Wed Dec 15 06:48:52 UTC 2021 I: starting to build samtools/buster/amd64 on jenkins on '2021-12-15 06:48' Wed Dec 15 06:48:52 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/39485/console.log Wed Dec 15 06:48:52 UTC 2021 I: Downloading source for buster/samtools=1.9-4 --2021-12-15 06:48:53-- http://deb.debian.org/debian/pool/main/s/samtools/samtools_1.9-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2199 (2.1K) Saving to: ‘samtools_1.9-4.dsc’ 0K .. 100% 121M=0s 2021-12-15 06:48:53 (121 MB/s) - ‘samtools_1.9-4.dsc’ saved [2199/2199] Wed Dec 15 06:48:53 UTC 2021 I: samtools_1.9-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.9-4 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: http://www.htslib.org/ Standards-Version: 4.3.0 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 (>= 12~), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.9), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0) Package-List: samtools deb science optional arch=any samtools-test deb science optional arch=all Checksums-Sha1: d5e163f7d7b232f99ac36d7749d5786b77af59d9 4098992 samtools_1.9.orig.tar.gz 101923e6658b76c53fc7aa15676c467ad6f9a6cd 20684 samtools_1.9-4.debian.tar.xz Checksums-Sha256: 211600bd180d01030b3fe25baa7ae1c105106bed6c3f8d993f41dd278d44c637 4098992 samtools_1.9.orig.tar.gz 24c7be2bbd0f53e825e608f5631270266e83a0f0c27f0612f76bff07e6989a04 20684 samtools_1.9-4.debian.tar.xz Files: e2f2e401af7e8309075ba4545118819d 4098992 samtools_1.9.orig.tar.gz 9586773a217b50161bf203fba7066d8f 20684 samtools_1.9-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxu4U4RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFpcBAAge3Id0hPpM1M6wVwC7uk5dkhw59ePBrN Ea1NmdpUOCv99eYX3m7n1XxHG7CiXqdk0DMRz0236YpJ2HfseooUB07caRjfxv3g MqwIPxcWzlb6ElFxh6rNsqFplM5Q+iAfnkJD9WNBWwBUEIgePpYFeS77QAjSVgIi cvMU6Dn/Bxnnuxkn7HjkaCS2QP8CS9CoBs9PmsWkToioqwY5xNsojmM2RfI7ep5q kbOYmj/FUKFxWs3Tqx7jqMYKvhoDChz7kj2hasmie3mneEwBX8+0jb75kpK8HtEz cmlH1FUlQkCGwHkAQo71SptRGmPonIbPTdijZ82/O7w1cXD7V95tCSEERC599Ag+ KodqMyXsbINKI7nwIlUUnSE0ZyoxlX9RZ57slhx9U3MdhcEjrOZub+HUubVbFkBF lri098SymwLcra415csMtbt09wt8BIoN+4qta/P0OtkO9/q+k+dJdxWHcr38XuYV 4HAIY2J1XiirQQRY1m7wlTOOBKCSnue006P6ShPGRsCoMSsTDaZIE9p3ZG/Z9VeO ypj1vAb5UVUQsDJA//bFqYn9hw2u1zP9KAvUIAsEyINA6eHiEI4JLc+87FcS9Rch vKnE5vvFCk6Wv66x/IwWTBtS+gXDRgdFp6WTP/TzgBKvL05dIg72HuXIvG57AkW8 /+YwJ9d8Z1Y= =03lc -----END PGP SIGNATURE----- Wed Dec 15 06:48:53 UTC 2021 I: Checking whether the package is not for us Wed Dec 15 06:48:53 UTC 2021 I: Starting 1st build on remote node ionos15-amd64.debian.net. Wed Dec 15 06:48:53 UTC 2021 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Wed Dec 15 06:50:39 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 17 01:11:56 -12 2023 I: pbuilder-time-stamp: 1673961116 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_1.9-4.dsc] I: copying [./samtools_1.9.orig.tar.gz] I: copying [./samtools_1.9-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Feb 21 05:35:10 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./samtools_1.9-4.dsc dpkg-source: info: extracting samtools in samtools-1.9 dpkg-source: info: unpacking samtools_1.9.orig.tar.gz dpkg-source: info: unpacking samtools_1.9-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch dpkg-source: info: applying sort-tests-memory-limit.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1882377/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ad73610aac984d0e85d8e9b332d3d992' 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='1882377' 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/tmp.cjLObFpaCN/pbuilderrc_Drmc --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/b1 --logfile b1/build.log samtools_1.9-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 10 16:20 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/1882377/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.9), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 12~); however: Package debhelper 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 libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.9); 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 pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on tabix (>= 1.0); however: Package tabix 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 29.3 MB of archives. After unpacking 97.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 autoconf-archive all 20180313-1 [749 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 bash-completion all 1:2.8-6 [208 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libncurses-dev amd64 6.1+20181013-2+deb10u2 [333 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libncurses5-dev amd64 6.1+20181013-2+deb10u2 [948 B] Get: 59 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 tabix amd64 1.9-12~deb10u1 [292 kB] Fetched 29.3 MB in 0s (79.