Running as unit: rb-build-armhf_10-6067.service ==================================================================================== Fri Nov 22 17:31:11 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_armhf_10) on jenkins, called using "wbq0-armhf-rb virt64a-armhf-rb" as arguments. Fri Nov 22 17:31:11 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-K0zZnBvW" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 17:31:11 UTC 2024 - checking /var/lib/jenkins/offline_nodes if wbq0-armhf-rb.debian.net is marked as down. Fri Nov 22 17:31:11 UTC 2024 - checking via ssh if wbq0-armhf-rb.debian.net is up. removed '/tmp/read-only-fs-test-MoS0a6' Fri Nov 22 17:31:14 UTC 2024 - checking /var/lib/jenkins/offline_nodes if virt64a-armhf-rb.debian.net is marked as down. Fri Nov 22 17:31:14 UTC 2024 - checking via ssh if virt64a-armhf-rb.debian.net is up. removed '/tmp/read-only-fs-test-luqtAk' ok, let's check if samtools is building anywhere yet… ok, samtools is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of samtools in experimental on armhf on jenkins now. 1st build will be done on wbq0-armhf-rb.debian.net. 2nd build will be done on virt64a-armhf-rb.debian.net. ============================================================================= Fri Nov 22 17:31:31 UTC 2024 I: starting to build samtools/experimental/armhf on jenkins on '2024-11-22 17:31' Fri Nov 22 17:31:31 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_10/6067/console.log 1732296691 armhf experimental samtools Fri Nov 22 17:31:31 UTC 2024 I: Downloading source for experimental/samtools=1.21-0+exp1 --2024-11-22 17:31:32-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/samtools/samtools_1.21-0%2bexp1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2272 (2.2K) [text/prs.lines.tag] Saving to: ‘samtools_1.21-0+exp1.dsc’ 0K .. 100% 275M=0s 2024-11-22 17:31:32 (275 MB/s) - ‘samtools_1.21-0+exp1.dsc’ saved [2272/2272] --2024-11-22 17:31:32-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/samtools/samtools_1.21-0%2bexp1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2272 (2.2K) [text/prs.lines.tag] Saving to: ‘samtools_1.21-0+exp1.dsc’ 0K .. 100% 275M=0s 2024-11-22 17:31:32 (275 MB/s) - ‘samtools_1.21-0+exp1.dsc’ saved [2272/2272] Fri Nov 22 17:31:32 UTC 2024 I: samtools_1.21-0+exp1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.21-0+exp1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://www.htslib.org/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/samtools Vcs-Git: https://salsa.debian.org/med-team/samtools.git Testsuite: autopkgtest Testsuite-Triggers: tabix Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl , libncurses-dev, libhts-dev (>= 1.21~), 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: fbca1838a28b3b74acd2db307e3060ee28683626 5682709 samtools_1.21.orig.tar.gz 61de9e05555a8086a152ca83553239a19c29b08d 22052 samtools_1.21-0+exp1.debian.tar.xz Checksums-Sha256: b327b85d3d60771ede370c8bcae0570e7704da39abddfe8e930a85b80aabffac 5682709 samtools_1.21.orig.tar.gz 09977260dcb343190558529b1ba1aaccc3c0a9914c61eeb6b56a3e1252d0e64f 22052 samtools_1.21-0+exp1.debian.tar.xz Files: 2c02716872a6b36be66591448ecbe8c4 5682709 samtools_1.21.orig.tar.gz 93aa2747f5933e7fa62b6e58054f6034 22052 samtools_1.21-0+exp1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmc2T8sACgkQPCZ2P2xn 5uJ4AA//QkQEICyCuSe99m4/JwcENIYfQkr350D9+e8HfTPeHZozN50Z7FXFa3H6 EcPWWZTwws2QIzAJ8BksjBLIPx6t3RMGvNyuSa7rFJpMtv78lZQTGDnq00oPP0Z/ uZV6FbtP3YOCgFYxbh6fR9THfra6Ouh6khSJ2dWMoekNWmplds1h8jr8cGBrqhRp Tb7zB8QDIEC0UtjjKOIiML24Ra2v07+EAANVsU2lNH4iQVzlt06V+42mdq8m/xU3 gPmTmmLzWNGGa8cDBCHdlJkf9Ae9VGyvKamVCWn3N1PDbRUHmsGL+0omvw9wT03J DG73N21MM+CbF6KMwt7XC+ZdfVkADqUqiK5kEruiPYDiHlEA3JVb5kHMA/AA+OOv F7I7Gr6wEBmanfKxVTitBad8grzHc6Q3H6U6I79GEZe2K3ngZ0rHdFpf/rMPP7AB tXkj9xnIFH51aHhvU2mdd8xAzVb7wwKM19fUHBlo2TK7N0ALQI8T8jcTasBH+ebE /HdJA6H+WfE5PytNf0IlA/YTrWA/8nj5pJQJV7sPG0kdo/fJ8GTWLq2cC2/5xgiP CqusKkAiI5EvKxLlFbspvjcOekxlim9VLg7HtqoNWN0l3BVtdsDmz5VizpOWnFaN s+gddiF8JKf9+NV/1i/NdF+rLah8EE3I4KdQM3lfn3PRwWtynU0= =F6QJ -----END PGP SIGNATURE----- Fri Nov 22 17:31:32 UTC 2024 I: Checking whether the package is not for us Fri Nov 22 17:31:32 UTC 2024 I: Starting 1st build on remote node wbq0-armhf-rb.debian.net. Fri Nov 22 17:31:32 UTC 2024 I: Preparing to do remote build '1' on wbq0-armhf-rb.debian.net. Fri Nov 22 17:31:32 UTC 2024 - checking /var/lib/jenkins/offline_nodes if wbq0-armhf-rb.debian.net is marked as down. Fri Nov 22 17:31:32 UTC 2024 - checking via ssh if wbq0-armhf-rb.debian.net is up. removed '/tmp/read-only-fs-test-OfRqYC' ==================================================================================== Fri Nov 22 17:31:37 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on wbq0, called using "1 samtools experimental /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi 1.21-0+exp1" as arguments. Fri Nov 22 17:31:37 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-TIFAzemq" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 17:31:37 UTC 2024 I: Downloading source for experimental/samtools=1.21-0+exp1 Reading package lists... NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools.git Please use: git clone https://salsa.debian.org/med-team/samtools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5707 kB of source archives. Get:1 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (dsc) [2272 B] Get:2 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (tar) [5683 kB] Get:3 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (diff) [22.1 kB] Fetched 5707 kB in 1s (4784 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools.git Please use: git clone https://salsa.debian.org/med-team/samtools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5707 kB of source archives. Get:1 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (dsc) [2272 B] Get:2 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (tar) [5683 kB] Get:3 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (diff) [22.1 kB] Fetched 5707 kB in 1s (4784 kB/s) Download complete and in download only mode ============================================================================= Building samtools in experimental on armhf on wbq0 now. Date: Fri Nov 22 09:31:39 PST 2024 Date UTC: Fri Nov 22 17:31:39 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 22 05:31:41 -12 2024 I: pbuilder-time-stamp: 1732296701 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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_1.21-0+exp1.dsc] I: copying [./samtools_1.21.orig.tar.gz] I: copying [./samtools_1.21-0+exp1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 14 19:30:19 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./samtools_1.21-0+exp1.dsc: no acceptable signature found dpkg-source: info: extracting samtools in samtools-1.21 dpkg-source: info: unpacking samtools_1.21.orig.tar.gz dpkg-source: info: unpacking samtools_1.21-0+exp1.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/6550/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='c1a3c51aae2d4667b8d039d1ac72f79b' 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='6550' 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.RfmZQeJi/pbuilderrc_Qrp7 --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b1 --logfile b1/build.log samtools_1.21-0+exp1.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux wbq0 6.1.0-27-armmp #1 SMP Debian 6.1.115-1 (2024-11-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/6550/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.21~), 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 ... 19686 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 (>= 1.21~); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on automake; however: Package automake is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 22.5 MB of archives. After unpacking 84.3 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libhts-dev (>= 1.21~) but it is not going to be installed The following actions will resolve these dependencies: Install the following packages: 1) comerr-dev [2.1-1.47.1-1+b1 (unstable)] 2) krb5-multidev [1.21.3-3 (unstable)] 3) libbrotli-dev [1.1.0-2+b6 (unstable)] 4) libbrotli1 [1.1.0-2+b6 (unstable)] 5) libcom-err2 [1.47.1-1+b1 (unstable)] 6) libcurl3t64-gnutls [8.11.0-1 (unstable)] 7) libcurl4-gnutls-dev [8.11.0-1 (unstable)] 8) libdeflate-dev [1.22-1 (unstable)] 9) libevent-2.1-7t64 [2.1.12-stable-10+b1 (unstable)] 10) libgmp-dev [2:6.3.0+dfsg-2+b2 (unstable)] 11) libgmpxx4ldbl [2:6.3.0+dfsg-2+b2 (unstable)] 12) libgnutls-dane0t64 [3.8.8-2 (unstable)] 13) libgnutls-openssl27t64 [3.8.8-2 (unstable)] 14) libgnutls28-dev [3.8.8-2 (unstable)] 15) libgssapi-krb5-2 [1.21.3-3 (unstable)] 16) libgssrpc4t64 [1.21.3-3 (unstable)] 17) libhts-dev [1.21+ds-0+exp2 (experimental)] 18) libhts3t64 [1.21+ds-0+exp2 (experimental)] 19) libidn2-dev [2.3.7-2+b1 (unstable)] 20) libk5crypto3 [1.21.3-3 (unstable)] 21) libkadm5clnt-mit12 [1.21.3-3 (unstable)] 22) libkadm5srv-mit12 [1.21.3-3 (unstable)] 23) libkdb5-10t64 [1.21.3-3 (unstable)] 24) libkeyutils1 [1.6.3-4 (unstable)] 25) libkrb5-3 [1.21.3-3 (unstable)] 26) libkrb5-dev [1.21.3-3 (unstable)] 27) libkrb5support0 [1.21.3-3 (unstable)] 28) libldap-2.5-0 [2.5.18+dfsg-3+b1 (unstable)] 29) libldap-dev [2.6.8+dfsg-1~exp4+b1 (experimental)] 30) libldap2 [2.6.8+dfsg-1~exp4+b1 (experimental)] 31) libnghttp2-14 [1.64.0-1 (unstable)] 32) libnghttp2-dev [1.64.0-1 (unstable)] 33) libnghttp3-9 [1.4.0-1+b1 (unstable)] 34) libnghttp3-dev [1.4.0-1+b1 (unstable)] 35) libngtcp2-16 [1.6.0-1 (unstable)] 36) libngtcp2-crypto-gnutls-dev [1.6.0-1 (unstable)] 37) libngtcp2-crypto-gnutls8 [1.6.0-1 (unstable)] 38) libngtcp2-dev [1.6.0-1 (unstable)] 39) libp11-kit-dev [0.25.5-2+b1 (unstable)] 40) libpsl-dev [0.21.2-1.1+b1 (unstable)] 41) libpsl5t64 [0.21.2-1.1+b1 (unstable)] 42) librtmp-dev [2.4+20151223.gitfa8646d.1-2+b5 (unstable)] 43) librtmp1 [2.4+20151223.gitfa8646d.1-2+b5 (unstable)] 44) libsasl2-2 [2.1.28+dfsg1-8 (unstable)] 45) libsasl2-modules-db [2.1.28+dfsg1-8 (unstable)] 46) libssh2-1-dev [1.11.1-1 (unstable)] 47) libssh2-1t64 [1.11.1-1 (unstable)] 48) libssl-dev [3.4.0-1 (experimental)] 49) libtasn1-6-dev [4.19.0-3+b3 (unstable)] 50) libunbound8 [1.22.0-1 (unstable)] 51) libzstd-dev [1.5.6+dfsg-1+b1 (unstable)] 52) nettle-dev [3.10-1+b1 (unstable)] Upgrade the following packages: 53) libssl3t64 [3.3.2-2 (now, unstable) -> 3.4.0-1 (experimental)] 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} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{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-2.5-0{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} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages will be upgraded: libssl3t64 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 1 packages upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 39.1 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian experimental/main armhf libssl3t64 armhf 3.4.0-1 [1883 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf bash-completion all 1:2.14.0-2 [310 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.1-1+b1 [54.3 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 27 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 38 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-3 [52.5 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-3 [37.0 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-3 [37.1 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-3 [46.7 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-3 [126 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.4.0-1+b1 [55.0 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.11.0-1 [310 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1 [539 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.8-2 [440 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.8-2 [440 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-2+b1 [208 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b2 [328 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b2 [593 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.8-2 [1328 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-3 [15.8 kB] Get: 71 http://deb.debian.org/debian experimental/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4+b1 [162 kB] Get: 72 http://deb.debian.org/debian experimental/main armhf libldap-dev armhf 2.6.8+dfsg-1~exp4+b1 [282 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libnghttp3-dev armhf 1.4.0-1+b1 [79.8 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls-dev armhf 1.6.0-1 [22.1 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libngtcp2-dev armhf 1.6.0-1 [168 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 83 http://deb.debian.org/debian experimental/main armhf libssl-dev armhf 3.4.0-1 [2428 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-1+b1 [327 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.11.0-1 [434 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libdeflate-dev armhf 1.22-1 [44.5 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB] Get: 90 http://deb.debian.org/debian experimental/main armhf libhts3t64 armhf 1.21+ds-0+exp2 [407 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf liblzma-dev armhf 5.6.3-1+b1 [304 kB] Get: 92 http://deb.debian.org/debian experimental/main armhf libhts-dev armhf 1.21+ds-0+exp2 [1655 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf libio-pty-perl armhf 1:1.20-1+b2 [33.8 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libncurses-dev armhf 6.5-2+b1 [310 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf tabix armhf 1.20+ds-2 [418 kB] Fetched 39.1 MB in 6s (6859 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19686 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Preparing to unpack .../libssl3t64_3.4.0-1_armhf.deb ... Unpacking libssl3t64:armhf (3.4.0-1) over (3.3.2-2) ... Setting up libssl3t64:armhf (3.4.0-1) ... Selecting previously unselected package sensible-utils. (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 ... 20868 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package bash-completion. Preparing to unpack .../01-bash-completion_1%3a2.14.0-2_all.deb ... Unpacking bash-completion (1:2.14.0-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_armhf.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../16-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package comerr-dev:armhf. Preparing to unpack .../17-comerr-dev_2.1-1.47.1-1+b1_armhf.deb ... Unpacking comerr-dev:armhf (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-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 .../22-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../24-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../26-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../32-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../33-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../34-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../35-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../36-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libgssrpc4t64:armhf. Preparing to unpack .../37-libgssrpc4t64_1.21.3-3_armhf.deb ... Unpacking libgssrpc4t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:armhf. Preparing to unpack .../38-libkadm5clnt-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5clnt-mit12:armhf (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:armhf. Preparing to unpack .../39-libkdb5-10t64_1.21.3-3_armhf.deb ... Unpacking libkdb5-10t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:armhf. Preparing to unpack .../40-libkadm5srv-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5srv-mit12:armhf (1.21.3-3) ... Selecting previously unselected package krb5-multidev:armhf. Preparing to unpack .../41-krb5-multidev_1.21.3-3_armhf.deb ... Unpacking krb5-multidev:armhf (1.21.3-3) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../42-libbrotli1_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:armhf. Preparing to unpack .../43-libbrotli-dev_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli-dev:armhf (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../44-libbz2-dev_1.0.8-6_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../45-libsasl2-modules-db_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../46-libsasl2-2_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../47-libldap-2.5-0_2.5.18+dfsg-3+b1_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../48-libnghttp2-14_1.64.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:armhf. Preparing to unpack .../49-libnghttp3-9_1.4.0-1+b1_armhf.deb ... Unpacking libnghttp3-9:armhf (1.4.0-1+b1) ... Selecting previously unselected package libngtcp2-16:armhf. Preparing to unpack .../50-libngtcp2-16_1.6.0-1_armhf.deb ... Unpacking libngtcp2-16:armhf (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:armhf. Preparing to unpack .../51-libngtcp2-crypto-gnutls8_1.6.0-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../52-libpsl5t64_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../53-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../54-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:armhf. Preparing to unpack .../55-libcurl3t64-gnutls_8.11.0-1_armhf.deb ... Unpacking libcurl3t64-gnutls:armhf (8.11.0-1) ... Selecting previously unselected package libevent-2.1-7t64:armhf. Preparing to unpack .../56-libevent-2.1-7t64_2.1.12-stable-10+b1_armhf.deb ... Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:armhf. Preparing to unpack .../57-libunbound8_1.22.0-1_armhf.deb ... Unpacking libunbound8:armhf (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:armhf. Preparing to unpack .../58-libgnutls-dane0t64_3.8.8-2_armhf.deb ... Unpacking libgnutls-dane0t64:armhf (3.8.8-2) ... Selecting previously unselected package libgnutls-openssl27t64:armhf. Preparing to unpack .../59-libgnutls-openssl27t64_3.8.8-2_armhf.deb ... Unpacking libgnutls-openssl27t64:armhf (3.8.8-2) ... Selecting previously unselected package libidn2-dev:armhf. Preparing to unpack .../60-libidn2-dev_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-dev:armhf (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:armhf. Preparing to unpack .../61-libp11-kit-dev_0.25.5-2+b1_armhf.deb ... Unpacking libp11-kit-dev:armhf (0.25.5-2+b1) ... Selecting previously unselected package libtasn1-6-dev:armhf. Preparing to unpack .../62-libtasn1-6-dev_4.19.0-3+b3_armhf.deb ... Unpacking libtasn1-6-dev:armhf (4.19.0-3+b3) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../63-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b2_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../64-libgmp-dev_2%3a6.3.0+dfsg-2+b2_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package nettle-dev:armhf. Preparing to unpack .../65-nettle-dev_3.10-1+b1_armhf.deb ... Unpacking nettle-dev:armhf (3.10-1+b1) ... Selecting previously unselected package libgnutls28-dev:armhf. Preparing to unpack .../66-libgnutls28-dev_3.8.8-2_armhf.deb ... Unpacking libgnutls28-dev:armhf (3.8.8-2) ... Selecting previously unselected package libkrb5-dev:armhf. Preparing to unpack .../67-libkrb5-dev_1.21.3-3_armhf.deb ... Unpacking libkrb5-dev:armhf (1.21.3-3) ... Selecting previously unselected package libldap2:armhf. Preparing to unpack .../68-libldap2_2.6.8+dfsg-1~exp4+b1_armhf.deb ... Unpacking libldap2:armhf (2.6.8+dfsg-1~exp4+b1) ... Selecting previously unselected package libldap-dev:armhf. Preparing to unpack .../69-libldap-dev_2.6.8+dfsg-1~exp4+b1_armhf.deb ... Unpacking libldap-dev:armhf (2.6.8+dfsg-1~exp4+b1) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../70-libpkgconf3_1.8.1-4_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../71-pkgconf-bin_1.8.1-4_armhf.