtools_1.22.1-1_arm64.changes: Format: 1.8 Date: Sun, 17 Aug 2025 21:29:26 +0200 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: arm64 all Version: 1.22.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats samtools-test - test files for the samtools package Changes: samtools (1.22.1-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.7.2 (routine-update) Checksums-Sha1: a83d44c00d3c49456e3ab0fbedc78c001ec96d86 1034284 samtools-dbgsym_1.22.1-1_arm64.deb ed83614982fd726624c7429f80f1ea8c4d9052b2 2389308 samtools-test_1.22.1-1_all.deb 6ff0ffeea8bfa24da51f5e8c1d75d438f9e1e8ff 7414 samtools_1.22.1-1_arm64.buildinfo e94d028801373a70d083d0f2f5677b1184f0bdb4 665736 samtools_1.22.1-1_arm64.deb Checksums-Sha256: f94179404e739b3f2cb9dc4cfc1c784ba8def758f3d05aeb39978c88a5a9b299 1034284 samtools-dbgsym_1.22.1-1_arm64.deb 4e4341beed458f2f4ed91eb19d440427757f449726e00a8814ad408de3686bc1 2389308 samtools-test_1.22.1-1_all.deb d08313695bafece1d0b7602ff8db56bba4dc66a587d53eb1a0a54b34fa9ddffe 7414 samtools_1.22.1-1_arm64.buildinfo b4347dc207e520e529579704094e9cf62437160894ddef86a98cb537adeac903 665736 samtools_1.22.1-1_arm64.deb Files: a8c4b1d1b12a0550b73f7ac59af62abe 1034284 debug optional samtools-dbgsym_1.22.1-1_arm64.deb 9e0dcabc8f81eec341de742dd700d993 2389308 science optional samtools-test_1.22.1-1_all.deb af4bc671da13873a67d89c125126913b 7414 science optional samtools_1.22.1-1_arm64.buildinfo b97753e0a916277e0696037b81732151 665736 science optional samtools_1.22.1-1_arm64.deb Tue Sep 9 14:48:36 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_7-95816.service; invocation ID: 7a73cbf410ff4c7b811cdf77f83e9b20 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.TiC0FOk1/samtools_1.22.1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TiC0FOk1/samtools_1.22.1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TiC0FOk1/samtools_1.22.1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TiC0FOk1/b1/samtools_1.22.1-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.TiC0FOk1/b2/samtools_1.22.1-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 233ms CPU time consumed: 176ms Memory peak: 17.5M (swap: 0B) Tue Sep 9 14:48:36 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Sep 9 14:48:36 UTC 2025 I: samtools from forky built successfully and reproducibly on arm64. Tue Sep 9 14:48:37 UTC 2025 I: Removing signed samtools_1.22.1-1_arm64.buildinfo.asc files: removed './b1/samtools_1.22.1-1_arm64.buildinfo.asc' removed './b2/samtools_1.22.1-1_arm64.buildinfo.asc'