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package autoconf-archive. Preparing to unpack .../06-autoconf-archive_20180313-1_all.deb ... Unpacking autoconf-archive (20180313-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package bash-completion. Preparing to unpack .../08-bash-completion_1%3a2.8-6_all.deb ... Unpacking bash-completion (1:2.8-6) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../09-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../10-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../11-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../12-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../13-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../16-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../17-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../18-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../24-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../26-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../27-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../28-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../29-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../30-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../31-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../32-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../33-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../34-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../35-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../36-libkrb5support0_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../37-libk5crypto3_1.17-3+deb10u3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../38-libssl1.1_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../39-libkrb5-3_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../40-libgssapi-krb5-2_1.17-3+deb10u3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../41-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../42-libsasl2-2_2.1.27+dfsg-1+deb10u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../43-libldap-common_2.4.47+dfsg-3+deb10u6_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../44-libldap-2.4-2_2.4.47+dfsg-3+deb10u6_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../45-libnghttp2-14_1.36.0-2+deb10u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../46-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../47-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../48-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../49-libcurl3-gnutls_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../50-libdeflate0_1.2-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.2-1) ... Selecting previously unselected package libhts2:amd64. Preparing to unpack .../51-libhts2_1.9-12~deb10u1_amd64.deb ... Unpacking libhts2:amd64 (1.9-12~deb10u1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../52-liblzma-dev_5.2.4-1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.2.4-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../53-zlib1g-dev_1%3a1.2.11.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../54-libhts-dev_1.9-12~deb10u1_amd64.deb ... Unpacking libhts-dev:amd64 (1.9-12~deb10u1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../55-libio-pty-perl_1%3a1.08-1.1+b5_amd64.deb ... Unpacking libio-pty-perl (1:1.08-1.1+b5) ... Selecting previously unselected package libncurses-dev:amd64. Preparing to unpack .../56-libncurses-dev_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses-dev:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libncurses5-dev:amd64. Preparing to unpack .../57-libncurses5-dev_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses5-dev:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package pkg-config. Preparing to unpack .../58-pkg-config_0.29-6_amd64.deb ... Unpacking pkg-config (0.29-6) ... Selecting previously unselected package tabix. Preparing to unpack .../59-tabix_1.9-12~deb10u1_amd64.deb ... Unpacking tabix (1.9-12~deb10u1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up autoconf-archive (20180313-1) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up bash-completion (1:2.8-6) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libncurses-dev:amd64 (6.1+20181013-2+deb10u2) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libncurses5-dev:amd64 (6.1+20181013-2+deb10u2) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up tabix (1.9-12~deb10u1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.9-12~deb10u1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/samtools-1.9/ && 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_1.9-4_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.9-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from samtools-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/samtools-1.9' rm -f config.mk touch config.mk dh_auto_clean -- make -j16 distclean make[2]: Entering directory '/build/samtools-1.9' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a 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/samtools-1.9' make[1]: Leaving directory '/build/samtools-1.9' 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build 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:56: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:56: the top level configure.ac:56: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:56: the top level configure.ac:56: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:56: the top level configure.ac:56: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:56: 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/samtools-1.9' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal configure.ac:56: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:56: the top level autoconf configure.ac:56: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:56: the top level dh_auto_configure -- --with-htslib=system ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for 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/samtools-1.9' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/samtools-1.9' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j16 "CFLAGS=-g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/samtools-1.9' gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.9"' > version.h gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c ar -rcs libst.a sam_opts.o sam_utils.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -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 ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lz 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_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_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.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 ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.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 libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/samtools-1.9' make[1]: Leaving directory '/build/samtools-1.9' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/samtools-1.9' dh_auto_test -- \ BGZIP=/usr/bin/bgzip make -j16 test VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/samtools-1.9' REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} /usr/bin/bgzip -c -b 65272 -s 5 /tmp/vwAFHEfE6l/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/vwAFHEfE6l/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/vwAFHEfE6l/bgzip.dat.gz .. ok /build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/samtools-1.9/samtools faidx /tmp/vwAFHEfE6l/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq 3:11-13 .. ok .. ok /build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq.gz 3:11-13 .. ok .. ok /build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq 2:998-1003 .. ok .. ok /build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq 1:100-104 .. ok .. ok /build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq.gz 1:100-104 .. ok .. ok /build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq 1:99998-100007 .. ok .. ok /build/samtools-1.9/samtools fqidx /tmp/vwAFHEfE6l/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/samtools-1.9/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/samtools-1.9/test/dat/dict.fa .. ok test_dict: /build/samtools-1.9/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/vwAFHEfE6l/dict.fa.gz .. ok test_dict: cat /build/samtools-1.9/test/dat/dict.fa | /build/samtools-1.9/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_index: /build/samtools-1.9/samtools view /tmp/vwAFHEfE6l/large_chrom.bam ref2 .. ok test_index: /build/samtools-1.9/samtools view /tmp/vwAFHEfE6l/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-1.9/samtools index /build/samtools-1.9/test/dat/test_input_1_a.bam && cat /build/samtools-1.9/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-1.9/samtools view -@ 2 /tmp/vwAFHEfE6l/large_chrom.bam ref2 .. ok test_index: /build/samtools-1.9/samtools view -@ 2 /tmp/vwAFHEfE6l/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-1.9/samtools index -@ 2 /build/samtools-1.9/test/dat/test_input_1_a.bam && cat /build/samtools-1.9/test/dat/test_input_1_a.bam.bai .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -b /tmp/vwAFHEfE6l/mpileup.bam.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -b /tmp/vwAFHEfE6l/mpileup.cram.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -b /tmp/vwAFHEfE6l/mpileup.bam.urllist -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -b /tmp/vwAFHEfE6l/mpileup.cram.urllist -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -uvDV -b /tmp/vwAFHEfE6l/mpileup.bam.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -uvDV -b /tmp/vwAFHEfE6l/mpileup.cram.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/vwAFHEfE6l/mpileup.cram.