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../72-pkgconf_1.8.1-4_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:armhf. Preparing to unpack .../73-libnghttp2-dev_1.64.0-1_armhf.deb ... Unpacking libnghttp2-dev:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:armhf. Preparing to unpack .../74-libnghttp3-dev_1.4.0-1+b1_armhf.deb ... Unpacking libnghttp3-dev:armhf (1.4.0-1+b1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:armhf. Preparing to unpack .../75-libngtcp2-crypto-gnutls-dev_1.6.0-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls-dev:armhf (1.6.0-1) ... Selecting previously unselected package libngtcp2-dev:armhf. Preparing to unpack .../76-libngtcp2-dev_1.6.0-1_armhf.deb ... Unpacking libngtcp2-dev:armhf (1.6.0-1) ... Selecting previously unselected package libpsl-dev:armhf. Preparing to unpack .../77-libpsl-dev_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl-dev:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../78-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:armhf. Preparing to unpack .../79-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../80-libssl-dev_3.4.0-1_armhf.deb ... Unpacking libssl-dev:armhf (3.4.0-1) ... Selecting previously unselected package libssh2-1-dev:armhf. Preparing to unpack .../81-libssh2-1-dev_1.11.1-1_armhf.deb ... Unpacking libssh2-1-dev:armhf (1.11.1-1) ... Selecting previously unselected package libzstd-dev:armhf. Preparing to unpack .../82-libzstd-dev_1.5.6+dfsg-1+b1_armhf.deb ... Unpacking libzstd-dev:armhf (1.5.6+dfsg-1+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../83-libcurl4-gnutls-dev_8.11.0-1_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (8.11.0-1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../84-libdeflate0_1.22-1_armhf.deb ... Unpacking libdeflate0:armhf (1.22-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../85-libdeflate-dev_1.22-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.22-1) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../86-libhtscodecs2_1.6.1-1_armhf.deb ... Unpacking libhtscodecs2:armhf (1.6.1-1) ... Selecting previously unselected package libhts3t64:armhf. Preparing to unpack .../87-libhts3t64_1.21+ds-0+exp2_armhf.deb ... Unpacking libhts3t64:armhf (1.21+ds-0+exp2) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../88-liblzma-dev_5.6.3-1+b1_armhf.deb ... Unpacking liblzma-dev:armhf (5.6.3-1+b1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../89-libhts-dev_1.21+ds-0+exp2_armhf.deb ... Unpacking libhts-dev:armhf (1.21+ds-0+exp2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../90-libio-pty-perl_1%3a1.20-1+b2_armhf.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../91-libncurses6_6.5-2+b1_armhf.deb ... Unpacking libncurses6:armhf (6.5-2+b1) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../92-libncurses-dev_6.5-2+b1_armhf.deb ... Unpacking libncurses-dev:armhf (6.5-2+b1) ... Selecting previously unselected package tabix. Preparing to unpack .../93-tabix_1.20+ds-2_armhf.deb ... Unpacking tabix (1.20+ds-2) ... Setting up libhtscodecs2:armhf (1.6.1-1) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libgnutls-openssl27t64:armhf (3.8.8-2) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up libzstd-dev:armhf (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:armhf (1.22.0-1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Setting up libgnutls-dane0t64:armhf (3.8.8-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up bash-completion (1:2.14.0-2) ... Setting up libncurses6:armhf (6.5-2+b1) ... Setting up comerr-dev:armhf (2.1-1.47.1-1+b1) ... Setting up libssl-dev:armhf (3.4.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libidn2-dev:armhf (2.3.7-2+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:armhf (1.4.0-1+b1) ... Setting up libnghttp3-dev:armhf (1.4.0-1+b1) ... Setting up liblzma-dev:armhf (5.6.3-1+b1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libngtcp2-16:armhf (1.6.0-1) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libtasn1-6-dev:armhf (4.19.0-3+b3) ... Setting up libdeflate-dev:armhf (1.22-1) ... Setting up tabix (1.20+ds-2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:armhf (2.6.8+dfsg-1~exp4+b1) ... Setting up libbrotli-dev:armhf (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Setting up libp11-kit-dev:armhf (0.25.5-2+b1) ... Setting up libbz2-dev:armhf (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libncurses-dev:armhf (6.5-2+b1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:armhf (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up libngtcp2-crypto-gnutls-dev:armhf (1.6.0-1) ... Setting up libngtcp2-dev:armhf (1.6.0-1) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Setting up pkgconf:armhf (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:armhf (2.6.8+dfsg-1~exp4+b1) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libssh2-1-dev:armhf (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:armhf (3.8.8-2) ... Setting up libnghttp2-dev:armhf (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:armhf (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:armhf (1.21.3-3) ... Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:armhf (1.21+ds-0+exp2) ... Setting up libkadm5clnt-mit12:armhf (1.21.3-3) ... Setting up libkdb5-10t64:armhf (1.21.3-3) ... Setting up debhelper (13.20) ... Setting up libkadm5srv-mit12:armhf (1.21.3-3) ... Setting up krb5-multidev:armhf (1.21.3-3) ... Setting up libkrb5-dev:armhf (1.21.3-3) ... Setting up libcurl4-gnutls-dev:armhf (8.11.0-1) ... Setting up libhts-dev:armhf (1.21+ds-0+exp2) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/samtools-1.21/ && 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_1.21-0+exp1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.21-0+exp1 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from samtools-1.21/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-1.21' rm -f config.mk touch config.mk dh_auto_clean -- make -j3 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.21' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.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-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc option to enable large file support... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.21' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.21"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/reproducible-path/samtools-1.21@«BUILDPATH»@g' version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j3 test "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.21' 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-1.21/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/avw_tQpPKL/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/avw_tQpPKL/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/avw_tQpPKL/bgzip.dat.gz .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 1:99998-100007 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/reproducible-path/samtools-1.21/test/dat/dict.fa .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/avw_tQpPKL/dict.fa.gz .. ok test_dict: cat /build/reproducible-path/samtools-1.21/test/dat/dict.fa | /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -AH < /build/reproducible-path/samtools-1.21/test/dat/dict.alias.fa .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -H -l /build/reproducible-path/samtools-1.21/test/dat/dict.alt < /build/reproducible-path/samtools-1.21/test/dat/dict.alias.fa .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view /tmp/avw_tQpPKL/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view /tmp/avw_tQpPKL/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/avw_tQpPKL/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/avw_tQpPKL/auto_indexed.crai && cat /tmp/avw_tQpPKL/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/avw_tQpPKL/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/avw_tQpPKL/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/avw_tQpPKL/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/avw_tQpPKL/auto_indexed.crai && cat /tmp/avw_tQpPKL/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.bam.list -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.cram.list -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.bam.urllist -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.cram.urllist -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:1050-1060 /tmp/avw_tQpPKL/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:1050-1060 /tmp/avw_tQpPKL/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup /build/reproducible-path/samtools-1.21/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate .. ok test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools consensus .. ok test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools import .. ok test_usage_subcommand: samtools reference .. ok test_usage_subcommand: samtools reset .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth .. ok test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags .. ok test_usage_subcommand: samtools head .. ok test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools samples Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/avw_tQpPKL/view.001.forn (SAM input) .. ok 68: Count -N /tmp/avw_tQpPKL/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/avw_tQpPKL/view.001.forn (BAM input) .. ok 70: Count -N /tmp/avw_tQpPKL/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/avw_tQpPKL/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/avw_tQpPKL/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/avw_tQpPKL/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test115.sam -h -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test117.sam -h -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test119.sam -h -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test121.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test123.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test125.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /build/reproducible-path/samtools-1.21/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-1.21/samtools head /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 0 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 1 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 5 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 29 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 30 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 0 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 1 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 5 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 5 -n 5 < /build/reproducible-path/samtools-1.21/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-1.21/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -0 /build/reproducible-path/samtools-1.21/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -0 /build/reproducible-path/samtools-1.21/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -T RG,BC,QT -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/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-1.21/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.21/test/bc_split.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -T MD,ia -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -1 /build/reproducible-path/samtools-1.21/test/o.fq -2 /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fasta -N -1 /build/reproducible-path/samtools-1.21/test/o.fa -2 /build/reproducible-path/samtools-1.21/test/o.fa /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -o /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -s /tmp/avw_tQpPKL/bam2fq.discard.s.fq -0 /tmp/avw_tQpPKL/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.21/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.21/test/i1.fq --i2 /build/reproducible-path/samtools-1.21/test/i2.fq -0 /build/reproducible-path/samtools-1.21/test/0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -T '*' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d ia /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.21/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-1.21/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.21/test/bc_split.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -T MD,ia -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -1 /build/reproducible-path/samtools-1.21/test/o.fq -2 /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fasta -@ 2 -N -1 /build/reproducible-path/samtools-1.21/test/o.fa -2 /build/reproducible-path/samtools-1.21/test/o.fa /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -o /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -s /tmp/avw_tQpPKL/bam2fq.discard.s.fq -0 /tmp/avw_tQpPKL/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.21/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.21/test/i1.fq --i2 /build/reproducible-path/samtools-1.21/test/i2.fq -0 /build/reproducible-path/samtools-1.21/test/0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -T '*' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d ia /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.21/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-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa -i 0 /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -S RG -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -S RG -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -t /build/reproducible-path/samtools-1.21/test/stat/11.stats.targets /build/reproducible-path/samtools-1.21/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -g 4 -t /build/reproducible-path/samtools-1.21/test/stat/11.stats.targets /build/reproducible-path/samtools-1.21/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -g 4 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.21/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.21/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.21/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.21/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I s1 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I grp2 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I grp3 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I Sample /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/mpileup/ce.fa /build/reproducible-path/samtools-1.21/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam -b /tmp/3WYe1BIefS - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -r -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -cp -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -o - -s 1 -O sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.1.bam /tmp/avw_tQpPKL/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.3.bam /tmp/avw_tQpPKL/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/avw_tQpPKL/merge.bed.1.bam /tmp/avw_tQpPKL/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -r -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.2.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam -b /tmp/ctEC6DyYGi - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -r -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -cp -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -o - -s 1 -O sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.1.bam /tmp/avw_tQpPKL/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.3.bam /tmp/avw_tQpPKL/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/avw_tQpPKL/merge.bed.1.bam /tmp/avw_tQpPKL/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -r -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.2.sam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -N -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t AS -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t FI -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort --template-coordinate -m 10M /build/reproducible-path/samtools-1.21/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -M -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -MH -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -N -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t AS -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t FI -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 --template-coordinate -m 10M /build/reproducible-path/samtools-1.21/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -M -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -MH -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -O /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -o /build/reproducible-path/samtools-1.21/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -o /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -f /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -O /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.21/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -f /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/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-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/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-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bounds.sam - .. ok /build/reproducible-path/samtools-1.21/samtools calmd -uAr /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa .. ok /build/reproducible-path/samtools-1.21/samtools calmd -@ 2 -uAr /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck -v /build/reproducible-path/samtools-1.21/test/quickcheck/1.quickcheck.badeof.bam /build/reproducible-path/samtools-1.21/test/quickcheck/2.quickcheck.badheader.bam /build/reproducible-path/samtools-1.21/test/quickcheck/3.quickcheck.ok.bam /build/reproducible-path/samtools-1.21/test/quickcheck/4.quickcheck.ok.bam /build/reproducible-path/samtools-1.21/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/6.quickcheck.cram21.ok.cram /build/reproducible-path/samtools-1.21/test/quickcheck/7.quickcheck.cram30.ok.cram /build/reproducible-path/samtools-1.21/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck -uv /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader --in-place /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram && /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader --in-place /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram && /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m overwrite_all /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m orphan_only /build/reproducible-path/samtools-1.21/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -R '1#9' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/reproducible-path/samtools-1.21/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam -r --no-PG /build/reproducible-path/samtools-1.21/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.21/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam -r --no-PG /build/reproducible-path/samtools-1.21/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.21/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -j /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -g512 -G2048 /build/reproducible-path/samtools-1.21/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -c /build/reproducible-path/samtools-1.21/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d an -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d an -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/avw_tQpPKL/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/avw_tQpPKL/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /tmp/avw_tQpPKL/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -m 10M /build/reproducible-path/samtools-1.21/test/large_pos/longref_name.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools merge -O sam --no-PG - /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam /build/reproducible-path/samtools-1.21/test/large_pos/longref2.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools depth /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools depth -b /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/avw_tQpPKL/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/reproducible-path/samtools-1.21/samtools fixmate -O sam --no-PG - - | /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_hard_clipped.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/1_soft_clipped.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools reset --dupflag | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag < /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: cat /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.cram .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG sam_to_fixed_bam /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index --no-PG /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/reset/seq.sam -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset /build/reproducible-path/samtools-1.21/test/reset/seq.sam -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok Number of tests: total .. 990 passed .. 946 failed .. 0 expected failure .. 44 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 120 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 53 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh cram-size.reg === Testing cram-size.reg regressions === Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 65 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' rm -fr -- /tmp/dh-xdg-rundir-zsmxcL_q make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.21/debian/tmp make -j3 install DESTDIR=/build/reproducible-path/samtools-1.21/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.21' mkdir -p -m 755 /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' make clean make[2]: Entering directory '/build/reproducible-path/samtools-1.21' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.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-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/samtools-1.21' 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-1.21' 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-1.21' 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-1.21' 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-1.21' # 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-1.21' dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 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 1731584159 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1731584159 as canonical time Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/samtools cd debian/samtools-test chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian 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-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/reproducible-path/samtools-1.21' cd '/build/reproducible-path/samtools-1.21' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 debian/rules execute_after_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/samtools-1.21' chmod -x /build/reproducible-path/samtools-1.21/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' dh_missing dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 729158 new size 750642 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.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/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.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/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.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/67/e928e02c0111fee9a809fa505157999a001621.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.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/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.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/14/4f2a177ea7991a0822e26944c28ad098e39606.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.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/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.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/df/692591be73a860f596386f769a08d2034a2d43.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.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=144f2a177ea7991a0822e26944c28ad098e39606 48ca1f475bfbcda812a638c0eeea747ea9cc5f22 4a3389d400e7a3f36f8902d21b43794fc0e5302f 5d2a4e264350e4290193be9c8c57a1ed7add64ea 67e928e02c0111fee9a809fa505157999a001621 710f3c191656ce7f7f819003dbcaa4296e2973a0 df692591be73a860f596386f769a08d2034a2d43" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/samtools-test/DEBIAN echo misc:Depends= >> debian/samtools-test.substvars echo misc:Pre-Depends= >> debian/samtools-test.substvars dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb: building package 'samtools' in '../samtools_1.21-0+exp1_armhf.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.21-0+exp1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.21-0+exp1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.21-0+exp1_armhf.buildinfo dpkg-genchanges --build=binary -O../samtools_1.21-0+exp1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.21/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ 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/6550 and its subdirectories I: Current time: Fri Nov 22 05:45:11 -12 2024 I: pbuilder-time-stamp: 1732297511 Fri Nov 22 17:45:11 UTC 2024 I: Signing ./b1/samtools_1.21-0+exp1_armhf.buildinfo as samtools_1.21-0+exp1_armhf.buildinfo.asc Fri Nov 22 17:45:12 UTC 2024 I: Signed ./b1/samtools_1.21-0+exp1_armhf.buildinfo as ./b1/samtools_1.21-0+exp1_armhf.buildinfo.asc Fri Nov 22 17:45:12 UTC 2024 - build #1 for samtools/experimental/armhf on wbq0 done. Starting cleanup. All cleanup done. Fri Nov 22 17:45:12 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-TIFAzemq, removing. /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 17:45 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 17:31 b2 -rw------- 1 jenkins jenkins 3421 Nov 22 17:31 rbuildlog.jhts4YW -rw-r--r-- 1 jenkins jenkins 2272 Nov 14 19:34 samtools_1.21-0+exp1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b1: total 9784 -rw-r--r-- 1 jenkins jenkins 263000 Nov 22 17:45 build.log -rw-r--r-- 1 jenkins jenkins 993212 Nov 22 17:45 samtools-dbgsym_1.21-0+exp1_armhf.deb -rw-r--r-- 1 jenkins jenkins 2366700 Nov 22 17:45 samtools-test_1.21-0+exp1_all.deb -rw-r--r-- 1 jenkins jenkins 22052 Nov 22 17:45 samtools_1.21-0+exp1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2272 Nov 22 17:45 samtools_1.21-0+exp1.dsc -rw-r--r-- 1 jenkins jenkins 7433 Nov 22 17:45 samtools_1.21-0+exp1_armhf.buildinfo -rw-r--r-- 1 jenkins jenkins 8315 Nov 22 17:45 samtools_1.21-0+exp1_armhf.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1844 Nov 22 17:45 samtools_1.21-0+exp1_armhf.changes -rw-r--r-- 1 jenkins jenkins 631956 Nov 22 17:45 samtools_1.21-0+exp1_armhf.deb -rw-r--r-- 1 jenkins jenkins 1596 Nov 22 17:45 samtools_1.21-0+exp1_source.changes -rw-r--r-- 1 jenkins jenkins 5682709 Nov 22 17:45 samtools_1.21.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b2: total 0 Fri Nov 22 17:45:36 UTC 2024 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 22 05:31:41 -12 2024 I: pbuilder-time-stamp: 1732296701 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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_1.21-0+exp1.dsc] I: copying [./samtools_1.21.orig.tar.gz] I: copying [./samtools_1.21-0+exp1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 14 19:30:19 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./samtools_1.21-0+exp1.dsc: no acceptable signature found dpkg-source: info: extracting samtools in samtools-1.21 dpkg-source: info: unpacking samtools_1.21.orig.tar.gz dpkg-source: info: unpacking samtools_1.21-0+exp1.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/6550/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='c1a3c51aae2d4667b8d039d1ac72f79b' 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='6550' 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.RfmZQeJi/pbuilderrc_Qrp7 --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b1 --logfile b1/build.log samtools_1.21-0+exp1.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux wbq0 6.1.0-27-armmp #1 SMP Debian 6.1.115-1 (2024-11-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/6550/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.21~), 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 ... 19686 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 (>= 1.21~); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on automake; however: Package automake is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 22.5 MB of archives. After unpacking 84.3 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libhts-dev (>= 1.21~) but it is not going to be installed The following actions will resolve these dependencies: Install the following packages: 1) comerr-dev [2.1-1.47.1-1+b1 (unstable)] 2) krb5-multidev [1.21.3-3 (unstable)] 3) libbrotli-dev [1.1.0-2+b6 (unstable)] 4) libbrotli1 [1.1.0-2+b6 (unstable)] 5) libcom-err2 [1.47.1-1+b1 (unstable)] 6) libcurl3t64-gnutls [8.11.0-1 (unstable)] 7) libcurl4-gnutls-dev [8.11.0-1 (unstable)] 8) libdeflate-dev [1.22-1 (unstable)] 9) libevent-2.1-7t64 [2.1.12-stable-10+b1 (unstable)] 10) libgmp-dev [2:6.3.0+dfsg-2+b2 (unstable)] 11) libgmpxx4ldbl [2:6.3.0+dfsg-2+b2 (unstable)] 12) libgnutls-dane0t64 [3.8.8-2 (unstable)] 13) libgnutls-openssl27t64 [3.8.8-2 (unstable)] 14) libgnutls28-dev [3.8.8-2 (unstable)] 15) libgssapi-krb5-2 [1.21.3-3 (unstable)] 16) libgssrpc4t64 [1.21.3-3 (unstable)] 17) libhts-dev [1.21+ds-0+exp2 (experimental)] 18) libhts3t64 [1.21+ds-0+exp2 (experimental)] 19) libidn2-dev [2.3.7-2+b1 (unstable)] 20) libk5crypto3 [1.21.3-3 (unstable)] 21) libkadm5clnt-mit12 [1.21.3-3 (unstable)] 22) libkadm5srv-mit12 [1.21.3-3 (unstable)] 23) libkdb5-10t64 [1.21.3-3 (unstable)] 24) libkeyutils1 [1.6.3-4 (unstable)] 25) libkrb5-3 [1.21.3-3 (unstable)] 26) libkrb5-dev [1.21.3-3 (unstable)] 27) libkrb5support0 [1.21.3-3 (unstable)] 28) libldap-2.5-0 [2.5.18+dfsg-3+b1 (unstable)] 29) libldap-dev [2.6.8+dfsg-1~exp4+b1 (experimental)] 30) libldap2 [2.6.8+dfsg-1~exp4+b1 (experimental)] 31) libnghttp2-14 [1.64.0-1 (unstable)] 32) libnghttp2-dev [1.64.0-1 (unstable)] 33) libnghttp3-9 [1.4.0-1+b1 (unstable)] 34) libnghttp3-dev [1.4.0-1+b1 (unstable)] 35) libngtcp2-16 [1.6.0-1 (unstable)] 36) libngtcp2-crypto-gnutls-dev [1.6.0-1 (unstable)] 37) libngtcp2-crypto-gnutls8 [1.6.0-1 (unstable)] 38) libngtcp2-dev [1.6.0-1 (unstable)] 39) libp11-kit-dev [0.25.5-2+b1 (unstable)] 40) libpsl-dev [0.21.2-1.1+b1 (unstable)] 41) libpsl5t64 [0.21.2-1.1+b1 (unstable)] 42) librtmp-dev [2.4+20151223.gitfa8646d.1-2+b5 (unstable)] 43) librtmp1 [2.4+20151223.gitfa8646d.1-2+b5 (unstable)] 44) libsasl2-2 [2.1.28+dfsg1-8 (unstable)] 45) libsasl2-modules-db [2.1.28+dfsg1-8 (unstable)] 46) libssh2-1-dev [1.11.1-1 (unstable)] 47) libssh2-1t64 [1.11.1-1 (unstable)] 48) libssl-dev [3.4.0-1 (experimental)] 49) libtasn1-6-dev [4.19.0-3+b3 (unstable)] 50) libunbound8 [1.22.0-1 (unstable)] 51) libzstd-dev [1.5.6+dfsg-1+b1 (unstable)] 52) nettle-dev [3.10-1+b1 (unstable)] Upgrade the following packages: 53) libssl3t64 [3.3.2-2 (now, unstable) -> 3.4.0-1 (experimental)] 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} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{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-2.5-0{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} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages will be upgraded: libssl3t64 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 1 packages upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 39.1 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian experimental/main armhf libssl3t64 armhf 3.4.0-1 [1883 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf bash-completion all 1:2.14.0-2 [310 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.1-1+b1 [54.3 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 27 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 38 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-3 [52.5 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-3 [37.0 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-3 [37.1 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-3 [46.7 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-3 [126 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.4.0-1+b1 [55.0 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.11.0-1 [310 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1 [539 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.8-2 [440 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.8-2 [440 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-2+b1 [208 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b2 [328 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b2 [593 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.8-2 [1328 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-3 [15.8 kB] Get: 71 http://deb.debian.org/debian experimental/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4+b1 [162 kB] Get: 72 http://deb.debian.org/debian experimental/main armhf libldap-dev armhf 2.6.8+dfsg-1~exp4+b1 [282 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libnghttp3-dev armhf 1.4.0-1+b1 [79.8 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls-dev armhf 1.6.0-1 [22.1 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libngtcp2-dev armhf 1.6.0-1 [168 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 83 http://deb.debian.org/debian experimental/main armhf libssl-dev armhf 3.4.0-1 [2428 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-1+b1 [327 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.11.0-1 [434 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libdeflate-dev armhf 1.22-1 [44.5 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB] Get: 90 http://deb.debian.org/debian experimental/main armhf libhts3t64 armhf 1.21+ds-0+exp2 [407 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf liblzma-dev armhf 5.6.3-1+b1 [304 kB] Get: 92 http://deb.debian.org/debian experimental/main armhf libhts-dev armhf 1.21+ds-0+exp2 [1655 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf libio-pty-perl armhf 1:1.20-1+b2 [33.8 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libncurses-dev armhf 6.5-2+b1 [310 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf tabix armhf 1.20+ds-2 [418 kB] Fetched 39.1 MB in 6s (6859 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19686 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Preparing to unpack .../libssl3t64_3.4.0-1_armhf.deb ... Unpacking libssl3t64:armhf (3.4.0-1) over (3.3.2-2) ... Setting up libssl3t64:armhf (3.4.0-1) ... Selecting previously unselected package sensible-utils. (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 ... 20868 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package bash-completion. Preparing to unpack .../01-bash-completion_1%3a2.14.0-2_all.deb ... Unpacking bash-completion (1:2.14.0-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_armhf.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../16-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package comerr-dev:armhf. Preparing to unpack .../17-comerr-dev_2.1-1.47.1-1+b1_armhf.deb ... Unpacking comerr-dev:armhf (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-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 .../22-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../24-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../26-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../32-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../33-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../34-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../35-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../36-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libgssrpc4t64:armhf. Preparing to unpack .../37-libgssrpc4t64_1.21.3-3_armhf.deb ... Unpacking libgssrpc4t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:armhf. Preparing to unpack .../38-libkadm5clnt-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5clnt-mit12:armhf (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:armhf. Preparing to unpack .../39-libkdb5-10t64_1.21.3-3_armhf.deb ... Unpacking libkdb5-10t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:armhf. Preparing to unpack .../40-libkadm5srv-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5srv-mit12:armhf (1.21.3-3) ... Selecting previously unselected package krb5-multidev:armhf. Preparing to unpack .../41-krb5-multidev_1.21.3-3_armhf.deb ... Unpacking krb5-multidev:armhf (1.21.3-3) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../42-libbrotli1_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:armhf. Preparing to unpack .../43-libbrotli-dev_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli-dev:armhf (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../44-libbz2-dev_1.0.8-6_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../45-libsasl2-modules-db_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../46-libsasl2-2_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../47-libldap-2.5-0_2.5.18+dfsg-3+b1_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../48-libnghttp2-14_1.64.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:armhf. Preparing to unpack .../49-libnghttp3-9_1.4.0-1+b1_armhf.deb ... Unpacking libnghttp3-9:armhf (1.4.0-1+b1) ... Selecting previously unselected package libngtcp2-16:armhf. Preparing to unpack .../50-libngtcp2-16_1.6.0-1_armhf.deb ... Unpacking libngtcp2-16:armhf (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:armhf. Preparing to unpack .../51-libngtcp2-crypto-gnutls8_1.6.0-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../52-libpsl5t64_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../53-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../54-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:armhf. Preparing to unpack .../55-libcurl3t64-gnutls_8.11.0-1_armhf.deb ... Unpacking libcurl3t64-gnutls:armhf (8.11.0-1) ... Selecting previously unselected package libevent-2.1-7t64:armhf. Preparing to unpack .../56-libevent-2.1-7t64_2.1.12-stable-10+b1_armhf.deb ... Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:armhf. Preparing to unpack .../57-libunbound8_1.22.0-1_armhf.deb ... Unpacking libunbound8:armhf (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:armhf. Preparing to unpack .../58-libgnutls-dane0t64_3.8.8-2_armhf.deb ... Unpacking libgnutls-dane0t64:armhf (3.8.8-2) ... Selecting previously unselected package libgnutls-openssl27t64:armhf. Preparing to unpack .../59-libgnutls-openssl27t64_3.8.8-2_armhf.deb ... Unpacking libgnutls-openssl27t64:armhf (3.8.8-2) ... Selecting previously unselected package libidn2-dev:armhf. Preparing to unpack .../60-libidn2-dev_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-dev:armhf (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:armhf. Preparing to unpack .../61-libp11-kit-dev_0.25.5-2+b1_armhf.deb ... Unpacking libp11-kit-dev:armhf (0.25.5-2+b1) ... Selecting previously unselected package libtasn1-6-dev:armhf. Preparing to unpack .../62-libtasn1-6-dev_4.19.0-3+b3_armhf.deb ... Unpacking libtasn1-6-dev:armhf (4.19.0-3+b3) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../63-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b2_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../64-libgmp-dev_2%3a6.3.0+dfsg-2+b2_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package nettle-dev:armhf. Preparing to unpack .../65-nettle-dev_3.10-1+b1_armhf.deb ... Unpacking nettle-dev:armhf (3.10-1+b1) ... Selecting previously unselected package libgnutls28-dev:armhf. Preparing to unpack .../66-libgnutls28-dev_3.8.8-2_armhf.deb ... Unpacking libgnutls28-dev:armhf (3.8.8-2) ... Selecting previously unselected package libkrb5-dev:armhf. Preparing to unpack .../67-libkrb5-dev_1.21.3-3_armhf.deb ... Unpacking libkrb5-dev:armhf (1.21.3-3) ... Selecting previously unselected package libldap2:armhf. Preparing to unpack .../68-libldap2_2.6.8+dfsg-1~exp4+b1_armhf.deb ... Unpacking libldap2:armhf (2.6.8+dfsg-1~exp4+b1) ... Selecting previously unselected package libldap-dev:armhf. Preparing to unpack .../69-libldap-dev_2.6.8+dfsg-1~exp4+b1_armhf.deb ... Unpacking libldap-dev:armhf (2.6.8+dfsg-1~exp4+b1) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../70-libpkgconf3_1.8.1-4_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../71-pkgconf-bin_1.8.1-4_armhf.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../72-pkgconf_1.8.1-4_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:armhf. Preparing to unpack .../73-libnghttp2-dev_1.64.0-1_armhf.deb ... Unpacking libnghttp2-dev:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:armhf. Preparing to unpack .../74-libnghttp3-dev_1.4.0-1+b1_armhf.deb ... Unpacking libnghttp3-dev:armhf (1.4.0-1+b1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:armhf. Preparing to unpack .../75-libngtcp2-crypto-gnutls-dev_1.6.0-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls-dev:armhf (1.6.0-1) ... Selecting previously unselected package libngtcp2-dev:armhf. Preparing to unpack .../76-libngtcp2-dev_1.6.0-1_armhf.deb ... Unpacking libngtcp2-dev:armhf (1.6.0-1) ... Selecting previously unselected package libpsl-dev:armhf. Preparing to unpack .../77-libpsl-dev_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl-dev:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../78-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:armhf. Preparing to unpack .../79-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../80-libssl-dev_3.4.0-1_armhf.deb ... Unpacking libssl-dev:armhf (3.4.0-1) ... Selecting previously unselected package libssh2-1-dev:armhf. Preparing to unpack .../81-libssh2-1-dev_1.11.1-1_armhf.deb ... Unpacking libssh2-1-dev:armhf (1.11.1-1) ... Selecting previously unselected package libzstd-dev:armhf. Preparing to unpack .../82-libzstd-dev_1.5.6+dfsg-1+b1_armhf.deb ... Unpacking libzstd-dev:armhf (1.5.6+dfsg-1+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../83-libcurl4-gnutls-dev_8.11.0-1_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (8.11.0-1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../84-libdeflate0_1.22-1_armhf.deb ... Unpacking libdeflate0:armhf (1.22-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../85-libdeflate-dev_1.22-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.22-1) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../86-libhtscodecs2_1.6.1-1_armhf.deb ... Unpacking libhtscodecs2:armhf (1.6.1-1) ... Selecting previously unselected package libhts3t64:armhf. Preparing to unpack .../87-libhts3t64_1.21+ds-0+exp2_armhf.deb ... Unpacking libhts3t64:armhf (1.21+ds-0+exp2) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../88-liblzma-dev_5.6.3-1+b1_armhf.deb ... Unpacking liblzma-dev:armhf (5.6.3-1+b1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../89-libhts-dev_1.21+ds-0+exp2_armhf.deb ... Unpacking libhts-dev:armhf (1.21+ds-0+exp2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../90-libio-pty-perl_1%3a1.20-1+b2_armhf.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../91-libncurses6_6.5-2+b1_armhf.deb ... Unpacking libncurses6:armhf (6.5-2+b1) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../92-libncurses-dev_6.5-2+b1_armhf.deb ... Unpacking libncurses-dev:armhf (6.5-2+b1) ... Selecting previously unselected package tabix. Preparing to unpack .../93-tabix_1.20+ds-2_armhf.deb ... Unpacking tabix (1.20+ds-2) ... Setting up libhtscodecs2:armhf (1.6.1-1) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libgnutls-openssl27t64:armhf (3.8.8-2) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up libzstd-dev:armhf (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:armhf (1.22.0-1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Setting up libgnutls-dane0t64:armhf (3.8.8-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up bash-completion (1:2.14.0-2) ... Setting up libncurses6:armhf (6.5-2+b1) ... Setting up comerr-dev:armhf (2.1-1.47.1-1+b1) ... Setting up libssl-dev:armhf (3.4.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libidn2-dev:armhf (2.3.7-2+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:armhf (1.4.0-1+b1) ... Setting up libnghttp3-dev:armhf (1.4.0-1+b1) ... Setting up liblzma-dev:armhf (5.6.3-1+b1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libngtcp2-16:armhf (1.6.0-1) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libtasn1-6-dev:armhf (4.19.0-3+b3) ... Setting up libdeflate-dev:armhf (1.22-1) ... Setting up tabix (1.20+ds-2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:armhf (2.6.8+dfsg-1~exp4+b1) ... Setting up libbrotli-dev:armhf (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Setting up libp11-kit-dev:armhf (0.25.5-2+b1) ... Setting up libbz2-dev:armhf (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libncurses-dev:armhf (6.5-2+b1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:armhf (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up libngtcp2-crypto-gnutls-dev:armhf (1.6.0-1) ... Setting up libngtcp2-dev:armhf (1.6.0-1) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Setting up pkgconf:armhf (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:armhf (2.6.8+dfsg-1~exp4+b1) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libssh2-1-dev:armhf (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:armhf (3.8.8-2) ... Setting up libnghttp2-dev:armhf (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:armhf (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:armhf (1.21.3-3) ... Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:armhf (1.21+ds-0+exp2) ... Setting up libkadm5clnt-mit12:armhf (1.21.3-3) ... Setting up libkdb5-10t64:armhf (1.21.3-3) ... Setting up debhelper (13.20) ... Setting up libkadm5srv-mit12:armhf (1.21.3-3) ... Setting up krb5-multidev:armhf (1.21.3-3) ... Setting up libkrb5-dev:armhf (1.21.3-3) ... Setting up libcurl4-gnutls-dev:armhf (8.11.0-1) ... Setting up libhts-dev:armhf (1.21+ds-0+exp2) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/samtools-1.21/ && 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_1.21-0+exp1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.21-0+exp1 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from samtools-1.21/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-1.21' rm -f config.mk touch config.mk dh_auto_clean -- make -j3 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.21' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.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-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc option to enable large file support... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.21' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.21"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/reproducible-path/samtools-1.21@«BUILDPATH»@g' version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j3 test "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.21' 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-1.21/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/avw_tQpPKL/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/avw_tQpPKL/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/avw_tQpPKL/bgzip.dat.gz .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 1:99998-100007 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/reproducible-path/samtools-1.21/test/dat/dict.fa .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/avw_tQpPKL/dict.fa.gz .. ok test_dict: cat /build/reproducible-path/samtools-1.21/test/dat/dict.fa | /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -AH < /build/reproducible-path/samtools-1.21/test/dat/dict.alias.fa .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -H -l /build/reproducible-path/samtools-1.21/test/dat/dict.alt < /build/reproducible-path/samtools-1.21/test/dat/dict.alias.fa .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view /tmp/avw_tQpPKL/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view /tmp/avw_tQpPKL/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/avw_tQpPKL/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/avw_tQpPKL/auto_indexed.crai && cat /tmp/avw_tQpPKL/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/avw_tQpPKL/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/avw_tQpPKL/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/avw_tQpPKL/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/avw_tQpPKL/auto_indexed.crai && cat /tmp/avw_tQpPKL/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.bam.list -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.cram.list -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.bam.urllist -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.cram.urllist -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:1050-1060 /tmp/avw_tQpPKL/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:1050-1060 /tmp/avw_tQpPKL/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup /build/reproducible-path/samtools-1.21/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate .. ok test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools consensus .. ok test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools import .. ok test_usage_subcommand: samtools reference .. ok test_usage_subcommand: samtools reset .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth .. ok test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags .. ok test_usage_subcommand: samtools head .. ok test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools samples Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/avw_tQpPKL/view.001.forn (SAM input) .. ok 68: Count -N /tmp/avw_tQpPKL/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/avw_tQpPKL/view.001.forn (BAM input) .. ok 70: Count -N /tmp/avw_tQpPKL/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/avw_tQpPKL/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/avw_tQpPKL/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/avw_tQpPKL/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test115.sam -h -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test117.sam -h -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test119.sam -h -d TGCA /tmp/avw_tQpPKL/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test121.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test123.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test125.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/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-1.21/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /build/reproducible-path/samtools-1.21/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-1.21/samtools head /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 0 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 1 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 5 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 29 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 30 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 0 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 1 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 5 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 5 -n 5 < /build/reproducible-path/samtools-1.21/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-1.21/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -0 /build/reproducible-path/samtools-1.21/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -0 /build/reproducible-path/samtools-1.21/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -T RG,BC,QT -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/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-1.21/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.21/test/bc_split.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -T MD,ia -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -1 /build/reproducible-path/samtools-1.21/test/o.fq -2 /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fasta -N -1 /build/reproducible-path/samtools-1.21/test/o.fa -2 /build/reproducible-path/samtools-1.21/test/o.fa /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -o /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -s /tmp/avw_tQpPKL/bam2fq.discard.s.fq -0 /tmp/avw_tQpPKL/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.21/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.21/test/i1.fq --i2 /build/reproducible-path/samtools-1.21/test/i2.fq -0 /build/reproducible-path/samtools-1.21/test/0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -T '*' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d ia /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.21/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-1.21/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.21/test/bc_split.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -T MD,ia -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -1 /build/reproducible-path/samtools-1.21/test/o.fq -2 /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fasta -@ 2 -N -1 /build/reproducible-path/samtools-1.21/test/o.fa -2 /build/reproducible-path/samtools-1.21/test/o.fa /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -o /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -s /tmp/avw_tQpPKL/bam2fq.discard.s.fq -0 /tmp/avw_tQpPKL/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.21/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.21/test/i1.fq --i2 /build/reproducible-path/samtools-1.21/test/i2.fq -0 /build/reproducible-path/samtools-1.21/test/0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -T '*' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d ia /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.21/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-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa -i 0 /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -S RG -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -S RG -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -t /build/reproducible-path/samtools-1.21/test/stat/11.stats.targets /build/reproducible-path/samtools-1.21/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -g 4 -t /build/reproducible-path/samtools-1.21/test/stat/11.stats.targets /build/reproducible-path/samtools-1.21/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -g 4 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.21/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.21/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.21/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.21/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I s1 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I grp2 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I grp3 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I Sample /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/mpileup/ce.fa /build/reproducible-path/samtools-1.21/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam -b /tmp/3WYe1BIefS - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -r -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -cp -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -o - -s 1 -O sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.1.bam /tmp/avw_tQpPKL/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.3.bam /tmp/avw_tQpPKL/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/avw_tQpPKL/merge.bed.1.bam /tmp/avw_tQpPKL/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -r -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.2.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam -b /tmp/ctEC6DyYGi - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -r -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -cp -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -o - -s 1 -O sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.1.bam /tmp/avw_tQpPKL/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.3.bam /tmp/avw_tQpPKL/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/avw_tQpPKL/merge.bed.1.bam /tmp/avw_tQpPKL/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -r -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.2.sam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -N -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t AS -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t FI -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort --template-coordinate -m 10M /build/reproducible-path/samtools-1.21/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -M -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -MH -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -N -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t AS -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t FI -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 --template-coordinate -m 10M /build/reproducible-path/samtools-1.21/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -M -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -MH -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -O /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -o /build/reproducible-path/samtools-1.21/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -o /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -f /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -O /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.21/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -f /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/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-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/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-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bounds.sam - .. ok /build/reproducible-path/samtools-1.21/samtools calmd -uAr /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa .. ok /build/reproducible-path/samtools-1.21/samtools calmd -@ 2 -uAr /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck -v /build/reproducible-path/samtools-1.21/test/quickcheck/1.quickcheck.badeof.bam /build/reproducible-path/samtools-1.21/test/quickcheck/2.quickcheck.badheader.bam /build/reproducible-path/samtools-1.21/test/quickcheck/3.quickcheck.ok.bam /build/reproducible-path/samtools-1.21/test/quickcheck/4.quickcheck.ok.bam /build/reproducible-path/samtools-1.21/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/6.quickcheck.cram21.ok.cram /build/reproducible-path/samtools-1.21/test/quickcheck/7.quickcheck.cram30.ok.cram /build/reproducible-path/samtools-1.21/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck -uv /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader --in-place /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram && /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader --in-place /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram && /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m overwrite_all /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m orphan_only /build/reproducible-path/samtools-1.21/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -R '1#9' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/reproducible-path/samtools-1.21/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam -r --no-PG /build/reproducible-path/samtools-1.21/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.21/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam -r --no-PG /build/reproducible-path/samtools-1.21/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.21/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -j /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -g512 -G2048 /build/reproducible-path/samtools-1.21/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -c /build/reproducible-path/samtools-1.21/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d an -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d an -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/avw_tQpPKL/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/avw_tQpPKL/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /tmp/avw_tQpPKL/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -m 10M /build/reproducible-path/samtools-1.21/test/large_pos/longref_name.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools merge -O sam --no-PG - /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam /build/reproducible-path/samtools-1.21/test/large_pos/longref2.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools depth /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools depth -b /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/avw_tQpPKL/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/reproducible-path/samtools-1.21/samtools fixmate -O sam --no-PG - - | /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_hard_clipped.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/1_soft_clipped.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools reset --dupflag | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag < /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: cat /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.cram .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG sam_to_fixed_bam /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index --no-PG /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/reset/seq.sam -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset /build/reproducible-path/samtools-1.21/test/reset/seq.sam -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok Number of tests: total .. 990 passed .. 946 failed .. 0 expected failure .. 44 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 120 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 53 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh cram-size.reg === Testing cram-size.reg regressions === Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 65 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' rm -fr -- /tmp/dh-xdg-rundir-zsmxcL_q make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.21/debian/tmp make -j3 install DESTDIR=/build/reproducible-path/samtools-1.21/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.21' mkdir -p -m 755 /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' make clean make[2]: Entering directory '/build/reproducible-path/samtools-1.21' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.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-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/samtools-1.21' 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-1.21' 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-1.21' 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-1.21' 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-1.21' # 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-1.21' dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 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 1731584159 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1731584159 as canonical time Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/samtools cd debian/samtools-test chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian 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-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/reproducible-path/samtools-1.21' cd '/build/reproducible-path/samtools-1.21' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 debian/rules execute_after_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/samtools-1.21' chmod -x /build/reproducible-path/samtools-1.21/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' dh_missing dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 729158 new size 750642 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.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/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.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/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.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/67/e928e02c0111fee9a809fa505157999a001621.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.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/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.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/14/4f2a177ea7991a0822e26944c28ad098e39606.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.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/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.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/df/692591be73a860f596386f769a08d2034a2d43.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.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=144f2a177ea7991a0822e26944c28ad098e39606 48ca1f475bfbcda812a638c0eeea747ea9cc5f22 4a3389d400e7a3f36f8902d21b43794fc0e5302f 5d2a4e264350e4290193be9c8c57a1ed7add64ea 67e928e02c0111fee9a809fa505157999a001621 710f3c191656ce7f7f819003dbcaa4296e2973a0 df692591be73a860f596386f769a08d2034a2d43" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/samtools-test/DEBIAN echo misc:Depends= >> debian/samtools-test.substvars echo misc:Pre-Depends= >> debian/samtools-test.substvars dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb: building package 'samtools' in '../samtools_1.21-0+exp1_armhf.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.21-0+exp1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.21-0+exp1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.21-0+exp1_armhf.buildinfo dpkg-genchanges --build=binary -O../samtools_1.21-0+exp1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.21/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ 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/6550 and its subdirectories I: Current time: Fri Nov 22 05:45:11 -12 2024 I: pbuilder-time-stamp: 1732297511 Fri Nov 22 17:45:39 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Fri Nov 22 17:45:39 UTC 2024 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Fri Nov 22 17:45:39 UTC 2024 - checking /var/lib/jenkins/offline_nodes if virt64a-armhf-rb.debian.net is marked as down. Fri Nov 22 17:45:39 UTC 2024 - checking via ssh if virt64a-armhf-rb.debian.net is up. removed '/tmp/read-only-fs-test-tlwx1B' ==================================================================================== Fri Nov 22 17:45:44 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on virt64a, called using "2 samtools experimental /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi 1.21-0+exp1" as arguments. Fri Nov 22 17:45:44 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-pUuLmiNl" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 17:45:44 UTC 2024 I: Downloading source for experimental/samtools=1.21-0+exp1 Reading package lists... NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools.git Please use: git clone https://salsa.debian.org/med-team/samtools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5707 kB of source archives. Get:1 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (dsc) [2272 B] Get:2 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (tar) [5683 kB] Get:3 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (diff) [22.1 kB] Fetched 5707 kB in 0s (47.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools.git Please use: git clone https://salsa.debian.org/med-team/samtools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5707 kB of source archives. Get:1 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (dsc) [2272 B] Get:2 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (tar) [5683 kB] Get:3 http://cdn-fastly.deb.debian.org/debian experimental/main samtools 1.21-0+exp1 (diff) [22.1 kB] Fetched 5707 kB in 0s (47.1 MB/s) Download complete and in download only mode ============================================================================= Re-Building samtools in experimental on armhf on virt64a now. Date: Fri Nov 22 17:45:44 UTC 2024 Date UTC: Fri Nov 22 17:45:44 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/pbuilderrc_RhZo + case ${ARCH} in + case $NUM_CPU in + case $ARCH in + locale=it_CH + language=it + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' samtools = debian-installer -o samtools = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' samtools = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/pbuilderrc_RhZo --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b2 --logfile b2/build.log samtools_1.21-0+exp1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 23 07:45:45 +14 2024 I: pbuilder-time-stamp: 1732297545 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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_1.21-0+exp1.dsc] I: copying [./samtools_1.21.orig.tar.gz] I: copying [./samtools_1.21-0+exp1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 14 19:30:19 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./samtools_1.21-0+exp1.dsc: no acceptable signature found dpkg-source: info: extracting samtools in samtools-1.21 dpkg-source: info: unpacking samtools_1.21.orig.tar.gz dpkg-source: info: unpacking samtools_1.21-0+exp1.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/20800/tmp/hooks/D01_modify_environment starting debug: Running on virt64a. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 22 17:45 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=experimental EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=9b34ed21d43f4555ac03c1401bbfe047 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=20800 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/pbuilderrc_RhZo --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b2 --logfile b2/build.log samtools_1.21-0+exp1.dsc' SUDO_GID=114 SUDO_UID=108 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-27-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.21~), 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 ... 19686 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 (>= 1.21~); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on automake; however: Package automake is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 22.5 MB of archives. After unpacking 84.3 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libhts-dev (>= 1.21~) but it is not going to be installed The following actions will resolve these dependencies: Install the following packages: 1) comerr-dev [2.1-1.47.1-1+b1 (unstable)] 2) krb5-multidev [1.21.3-3 (unstable)] 3) libbrotli-dev [1.1.0-2+b6 (unstable)] 4) libbrotli1 [1.1.0-2+b6 (unstable)] 5) libcom-err2 [1.47.1-1+b1 (unstable)] 6) libcurl3t64-gnutls [8.11.0-1 (unstable)] 7) libcurl4-gnutls-dev [8.11.0-1 (unstable)] 8) libdeflate-dev [1.22-1 (unstable)] 9) libevent-2.1-7t64 [2.1.12-stable-10+b1 (unstable)] 10) libgmp-dev [2:6.3.0+dfsg-2+b2 (unstable)] 11) libgmpxx4ldbl [2:6.3.0+dfsg-2+b2 (unstable)] 12) libgnutls-dane0t64 [3.8.8-2 (unstable)] 13) libgnutls-openssl27t64 [3.8.8-2 (unstable)] 14) libgnutls28-dev [3.8.8-2 (unstable)] 15) libgssapi-krb5-2 [1.21.3-3 (unstable)] 16) libgssrpc4t64 [1.21.3-3 (unstable)] 17) libhts-dev [1.21+ds-0+exp2 (experimental)] 18) libhts3t64 [1.21+ds-0+exp2 (experimental)] 19) libidn2-dev [2.3.7-2+b1 (unstable)] 20) libk5crypto3 [1.21.3-3 (unstable)] 21) libkadm5clnt-mit12 [1.21.3-3 (unstable)] 22) libkadm5srv-mit12 [1.21.3-3 (unstable)] 23) libkdb5-10t64 [1.21.3-3 (unstable)] 24) libkeyutils1 [1.6.3-4 (unstable)] 25) libkrb5-3 [1.21.3-3 (unstable)] 26) libkrb5-dev [1.21.3-3 (unstable)] 27) libkrb5support0 [1.21.3-3 (unstable)] 28) libldap-2.5-0 [2.5.18+dfsg-3+b1 (unstable)] 29) libldap-dev [2.6.8+dfsg-1~exp4+b1 (experimental)] 30) libldap2 [2.6.8+dfsg-1~exp4+b1 (experimental)] 31) libnghttp2-14 [1.64.0-1 (unstable)] 32) libnghttp2-dev [1.64.0-1 (unstable)] 33) libnghttp3-9 [1.4.0-1+b1 (unstable)] 34) libnghttp3-dev [1.4.0-1+b1 (unstable)] 35) libngtcp2-16 [1.6.0-1 (unstable)] 36) libngtcp2-crypto-gnutls-dev [1.6.0-1 (unstable)] 37) libngtcp2-crypto-gnutls8 [1.6.0-1 (unstable)] 38) libngtcp2-dev [1.6.0-1 (unstable)] 39) libp11-kit-dev [0.25.5-2+b1 (unstable)] 40) libpsl-dev [0.21.2-1.1+b1 (unstable)] 41) libpsl5t64 [0.21.2-1.1+b1 (unstable)] 42) librtmp-dev [2.4+20151223.gitfa8646d.1-2+b5 (unstable)] 43) librtmp1 [2.4+20151223.gitfa8646d.1-2+b5 (unstable)] 44) libsasl2-2 [2.1.28+dfsg1-8 (unstable)] 45) libsasl2-modules-db [2.1.28+dfsg1-8 (unstable)] 46) libssh2-1-dev [1.11.1-1 (unstable)] 47) libssh2-1t64 [1.11.1-1 (unstable)] 48) libssl-dev [3.4.0-1 (experimental)] 49) libtasn1-6-dev [4.19.0-3+b3 (unstable)] 50) libunbound8 [1.22.0-1 (unstable)] 51) libzstd-dev [1.5.6+dfsg-1+b1 (unstable)] 52) nettle-dev [3.10-1+b1 (unstable)] Upgrade the following packages: 53) libssl3t64 [3.3.2-2 (now, unstable) -> 3.4.0-1 (experimental)] 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} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{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-2.5-0{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} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages will be upgraded: libssl3t64 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 1 packages upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 39.1 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian experimental/main armhf libssl3t64 armhf 3.4.0-1 [1883 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf bash-completion all 1:2.14.0-2 [310 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.1-1+b1 [54.3 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 27 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 38 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-3 [52.5 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-3 [37.0 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-3 [37.1 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-3 [46.7 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-3 [126 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.4.0-1+b1 [55.0 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.11.0-1 [310 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1 [539 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.8-2 [440 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.8-2 [440 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-2+b1 [208 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b2 [328 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b2 [593 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.8-2 [1328 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-3 [15.8 kB] Get: 71 http://deb.debian.org/debian experimental/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4+b1 [162 kB] Get: 72 http://deb.debian.org/debian experimental/main armhf libldap-dev armhf 2.6.8+dfsg-1~exp4+b1 [282 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libnghttp3-dev armhf 1.4.0-1+b1 [79.8 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls-dev armhf 1.6.0-1 [22.1 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libngtcp2-dev armhf 1.6.0-1 [168 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 83 http://deb.debian.org/debian experimental/main armhf libssl-dev armhf 3.4.0-1 [2428 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-1+b1 [327 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.11.0-1 [434 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libdeflate-dev armhf 1.22-1 [44.5 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB] Get: 90 http://deb.debian.org/debian experimental/main armhf libhts3t64 armhf 1.21+ds-0+exp2 [407 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf liblzma-dev armhf 5.6.3-1+b1 [304 kB] Get: 92 http://deb.debian.org/debian experimental/main armhf libhts-dev armhf 1.21+ds-0+exp2 [1655 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf libio-pty-perl armhf 1:1.20-1+b2 [33.8 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libncurses-dev armhf 6.5-2+b1 [310 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf tabix armhf 1.20+ds-2 [418 kB] Fetched 39.1 MB in 1s (26.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19686 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Preparing to unpack .../libssl3t64_3.4.0-1_armhf.deb ... Unpacking libssl3t64:armhf (3.4.0-1) over (3.3.2-2) ... Setting up libssl3t64:armhf (3.4.0-1) ... Selecting previously unselected package sensible-utils. (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 ... 20868 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package bash-completion. Preparing to unpack .../01-bash-completion_1%3a2.14.0-2_all.deb ... Unpacking bash-completion (1:2.14.0-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_armhf.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../16-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package comerr-dev:armhf. Preparing to unpack .../17-comerr-dev_2.1-1.47.1-1+b1_armhf.deb ... Unpacking comerr-dev:armhf (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-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 .../22-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../24-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../26-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../32-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../33-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../34-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../35-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../36-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libgssrpc4t64:armhf. Preparing to unpack .../37-libgssrpc4t64_1.21.3-3_armhf.deb ... Unpacking libgssrpc4t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:armhf. Preparing to unpack .../38-libkadm5clnt-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5clnt-mit12:armhf (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:armhf. Preparing to unpack .../39-libkdb5-10t64_1.21.3-3_armhf.deb ... Unpacking libkdb5-10t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:armhf. Preparing to unpack .../40-libkadm5srv-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5srv-mit12:armhf (1.21.3-3) ... Selecting previously unselected package krb5-multidev:armhf. Preparing to unpack .../41-krb5-multidev_1.21.3-3_armhf.deb ... Unpacking krb5-multidev:armhf (1.21.3-3) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../42-libbrotli1_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:armhf. Preparing to unpack .../43-libbrotli-dev_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli-dev:armhf (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../44-libbz2-dev_1.0.8-6_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../45-libsasl2-modules-db_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../46-libsasl2-2_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../47-libldap-2.5-0_2.5.18+dfsg-3+b1_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../48-libnghttp2-14_1.64.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:armhf. Preparing to unpack .../49-libnghttp3-9_1.4.0-1+b1_armhf.deb ... Unpacking libnghttp3-9:armhf (1.4.0-1+b1) ... Selecting previously unselected package libngtcp2-16:armhf. Preparing to unpack .../50-libngtcp2-16_1.6.0-1_armhf.deb ... Unpacking libngtcp2-16:armhf (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:armhf. Preparing to unpack .../51-libngtcp2-crypto-gnutls8_1.6.0-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../52-libpsl5t64_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../53-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../54-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:armhf. Preparing to unpack .../55-libcurl3t64-gnutls_8.11.0-1_armhf.deb ... Unpacking libcurl3t64-gnutls:armhf (8.11.0-1) ... Selecting previously unselected package libevent-2.1-7t64:armhf. Preparing to unpack .../56-libevent-2.1-7t64_2.1.12-stable-10+b1_armhf.deb ... Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:armhf. Preparing to unpack .../57-libunbound8_1.22.0-1_armhf.deb ... Unpacking libunbound8:armhf (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:armhf. Preparing to unpack .../58-libgnutls-dane0t64_3.8.8-2_armhf.deb ... Unpacking libgnutls-dane0t64:armhf (3.8.8-2) ... Selecting previously unselected package libgnutls-openssl27t64:armhf. Preparing to unpack .../59-libgnutls-openssl27t64_3.8.8-2_armhf.deb ... Unpacking libgnutls-openssl27t64:armhf (3.8.8-2) ... Selecting previously unselected package libidn2-dev:armhf. Preparing to unpack .../60-libidn2-dev_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-dev:armhf (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:armhf. Preparing to unpack .../61-libp11-kit-dev_0.25.5-2+b1_armhf.deb ... Unpacking libp11-kit-dev:armhf (0.25.5-2+b1) ... Selecting previously unselected package libtasn1-6-dev:armhf. Preparing to unpack .../62-libtasn1-6-dev_4.19.0-3+b3_armhf.deb ... Unpacking libtasn1-6-dev:armhf (4.19.0-3+b3) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../63-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b2_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../64-libgmp-dev_2%3a6.3.0+dfsg-2+b2_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package nettle-dev:armhf. Preparing to unpack .../65-nettle-dev_3.10-1+b1_armhf.deb ... Unpacking nettle-dev:armhf (3.10-1+b1) ... Selecting previously unselected package libgnutls28-dev:armhf. Preparing to unpack .../66-libgnutls28-dev_3.8.8-2_armhf.deb ... Unpacking libgnutls28-dev:armhf (3.8.8-2) ... Selecting previously unselected package libkrb5-dev:armhf. Preparing to unpack .../67-libkrb5-dev_1.21.3-3_armhf.deb ... Unpacking libkrb5-dev:armhf (1.21.3-3) ... Selecting previously unselected package libldap2:armhf. Preparing to unpack .../68-libldap2_2.6.8+dfsg-1~exp4+b1_armhf.deb ... Unpacking libldap2:armhf (2.6.8+dfsg-1~exp4+b1) ... Selecting previously unselected package libldap-dev:armhf. Preparing to unpack .../69-libldap-dev_2.6.8+dfsg-1~exp4+b1_armhf.deb ... Unpacking libldap-dev:armhf (2.6.8+dfsg-1~exp4+b1) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../70-libpkgconf3_1.8.1-4_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../71-pkgconf-bin_1.8.1-4_armhf.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../72-pkgconf_1.8.1-4_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:armhf. Preparing to unpack .../73-libnghttp2-dev_1.64.0-1_armhf.deb ... Unpacking libnghttp2-dev:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:armhf. Preparing to unpack .../74-libnghttp3-dev_1.4.0-1+b1_armhf.deb ... Unpacking libnghttp3-dev:armhf (1.4.0-1+b1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:armhf. Preparing to unpack .../75-libngtcp2-crypto-gnutls-dev_1.6.0-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls-dev:armhf (1.6.0-1) ... Selecting previously unselected package libngtcp2-dev:armhf. Preparing to unpack .../76-libngtcp2-dev_1.6.0-1_armhf.deb ... Unpacking libngtcp2-dev:armhf (1.6.0-1) ... Selecting previously unselected package libpsl-dev:armhf. Preparing to unpack .../77-libpsl-dev_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl-dev:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../78-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:armhf. Preparing to unpack .../79-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../80-libssl-dev_3.4.0-1_armhf.deb ... Unpacking libssl-dev:armhf (3.4.0-1) ... Selecting previously unselected package libssh2-1-dev:armhf. Preparing to unpack .../81-libssh2-1-dev_1.11.1-1_armhf.deb ... Unpacking libssh2-1-dev:armhf (1.11.1-1) ... Selecting previously unselected package libzstd-dev:armhf. Preparing to unpack .../82-libzstd-dev_1.5.6+dfsg-1+b1_armhf.deb ... Unpacking libzstd-dev:armhf (1.5.6+dfsg-1+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../83-libcurl4-gnutls-dev_8.11.0-1_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (8.11.0-1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../84-libdeflate0_1.22-1_armhf.deb ... Unpacking libdeflate0:armhf (1.22-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../85-libdeflate-dev_1.22-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.22-1) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../86-libhtscodecs2_1.6.1-1_armhf.deb ... Unpacking libhtscodecs2:armhf (1.6.1-1) ... Selecting previously unselected package libhts3t64:armhf. Preparing to unpack .../87-libhts3t64_1.21+ds-0+exp2_armhf.deb ... Unpacking libhts3t64:armhf (1.21+ds-0+exp2) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../88-liblzma-dev_5.6.3-1+b1_armhf.deb ... Unpacking liblzma-dev:armhf (5.6.3-1+b1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../89-libhts-dev_1.21+ds-0+exp2_armhf.deb ... Unpacking libhts-dev:armhf (1.21+ds-0+exp2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../90-libio-pty-perl_1%3a1.20-1+b2_armhf.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../91-libncurses6_6.5-2+b1_armhf.deb ... Unpacking libncurses6:armhf (6.5-2+b1) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../92-libncurses-dev_6.5-2+b1_armhf.deb ... Unpacking libncurses-dev:armhf (6.5-2+b1) ... Selecting previously unselected package tabix. Preparing to unpack .../93-tabix_1.20+ds-2_armhf.deb ... Unpacking tabix (1.20+ds-2) ... Setting up libhtscodecs2:armhf (1.6.1-1) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libgnutls-openssl27t64:armhf (3.8.8-2) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up libzstd-dev:armhf (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:armhf (1.22.0-1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Setting up libgnutls-dane0t64:armhf (3.8.8-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up bash-completion (1:2.14.0-2) ... Setting up libncurses6:armhf (6.5-2+b1) ... Setting up comerr-dev:armhf (2.1-1.47.1-1+b1) ... Setting up libssl-dev:armhf (3.4.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libidn2-dev:armhf (2.3.7-2+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:armhf (1.4.0-1+b1) ... Setting up libnghttp3-dev:armhf (1.4.0-1+b1) ... Setting up liblzma-dev:armhf (5.6.3-1+b1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libngtcp2-16:armhf (1.6.0-1) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libtasn1-6-dev:armhf (4.19.0-3+b3) ... Setting up libdeflate-dev:armhf (1.22-1) ... Setting up tabix (1.20+ds-2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:armhf (2.6.8+dfsg-1~exp4+b1) ... Setting up libbrotli-dev:armhf (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Setting up libp11-kit-dev:armhf (0.25.5-2+b1) ... Setting up libbz2-dev:armhf (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libncurses-dev:armhf (6.5-2+b1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:armhf (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up libngtcp2-crypto-gnutls-dev:armhf (1.6.0-1) ... Setting up libngtcp2-dev:armhf (1.6.0-1) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Setting up pkgconf:armhf (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:armhf (2.6.8+dfsg-1~exp4+b1) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libssh2-1-dev:armhf (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:armhf (3.8.8-2) ... Setting up libnghttp2-dev:armhf (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:armhf (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:armhf (1.21.3-3) ... Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:armhf (1.21+ds-0+exp2) ... Setting up libkadm5clnt-mit12:armhf (1.21.3-3) ... Setting up libkdb5-10t64:armhf (1.21.3-3) ... Setting up debhelper (13.20) ... Setting up libkadm5srv-mit12:armhf (1.21.3-3) ... Setting up krb5-multidev:armhf (1.21.3-3) ... Setting up libkrb5-dev:armhf (1.21.3-3) ... Setting up libcurl4-gnutls-dev:armhf (8.11.0-1) ... Setting up libhts-dev:armhf (1.21+ds-0+exp2) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/20800/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for experimental I: user script /srv/workspace/pbuilder/20800/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/samtools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../samtools_1.21-0+exp1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.21-0+exp1 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from samtools-1.21/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-1.21' rm -f config.mk touch config.mk dh_auto_clean -- make -j4 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.21' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.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-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc option to enable large file support... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j4 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.21' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option '-frelease' is valid for D but not for C 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.21"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/reproducible-path/samtools-1.21@«BUILDPATH»@g' version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/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_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.21' 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-1.21/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/lLvf1KLWi4/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/lLvf1KLWi4/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/lLvf1KLWi4/bgzip.dat.gz .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 3:11-13 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 1:100-104 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 1:99998-100007 .. ok .. ok /build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/reproducible-path/samtools-1.21/test/dat/dict.fa .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/lLvf1KLWi4/dict.fa.gz .. ok test_dict: cat /build/reproducible-path/samtools-1.21/test/dat/dict.fa | /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -AH < /build/reproducible-path/samtools-1.21/test/dat/dict.alias.fa .. ok test_dict: /build/reproducible-path/samtools-1.21/samtools dict -H -l /build/reproducible-path/samtools-1.21/test/dat/dict.alt < /build/reproducible-path/samtools-1.21/test/dat/dict.alias.fa .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view /tmp/lLvf1KLWi4/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view /tmp/lLvf1KLWi4/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/lLvf1KLWi4/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/lLvf1KLWi4/auto_indexed.crai && cat /tmp/lLvf1KLWi4/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/lLvf1KLWi4/large_chrom.bam ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/lLvf1KLWi4/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/lLvf1KLWi4/test_input_1_b.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/lLvf1KLWi4/auto_indexed.crai && cat /tmp/lLvf1KLWi4/auto_indexed.crai .. ok test_index: /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.bam.list -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.cram.list -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.bam.urllist -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.cram.urllist -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lLvf1KLWi4/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lLvf1KLWi4/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/reproducible-path/samtools-1.21/samtools mpileup /build/reproducible-path/samtools-1.21/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate .. ok test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools consensus .. ok test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools import .. ok test_usage_subcommand: samtools reference .. ok test_usage_subcommand: samtools reset .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth .. ok test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags .. ok test_usage_subcommand: samtools head .. ok test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools samples Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/lLvf1KLWi4/view.001.forn (SAM input) .. ok 68: Count -N /tmp/lLvf1KLWi4/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/lLvf1KLWi4/view.001.forn (BAM input) .. ok 70: Count -N /tmp/lLvf1KLWi4/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/lLvf1KLWi4/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/lLvf1KLWi4/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/lLvf1KLWi4/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test115.sam -h -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test117.sam -h -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test119.sam -h -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test121.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test123.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test125.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /build/reproducible-path/samtools-1.21/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-1.21/samtools head /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 0 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 1 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 5 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 29 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 30 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 0 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 1 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -n 5 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam .. ok test_head: /build/reproducible-path/samtools-1.21/samtools head -h 5 -n 5 < /build/reproducible-path/samtools-1.21/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-1.21/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -0 /build/reproducible-path/samtools-1.21/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -0 /build/reproducible-path/samtools-1.21/test/0.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -T RG,BC,QT -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/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-1.21/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.21/test/bc_split.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -T MD,ia -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -1 /build/reproducible-path/samtools-1.21/test/o.fq -2 /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fasta -N -1 /build/reproducible-path/samtools-1.21/test/o.fa -2 /build/reproducible-path/samtools-1.21/test/o.fa /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -o /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -s /tmp/lLvf1KLWi4/bam2fq.discard.s.fq -0 /tmp/lLvf1KLWi4/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.21/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.21/test/i1.fq --i2 /build/reproducible-path/samtools-1.21/test/i2.fq -0 /build/reproducible-path/samtools-1.21/test/0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -t -T '*' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -N -T '*' -d ia /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.21/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-1.21/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.21/test/bc_split.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -T MD,ia -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -1 /build/reproducible-path/samtools-1.21/test/o.fq -2 /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fasta -@ 2 -N -1 /build/reproducible-path/samtools-1.21/test/o.fa -2 /build/reproducible-path/samtools-1.21/test/o.fa /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -o /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -s /tmp/lLvf1KLWi4/bam2fq.discard.s.fq -0 /tmp/lLvf1KLWi4/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.21/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.21/test/i1.fq --i2 /build/reproducible-path/samtools-1.21/test/i2.fq -0 /build/reproducible-path/samtools-1.21/test/0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -T '*' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d ia /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.21/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-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa -i 0 /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -S RG -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -S RG -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -t /build/reproducible-path/samtools-1.21/test/stat/11.stats.targets /build/reproducible-path/samtools-1.21/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -g 4 -t /build/reproducible-path/samtools-1.21/test/stat/11.stats.targets /build/reproducible-path/samtools-1.21/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -g 4 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.21/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.21/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.21/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.21/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I s1 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I grp2 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I grp3 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -I Sample /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/mpileup/ce.fa /build/reproducible-path/samtools-1.21/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam -b /tmp/DwsJpoalnw - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -r -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -cp -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -o - -s 1 -O sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.1.bam /tmp/lLvf1KLWi4/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.3.bam /tmp/lLvf1KLWi4/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/lLvf1KLWi4/merge.bed.1.bam /tmp/lLvf1KLWi4/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -r -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.2.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam -b /tmp/_oeRhjRfcI - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -r -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -cp -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -o - -s 1 -O sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.1.bam /tmp/lLvf1KLWi4/merge.tag.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.3.bam /tmp/lLvf1KLWi4/merge.tag.4.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/lLvf1KLWi4/merge.bed.1.bam /tmp/lLvf1KLWi4/merge.bed.2.bam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -r -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.2.sam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -N -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -n -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t AS -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -t FI -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort --template-coordinate -m 10M /build/reproducible-path/samtools-1.21/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -M -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -MH -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout.bam .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sorttmp .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -N -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t AS -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t FI -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools sort -@ 2 --template-coordinate -m 10M /build/reproducible-path/samtools-1.21/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -M -K10 -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -M -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -MH -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -O /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -o /build/reproducible-path/samtools-1.21/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -o /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -f /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -O /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.21/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate3.tmp .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -f /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/1_fast_collate.sam .. ok test_collate: /build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/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-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/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-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bounds.sam - .. ok /build/reproducible-path/samtools-1.21/samtools calmd -uAr /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa .. ok /build/reproducible-path/samtools-1.21/samtools calmd -@ 2 -uAr /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck -v /build/reproducible-path/samtools-1.21/test/quickcheck/1.quickcheck.badeof.bam /build/reproducible-path/samtools-1.21/test/quickcheck/2.quickcheck.badheader.bam /build/reproducible-path/samtools-1.21/test/quickcheck/3.quickcheck.ok.bam /build/reproducible-path/samtools-1.21/test/quickcheck/4.quickcheck.ok.bam /build/reproducible-path/samtools-1.21/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/6.quickcheck.cram21.ok.cram /build/reproducible-path/samtools-1.21/test/quickcheck/7.quickcheck.cram30.ok.cram /build/reproducible-path/samtools-1.21/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/reproducible-path/samtools-1.21/samtools quickcheck -uv /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader --in-place /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram && /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader --in-place /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram && /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/reproducible-path/samtools-1.21/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m overwrite_all /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m orphan_only /build/reproducible-path/samtools-1.21/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -R '1#9' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/reproducible-path/samtools-1.21/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -O sam -r --no-PG /build/reproducible-path/samtools-1.21/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.21/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/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-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/5_markdup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam -r --no-PG /build/reproducible-path/samtools-1.21/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/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-1.21/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/17_read_group.sam - .. ok test_markdup: /build/reproducible-path/samtools-1.21/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.21/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -j /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -g512 -G2048 /build/reproducible-path/samtools-1.21/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_bedcov: /build/reproducible-path/samtools-1.21/samtools bedcov -c /build/reproducible-path/samtools-1.21/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d an -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d an -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_split: /build/reproducible-path/samtools-1.21/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/lLvf1KLWi4/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/lLvf1KLWi4/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /tmp/lLvf1KLWi4/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -m 10M /build/reproducible-path/samtools-1.21/test/large_pos/longref_name.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools merge -O sam --no-PG - /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam /build/reproducible-path/samtools-1.21/test/large_pos/longref2.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools depth /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools depth -b /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/lLvf1KLWi4/longref.sam.gz .. ok test_large_positions: /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/reproducible-path/samtools-1.21/samtools fixmate -O sam --no-PG - - | /build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_hard_clipped.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/1_soft_clipped.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools reset --dupflag | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag < /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools view .. ok test_reset: cat /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.cram .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG sam_to_fixed_bam /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index --no-PG /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset --dupflag /build/reproducible-path/samtools-1.21/test/reset/seq.sam -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok test_reset: /build/reproducible-path/samtools-1.21/samtools reset /build/reproducible-path/samtools-1.21/test/reset/seq.sam -o /build/reproducible-path/samtools-1.21/test/reset/output .. ok Number of tests: total .. 990 passed .. 946 failed .. 0 expected failure .. 44 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 120 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 53 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh cram-size.reg === Testing cram-size.reg regressions === Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 65 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' rm -fr -- /tmp/dh-xdg-rundir-xD0B56gg make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.21/debian/tmp make -j4 install DESTDIR=/build/reproducible-path/samtools-1.21/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.21' mkdir -p -m 755 /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.21/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-1.21/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-1.21/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' make clean make[2]: Entering directory '/build/reproducible-path/samtools-1.21' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.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-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/samtools-1.21' 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-1.21' 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-1.21' 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-1.21' 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-1.21' # 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-1.21' dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 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 1731584159 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1731584159 as canonical time Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/samtools cd debian/samtools-test chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian chmod a-x usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian cd '/build/reproducible-path/samtools-1.21' cd '/build/reproducible-path/samtools-1.21' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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-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/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-1.21' chmod -x /build/reproducible-path/samtools-1.21/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' dh_missing dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 729158 new size 750642 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.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/df/692591be73a860f596386f769a08d2034a2d43.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.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/67/e928e02c0111fee9a809fa505157999a001621.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.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/14/4f2a177ea7991a0822e26944c28ad098e39606.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.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/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.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/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.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/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.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/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.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-test/DEBIAN echo misc:Depends= >> debian/samtools-test.substvars echo misc:Pre-Depends= >> debian/samtools-test.substvars dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=144f2a177ea7991a0822e26944c28ad098e39606 48ca1f475bfbcda812a638c0eeea747ea9cc5f22 4a3389d400e7a3f36f8902d21b43794fc0e5302f 5d2a4e264350e4290193be9c8c57a1ed7add64ea 67e928e02c0111fee9a809fa505157999a001621 710f3c191656ce7f7f819003dbcaa4296e2973a0 df692591be73a860f596386f769a08d2034a2d43" -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.21-0+exp1_armhf.deb'. dpkg-deb: building package 'samtools' in '../samtools_1.21-0+exp1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.21-0+exp1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.21-0+exp1_armhf.buildinfo dpkg-genchanges --build=binary -O../samtools_1.21-0+exp1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.21/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/20800/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/20800/tmp/hooks/B01_cleanup finished 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/20800 and its subdirectories I: Current time: Sat Nov 23 07:50:07 +14 2024 I: pbuilder-time-stamp: 1732297807 + false + set +x Fri Nov 22 17:50:07 UTC 2024 I: Signing ./b2/samtools_1.21-0+exp1_armhf.buildinfo as samtools_1.21-0+exp1_armhf.buildinfo.asc Fri Nov 22 17:50:07 UTC 2024 I: Signed ./b2/samtools_1.21-0+exp1_armhf.buildinfo as ./b2/samtools_1.21-0+exp1_armhf.buildinfo.asc Fri Nov 22 17:50:07 UTC 2024 - build #2 for samtools/experimental/armhf on virt64a done. Starting cleanup. All cleanup done. Fri Nov 22 17:50:07 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-pUuLmiNl, removing. /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi: total 280 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 17:45 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 17:50 b2 -rw------- 1 jenkins jenkins 266716 Nov 22 17:45 rbuildlog.jhts4YW -rw-r--r-- 1 jenkins jenkins 2272 Nov 14 19:34 samtools_1.21-0+exp1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b1: total 9800 -rw-r--r-- 1 jenkins jenkins 263000 Nov 22 17:45 build.log -rw-r--r-- 1 jenkins jenkins 993212 Nov 22 17:45 samtools-dbgsym_1.21-0+exp1_armhf.deb -rw-r--r-- 1 jenkins jenkins 2366700 Nov 22 17:45 samtools-test_1.21-0+exp1_all.deb -rw-r--r-- 1 jenkins jenkins 22052 Nov 22 17:45 samtools_1.21-0+exp1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2272 Nov 22 17:45 samtools_1.21-0+exp1.dsc -rw-r--r-- 1 jenkins jenkins 7433 Nov 22 17:45 samtools_1.21-0+exp1_armhf.buildinfo -rw-r--r-- 1 jenkins jenkins 8315 Nov 22 17:45 samtools_1.21-0+exp1_armhf.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1844 Nov 22 17:45 samtools_1.21-0+exp1_armhf.changes -rw-r--r-- 1 jenkins jenkins 631956 Nov 22 17:45 samtools_1.21-0+exp1_armhf.deb -rw-r--r-- 1 jenkins jenkins 1596 Nov 22 17:45 samtools_1.21-0+exp1_source.changes -rw-r--r-- 1 jenkins jenkins 5682709 Nov 22 17:45 samtools_1.21.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b2: total 9800 -rw-r--r-- 1 jenkins jenkins 265011 Nov 22 17:50 build.log -rw-r--r-- 1 jenkins jenkins 993212 Nov 22 17:50 samtools-dbgsym_1.21-0+exp1_armhf.deb -rw-r--r-- 1 jenkins jenkins 2366700 Nov 22 17:50 samtools-test_1.21-0+exp1_all.deb -rw-r--r-- 1 jenkins jenkins 22052 Nov 22 17:50 samtools_1.21-0+exp1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2272 Nov 22 17:50 samtools_1.21-0+exp1.dsc -rw-r--r-- 1 jenkins jenkins 7433 Nov 22 17:50 samtools_1.21-0+exp1_armhf.buildinfo -rw-r--r-- 1 jenkins jenkins 8315 Nov 22 17:50 samtools_1.21-0+exp1_armhf.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1844 Nov 22 17:50 samtools_1.21-0+exp1_armhf.changes -rw-r--r-- 1 jenkins jenkins 631956 Nov 22 17:50 samtools_1.21-0+exp1_armhf.deb -rw-r--r-- 1 jenkins jenkins 1596 Nov 22 17:50 samtools_1.21-0+exp1_source.changes -rw-r--r-- 1 jenkins jenkins 5682709 Nov 22 17:50 samtools_1.21.orig.tar.gz Fri Nov 22 17:50:35 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Fri Nov 22 17:50:37 UTC 2024 I: samtools_1.21-0+exp1_armhf.changes: Format: 1.8 Date: Thu, 14 Nov 2024 12:35:59 +0100 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: armhf all Version: 1.21-0+exp1 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats samtools-test - test files for the samtools package Closes: 1087456 Changes: samtools (1.21-0+exp1) experimental; urgency=medium . * Team upload. * New upstream version * d/rules: build-depend on newer htslib 1.21. Closes: #1087456 Checksums-Sha1: 55970b6e90e3684b7a80bb81932ebc10984819c8 993212 samtools-dbgsym_1.21-0+exp1_armhf.deb 9ff1d629f9fd5f173cd844bb1b784c88560e2d8a 2366700 samtools-test_1.21-0+exp1_all.deb 4a967568bf6b4348f927ae614b000d7544800fd9 7433 samtools_1.21-0+exp1_armhf.buildinfo 507ad797f8443ea111812a7e75a8136730553c2e 631956 samtools_1.21-0+exp1_armhf.deb Checksums-Sha256: 3476635df891f6900cd33cf04802c8193680482b14f7a7e7e74bfcd96c3cedb7 993212 samtools-dbgsym_1.21-0+exp1_armhf.deb 11b898f0fd5b8adc1e2a80947e53a77d09cdba9c36bbccba1f1dbf8e5f9f8dd4 2366700 samtools-test_1.21-0+exp1_all.deb b17067591a4dfc1fd9133bc45b5e747fbff062da88acf79419ae76c46f533ba5 7433 samtools_1.21-0+exp1_armhf.buildinfo 628a6ab1d79ef176801f520fd784165e8006164072f219d3402e85ce40b7b66a 631956 samtools_1.21-0+exp1_armhf.deb Files: 8bae8d62004f367b2c7a9643589c35e5 993212 debug optional samtools-dbgsym_1.21-0+exp1_armhf.deb 68b3e6880501aade5c874a0e6548236d 2366700 science optional samtools-test_1.21-0+exp1_all.deb 4a845e6b7b950558251fbbaa421f7304 7433 science optional samtools_1.21-0+exp1_armhf.buildinfo f83bce333d397bbb6f5f6c1301c918e1 631956 science optional samtools_1.21-0+exp1_armhf.deb Diff of the two buildlogs: -- --- b1/build.log 2024-11-22 17:45:16.670710419 +0000 +++ b2/build.log 2024-11-22 17:50:12.793276398 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 22 05:31:41 -12 2024 -I: pbuilder-time-stamp: 1732296701 +I: Current time: Sat Nov 23 07:45:45 +14 2024 +I: pbuilder-time-stamp: 1732297545 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying reproducible.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6550/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 22 17:45 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='c1a3c51aae2d4667b8d039d1ac72f79b' - 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='6550' - PS1='# ' - PS2='> ' + INVOCATION_ID=9b34ed21d43f4555ac03c1401bbfe047 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=20800 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.RfmZQeJi/pbuilderrc_Qrp7 --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b1 --logfile b1/build.log samtools_1.21-0+exp1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/pbuilderrc_RhZo --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b2 --logfile b2/build.log samtools_1.21-0+exp1.dsc' + SUDO_GID=114 + SUDO_UID=108 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux wbq0 6.1.0-27-armmp #1 SMP Debian 6.1.115-1 (2024-11-01) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/6550/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -297,7 +329,7 @@ Get: 94 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libncurses-dev armhf 6.5-2+b1 [310 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf tabix armhf 1.20+ds-2 [418 kB] -Fetched 39.1 MB in 6s (6859 kB/s) +Fetched 39.1 MB in 1s (26.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19686 files and directories currently installed.) @@ -696,7 +728,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/samtools-1.21/ && 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_1.21-0+exp1_source.changes +I: user script /srv/workspace/pbuilder/20800/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/20800/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/samtools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../samtools_1.21-0+exp1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.21-0+exp1 dpkg-buildpackage: info: source distribution experimental @@ -711,7 +747,7 @@ rm -f config.mk touch config.mk dh_auto_clean -- - make -j3 distclean + make -j4 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.21' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai @@ -798,15 +834,15 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" + make -j4 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.21' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option '-frelease' is valid for D but not for C 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -894,9 +930,9 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c 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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c @@ -908,9 +944,9 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C +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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c @@ -953,21 +989,21 @@ gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread +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_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' 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-1.21' dh_auto_test -- BGZIP=/usr/bin/bgzip - make -j3 test "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip + make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.21' test/split/test_count_rg test/split/test_expand_format_string @@ -1006,75 +1042,75 @@ /build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/avw_tQpPKL/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/lLvf1KLWi4/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/avw_tQpPKL/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/lLvf1KLWi4/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/avw_tQpPKL/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/lLvf1KLWi4/bgzip.dat.gz .. ok -/build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.21/samtools faidx /tmp/avw_tQpPKL/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 3:11-13 +/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 3:11-13 +/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 2:998-1003 +/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 2:998-1003 +/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 1:100-104 +/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 1:100-104 +/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq 1:99998-100007 +/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 1:99998-100007 .. ok .. ok -/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/avw_tQpPKL/fqidx.fq.gz 1:99998-100007 +/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -1084,7 +1120,7 @@ .. ok test_dict: - /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/avw_tQpPKL/dict.fa.gz + /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/lLvf1KLWi4/dict.fa.gz .. ok test_dict: @@ -1100,11 +1136,11 @@ .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view /tmp/avw_tQpPKL/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.21/samtools view /tmp/lLvf1KLWi4/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view /tmp/avw_tQpPKL/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.21/samtools view /tmp/lLvf1KLWi4/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -1112,19 +1148,19 @@ .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/avw_tQpPKL/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.21/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/lLvf1KLWi4/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b_opt.bam.bai ref2 + /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -1140,23 +1176,23 @@ .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi + /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/avw_tQpPKL/auto_indexed.crai && cat /tmp/avw_tQpPKL/auto_indexed.crai + /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/lLvf1KLWi4/auto_indexed.crai && cat /tmp/lLvf1KLWi4/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi + /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/avw_tQpPKL/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/lLvf1KLWi4/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/avw_tQpPKL/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/lLvf1KLWi4/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -1164,19 +1200,19 @@ .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/avw_tQpPKL/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/lLvf1KLWi4/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/avw_tQpPKL/test_input_1_b_opt.bam.bai ref2 + /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -1192,39 +1228,39 @@ .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi + /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/avw_tQpPKL/auto_indexed.crai && cat /tmp/avw_tQpPKL/auto_indexed.crai + /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/lLvf1KLWi4/auto_indexed.crai && cat /tmp/lLvf1KLWi4/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/avw_tQpPKL/auto_indexed.csi && cat /tmp/avw_tQpPKL/auto_indexed.csi + /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi .. ok test_mpileup: - /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.bam.list -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.bam.list -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.cram.list -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.cram.list -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.bam.urllist -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.bam.urllist -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/avw_tQpPKL/mpileup.cram.urllist -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.cram.urllist -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:1050-1060 /tmp/avw_tQpPKL/mpileup.1.bam | grep -v mpileup + /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lLvf1KLWi4/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/avw_tQpPKL/mpileup.ref.fa.gz -r17:1050-1060 /tmp/avw_tQpPKL/mpileup.1.cram | grep -v mpileup + /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lLvf1KLWi4/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1512,53 +1548,53 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/avw_tQpPKL/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok - 67: Filter -N /tmp/avw_tQpPKL/view.001.forn (SAM input) .. ok + 67: Filter -N /tmp/lLvf1KLWi4/view.001.forn (SAM input) .. ok - 68: Count -N /tmp/avw_tQpPKL/view.001.forn (SAM input) .. ok + 68: Count -N /tmp/lLvf1KLWi4/view.001.forn (SAM input) .. ok - 69: Filter -N /tmp/avw_tQpPKL/view.001.forn (BAM input) .. ok + 69: Filter -N /tmp/lLvf1KLWi4/view.001.forn (BAM input) .. ok - 70: Count -N /tmp/avw_tQpPKL/view.001.forn (BAM input) .. ok + 70: Count -N /tmp/lLvf1KLWi4/view.001.forn (BAM input) .. ok - 71: Filter -N /tmp/avw_tQpPKL/view.001.forn (CRAM input) .. ok + 71: Filter -N /tmp/lLvf1KLWi4/view.001.forn (CRAM input) .. ok - 72: Count -N /tmp/avw_tQpPKL/view.001.forn (CRAM input) .. ok + 72: Count -N /tmp/lLvf1KLWi4/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok @@ -1584,53 +1620,53 @@ 84: Count -d BC:TGCA (CRAM input) .. ok - 85: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input) .. ok + 85: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input) .. ok - 86: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input) .. ok + 86: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input) .. ok - 87: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input) .. ok + 87: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input) .. ok - 88: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input) .. ok + 88: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input) .. ok - 89: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input) .. ok + 89: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input) .. ok - 90: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input) .. ok + 90: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input) .. ok - 91: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (SAM input).. ok + 91: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (SAM input).. ok - 92: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (SAM input).. ok + 92: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (SAM input).. ok - 93: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (BAM input).. ok + 93: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (BAM input).. ok - 94: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (BAM input).. ok + 94: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (BAM input).. ok - 95: Filter -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (CRAM input).. ok + 95: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (CRAM input).. ok - 96: Count -D BC:/tmp/avw_tQpPKL/view.001.fobc -d BC:TGCA (CRAM input).. ok + 96: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (CRAM input).. ok - 97: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input).. ok + 97: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input).. ok - 98: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (SAM input).. ok + 98: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input).. ok - 99: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input).. ok + 99: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input).. ok - 100: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (BAM input).. ok + 100: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input).. ok - 101: Filter -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input).. ok + 101: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input).. ok - 102: Count -d BC:TGCA -D BC:/tmp/avw_tQpPKL/view.001.fobc (CRAM input).. ok + 102: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input).. ok - 103: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok + 103: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok - 104: Count -D RG:/tmp/avw_tQpPKL/view.001.fogn (SAM input) .. ok + 104: Count -D RG:/tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok - 105: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok + 105: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok - 106: Count -D RG:/tmp/avw_tQpPKL/view.001.fogn (BAM input) .. ok + 106: Count -D RG:/tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok - 107: Filter -D RG:/tmp/avw_tQpPKL/view.001.fogn (CRAM input).. ok + 107: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok - 108: Count -D RG:/tmp/avw_tQpPKL/view.001.fogn (CRAM input) .. ok + 108: Count -D RG:/tmp/lLvf1KLWi4/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok @@ -1646,126 +1682,126 @@ 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test115.sam -h -d TGCA /tmp/avw_tQpPKL/view.001.sam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test115.sam -h -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/view.001.sam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test117.sam -h -d TGCA /tmp/avw_tQpPKL/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test117.sam -h -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test119.sam -h -d TGCA /tmp/avw_tQpPKL/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test119.sam -h -d TGCA /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d TGCA /tmp/avw_tQpPKL/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/view.test006.cram --no-PG .. expected failure - 121: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" + 121: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test121.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.001.sam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test121.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.001.sam --no-PG .. expected failure - 122: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" + 122: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.001.sam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.001.sam --no-PG .. expected failure - 123: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" + 123: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test123.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test123.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test001.bam --no-PG .. expected failure - 124: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" + 124: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test001.bam --no-PG .. expected failure - 125: Filter -D BClong:/tmp/avw_tQpPKL/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" + 125: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.21/samtools view -o /tmp/avw_tQpPKL/view.test125.sam -h -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test125.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test006.cram --no-PG .. expected failure - 126: Count -D BClong:/tmp/avw_tQpPKL/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/avw_tQpPKL/view.001.fobc" + 126: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/avw_tQpPKL/view.001.fobc /tmp/avw_tQpPKL/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/view.001.sam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/view.001.sam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -o /tmp/avw_tQpPKL/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/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-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/avw_tQpPKL/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/view.test006.cram --no-PG .. expected failure @@ -2667,7 +2703,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.21/samtools fastq -N -s /tmp/avw_tQpPKL/bam2fq.discard.s.fq -0 /tmp/avw_tQpPKL/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.21/samtools fastq -N -s /tmp/lLvf1KLWi4/bam2fq.discard.s.fq -0 /tmp/lLvf1KLWi4/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2808,7 +2844,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -s /tmp/avw_tQpPKL/bam2fq.discard.s.fq -0 /tmp/avw_tQpPKL/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -s /tmp/lLvf1KLWi4/bam2fq.discard.s.fq -0 /tmp/lLvf1KLWi4/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -3025,7 +3061,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam -b /tmp/3WYe1BIefS - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam -b /tmp/DwsJpoalnw - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_merge: @@ -3049,11 +3085,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.1.bam /tmp/avw_tQpPKL/merge.tag.2.bam + /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.1.bam /tmp/lLvf1KLWi4/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.3.bam /tmp/avw_tQpPKL/merge.tag.4.bam + /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.3.bam /tmp/lLvf1KLWi4/merge.tag.4.bam .. ok test_merge: @@ -3061,7 +3097,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/avw_tQpPKL/merge.bed.1.bam /tmp/avw_tQpPKL/merge.bed.2.bam + /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/lLvf1KLWi4/merge.bed.1.bam /tmp/lLvf1KLWi4/merge.bed.2.bam .. ok test_merge: @@ -3081,7 +3117,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam -b /tmp/ctEC6DyYGi - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam -b /tmp/_oeRhjRfcI - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam .. ok test_merge: @@ -3105,11 +3141,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.1.bam /tmp/avw_tQpPKL/merge.tag.2.bam + /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.1.bam /tmp/lLvf1KLWi4/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/avw_tQpPKL/merge.tag.3.bam /tmp/avw_tQpPKL/merge.tag.4.bam + /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.3.bam /tmp/lLvf1KLWi4/merge.tag.4.bam .. ok test_merge: @@ -3117,7 +3153,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/avw_tQpPKL/merge.bed.1.bam /tmp/avw_tQpPKL/merge.bed.2.bam + /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/lLvf1KLWi4/merge.bed.1.bam /tmp/lLvf1KLWi4/merge.bed.2.bam .. ok test_merge: @@ -3129,15 +3165,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.21/samtools sort /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout + /build/reproducible-path/samtools-1.21/samtools sort /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.21/samtools sort -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout.bam + /build/reproducible-path/samtools-1.21/samtools sort -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.21/samtools sort -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sorttmp + /build/reproducible-path/samtools-1.21/samtools sort -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sorttmp .. ok test_sort: @@ -3189,15 +3225,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.21/samtools sort -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout + /build/reproducible-path/samtools-1.21/samtools sort -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sortout.bam + /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/avw_tQpPKL/sorttmp + /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sorttmp .. ok test_sort: @@ -3901,15 +3937,15 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/avw_tQpPKL/longref.sam.gz + /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/lLvf1KLWi4/longref.sam.gz .. ok test_large_positions: - /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/avw_tQpPKL/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/lLvf1KLWi4/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: - /build/reproducible-path/samtools-1.21/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /tmp/avw_tQpPKL/longref.sam.gz + /build/reproducible-path/samtools-1.21/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /tmp/lLvf1KLWi4/longref.sam.gz .. ok test_large_positions: @@ -3929,7 +3965,7 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.21/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/avw_tQpPKL/longref.sam.gz + /build/reproducible-path/samtools-1.21/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/lLvf1KLWi4/longref.sam.gz .. ok test_large_positions: @@ -4177,7 +4213,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.21' - rm -fr -- /tmp/dh-xdg-rundir-zsmxcL_q + rm -fr -- /tmp/dh-xdg-rundir-xD0B56gg make[1]: Leaving directory '/build/reproducible-path/samtools-1.21' create-stamp debian/debhelper-build-stamp dh_prep @@ -4189,7 +4225,7 @@ dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.21/debian/tmp - make -j3 install DESTDIR=/build/reproducible-path/samtools-1.21/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j4 install DESTDIR=/build/reproducible-path/samtools-1.21/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.21' mkdir -p -m 755 /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin @@ -4274,28 +4310,10 @@ dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 - mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 - mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 - mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 - mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 - mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 - mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 - mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 - mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 - mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 - mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 - mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 - mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 - mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 - mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 - mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 - mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 - mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 @@ -4306,14 +4324,7 @@ mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 - mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 - mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 - mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 - mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 - mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 - mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 - mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 @@ -4322,7 +4333,34 @@ mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 + mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 + mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 + mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 + mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 + mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 + mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 + mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 + mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 + mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 + mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 + mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 + mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 + mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 + mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 + mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 + mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 + mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 + mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 + mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 + mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 + mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 + mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 + mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 + mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 + mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 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 @@ -4341,9 +4379,9 @@ cd debian/samtools cd debian/samtools-test 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-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 + gzip -9nf usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian cd '/build/reproducible-path/samtools-1.21' cd '/build/reproducible-path/samtools-1.21' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz @@ -4357,8 +4395,8 @@ find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + 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-1.21' chmod -x /build/reproducible-path/samtools-1.21/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam @@ -4371,41 +4409,41 @@ objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.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/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug debian/samtools/usr/bin/md5fa - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.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/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug debian/samtools/usr/bin/samtools + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.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/df/692591be73a860f596386f769a08d2034a2d43.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.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/67/e928e02c0111fee9a809fa505157999a001621.debug debian/samtools/usr/bin/maq2sam-short - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.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/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.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/14/4f2a177ea7991a0822e26944c28ad098e39606.debug debian/samtools/usr/bin/maq2sam-long + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.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/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug debian/samtools/usr/bin/wgsim + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.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/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug debian/samtools/usr/bin/md5fa + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.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/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.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/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug debian/samtools/usr/bin/md5sum-lite - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.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/df/692591be73a860f596386f769a08d2034a2d43.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz @@ -4417,7 +4455,7 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect @@ -4426,15 +4464,15 @@ install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN dh_gencontrol + install -m0755 -d debian/samtools-test/DEBIAN + echo misc:Depends= >> debian/samtools-test.substvars + echo misc:Pre-Depends= >> debian/samtools-test.substvars + dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=144f2a177ea7991a0822e26944c28ad098e39606 48ca1f475bfbcda812a638c0eeea747ea9cc5f22 4a3389d400e7a3f36f8902d21b43794fc0e5302f 5d2a4e264350e4290193be9c8c57a1ed7add64ea 67e928e02c0111fee9a809fa505157999a001621 710f3c191656ce7f7f819003dbcaa4296e2973a0 df692591be73a860f596386f769a08d2034a2d43" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - install -m0755 -d debian/samtools-test/DEBIAN - echo misc:Depends= >> debian/samtools-test.substvars - echo misc:Pre-Depends= >> debian/samtools-test.substvars - dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools @@ -4454,10 +4492,10 @@ chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. - dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. -dpkg-deb: building package 'samtools' in '../samtools_1.21-0+exp1_armhf.deb'. + dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.21-0+exp1_armhf.deb'. +dpkg-deb: building package 'samtools' in '../samtools_1.21-0+exp1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.21-0+exp1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.21-0+exp1_armhf.buildinfo dpkg-genchanges --build=binary -O../samtools_1.21-0+exp1_armhf.changes @@ -4467,12 +4505,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/20800/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/20800/tmp/hooks/B01_cleanup finished 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/6550 and its subdirectories -I: Current time: Fri Nov 22 05:45:11 -12 2024 -I: pbuilder-time-stamp: 1732297511 +I: removing directory /srv/workspace/pbuilder/20800 and its subdirectories +I: Current time: Sat Nov 23 07:50:07 +14 2024 +I: pbuilder-time-stamp: 1732297807 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/armhf/samtools_1.21-0+exp1.diff: 88.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/armhf/samtools_1.21-0+exp1.diff.gz b2/build.log: 89.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 89.8% -- replaced with stdout Fri Nov 22 17:50:38 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_samtools_experimental_armhf_1732297838 + touch /var/log/reproducible-builds/diffoscope_stamp_samtools_experimental_armhf_1732297838 + RESULT=0 + systemd-run '--description=diffoscope on samtools/1.21-0+exp1 in experimental/armhf' --slice=rb-build-diffoscope.slice -u rb-diffoscope-armhf_10-6067 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi --run-session -c jenkins-reproducible-unstable-diffoscope-6c37286e-6744-4da5-b7c0-96977621c037 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/dbd-tmp-dSpOsd3 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/samtools_1.21-0+exp1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/samtools_1.21-0+exp1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/samtools_1.21-0+exp1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b1/samtools_1.21-0+exp1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b2/samtools_1.21-0+exp1_armhf.changes' + false + set +x Running as unit: rb-diffoscope-armhf_10-6067.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/samtools_1.21-0+exp1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/samtools_1.21-0+exp1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/samtools_1.21-0+exp1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b1/samtools_1.21-0+exp1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b2/samtools_1.21-0+exp1_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.417s) 0.417s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.058s) 0.058s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 773ms CPU time consumed: 765ms _ _ ___ __ _ _ __ ___ | |_ ___ ___ | |___ / __|/ _` | '_ ` _ \| __/ _ \ / _ \| / __| \__ \ (_| | | | | | | || (_) | (_) | \__ \ |___/\__,_|_| |_| |_|\__\___/ \___/|_|___/ Fri Nov 22 17:50:39 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 22 17:50:39 UTC 2024 I: samtools from experimental built successfully and reproducibly on armhf. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-22 17:50:40] INFO: Starting at 2024-11-22 17:50:40.072024 [2024-11-22 17:50:40] INFO: Generating the pages of 1 package(s) [2024-11-22 17:50:40] CRITICAL: https://tests.reproducible-builds.org/debian/experimental/armhf/samtools didn't produce a buildlog, even though it has been built. [2024-11-22 17:50:40] INFO: Finished at 2024-11-22 17:50:40.839683, took: 0:00:00.767664 Fri Nov 22 17:50:40 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/experimental/armhf/samtools.html Fri Nov 22 17:50:40 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 22 17:50:40 UTC 2024 I: Submitting 12K b1/samtools_1.21-0+exp1_armhf.buildinfo.asc https://buildinfo.debian.net/4a967568bf6b4348f927ae614b000d7544800fd9/samtools_1.21-0+exp1_all Fri Nov 22 17:50:41 UTC 2024 I: Submitting 12K b2/samtools_1.21-0+exp1_armhf.buildinfo.asc https://buildinfo.debian.net/51c52d18161d0e1378395e1c8cbc2e8591718b55/samtools_1.21-0+exp1_all Fri Nov 22 17:50:42 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 22 17:50:42 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 22 17:50:42 UTC 2024 I: Removing signed samtools_1.21-0+exp1_armhf.buildinfo.asc files: removed './b1/samtools_1.21-0+exp1_armhf.buildinfo.asc' removed './b2/samtools_1.21-0+exp1_armhf.buildinfo.asc' 1732297842 armhf experimental samtools Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/experimental/armhf/samtools_1.21-0+exp1.rbuild.log: 88.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/experimental/armhf/samtools_1.21-0+exp1.rbuild.log.gz [2024-11-22 17:50:43] INFO: Starting at 2024-11-22 17:50:43.214740 [2024-11-22 17:50:43] INFO: Generating the pages of 1 package(s) [2024-11-22 17:50:44] INFO: Finished at 2024-11-22 17:50:44.143065, took: 0:00:00.928334 All cleanup done. Fri Nov 22 17:50:44 UTC 2024 - total duration: 0h 19m 28s. Fri Nov 22 17:50:44 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-K0zZnBvW, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 19min 32.584s CPU time consumed: 8.703s