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/vwAFHEfE6l/mpileup.cram.list -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -B --ff 0x14 -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:1050-1060 /tmp/vwAFHEfE6l/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/samtools-1.9/samtools mpileup -B --ff 0x14 -f /tmp/vwAFHEfE6l/mpileup.ref.fa.gz -r17:1050-1060 /tmp/vwAFHEfE6l/mpileup.1.cram | grep -v mpileup .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad .. 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 collate Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure 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 bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools depth Usage on stderr rather than stdout .. expected failure 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 flags Usage on stderr rather than stdout .. expected failure 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_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/vwAFHEfE6l/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/vwAFHEfE6l/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/vwAFHEfE6l/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/vwAFHEfE6l/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/vwAFHEfE6l/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/vwAFHEfE6l/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/vwAFHEfE6l/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/vwAFHEfE6l/view.001.fogn (CRAM input).. ok 67: Filter -l Library 2 (SAM input) .. ok 68: Count -l Library 2 (SAM input) .. ok 69: Filter -l Library 2 (BAM input) .. ok 70: Count -l Library 2 (BAM input) .. ok 71: Filter -l Library 2 (CRAM input) .. ok 72: Count -l Library 2 (CRAM input) .. ok 73: Filter -l Library 3 (SAM input) .. ok 74: Count -l Library 3 (SAM input) .. ok 75: Filter -l Library 3 (BAM input) .. ok 76: Count -l Library 3 (BAM input) .. ok 77: Filter -l Library 3 (CRAM input) .. ok 78: Count -l Library 3 (CRAM input) .. ok 79: Filter -q 50 (SAM input) .. ok 80: Count -q 50 (SAM input) .. ok 81: Filter -q 50 (BAM input) .. ok 82: Count -q 50 (BAM input) .. ok 83: Filter -q 50 (CRAM input) .. ok 84: Count -q 50 (CRAM input) .. ok 85: Filter -q 99 (SAM input) .. ok 86: Count -q 99 (SAM input) .. ok 87: Filter -q 99 (BAM input) .. ok 88: Count -q 99 (BAM input) .. ok 89: Filter -q 99 (CRAM input) .. ok 90: Count -q 99 (CRAM input) .. ok 91: Filter -q 100 (SAM input) .. ok 92: Count -q 100 (SAM input) .. ok 93: Filter -q 100 (BAM input) .. ok 94: Count -q 100 (BAM input) .. ok 95: Filter -q 100 (CRAM input) .. ok 96: Count -q 100 (CRAM input) .. ok 97: Filter -x fa (SAM input) .. ok 98: Count -x fa (SAM input) .. ok 99: Filter -x fa (BAM input) .. ok 100: Count -x fa (BAM input) .. ok 101: Filter -x fa (CRAM input) .. ok 102: Count -x fa (CRAM input) .. ok 103: Filter -x fa -x ha (SAM input) .. ok 104: Count -x fa -x ha (SAM input) .. ok 105: Filter -x fa -x ha (BAM input) .. ok 106: Count -x fa -x ha (BAM input) .. ok 107: Filter -x fa -x ha (CRAM input) .. ok 108: Count -x fa -x ha (CRAM input) .. ok 109: Filter -x fa -r grp2 (SAM input) .. ok 110: Count -x fa -r grp2 (SAM input) .. ok 111: Filter -x fa -r grp2 (BAM input) .. ok 112: Count -x fa -r grp2 (BAM input) .. ok 113: Filter -x fa -r grp2 (CRAM input) .. ok 114: Count -x fa -r grp2 (CRAM input) .. ok 115: Filter -x RG -r grp2 (SAM input) .. ok 116: Count -x RG -r grp2 (SAM input) .. ok 117: Filter -x RG -r grp2 (BAM input) .. ok 118: Count -x RG -r grp2 (BAM input) .. ok 119: Filter -x RG -r grp2 (CRAM input) .. ok 120: Count -x RG -r grp2 (CRAM input) .. ok 121: Filter -m 10 (SAM input) .. ok 122: Count -m 10 (SAM input) .. ok 123: Filter -m 10 (BAM input) .. ok 124: Count -m 10 (BAM input) .. ok 125: Filter -m 10 (CRAM input) .. ok 126: Count -m 10 (CRAM input) .. ok 127: Filter -m 11 (SAM input) .. ok 128: Count -m 11 (SAM input) .. ok 129: Filter -m 11 (BAM input) .. ok 130: Count -m 11 (BAM input) .. ok 131: Filter -m 11 (CRAM input) .. ok 132: Count -m 11 (CRAM input) .. ok 133: Filter -m 15 (SAM input) .. ok 134: Count -m 15 (SAM input) .. ok 135: Filter -m 15 (BAM input) .. ok 136: Count -m 15 (BAM input) .. ok 137: Filter -m 15 (CRAM input) .. ok 138: Count -m 15 (CRAM input) .. ok 139: Filter -m 16 (SAM input) .. ok 140: Count -m 16 (SAM input) .. ok 141: Filter -m 16 (BAM input) .. ok 142: Count -m 16 (BAM input) .. ok 143: Filter -m 16 (CRAM input) .. ok 144: Count -m 16 (CRAM input) .. ok 145: 1bp reads file SAM -> BAM -> SAM .. ok 146: 1bp reads file SAM -> CRAM -> SAM .. ok 146: Region Z (BAM input) .. ok 147: Count Z (BAM input) .. ok 148: Region Z (CRAM input) .. ok 149: Count Z (CRAM input) .. ok 150: Region Z:30 (BAM input) .. ok 151: Count Z:30 (BAM input) .. ok 152: Region Z:30 (CRAM input) .. ok 153: Count Z:30 (CRAM input) .. ok 154: Region Z:20-40 (BAM input) .. ok 155: Count Z:20-40 (BAM input) .. ok 156: Region Z:20-40 (CRAM input) .. ok 157: Count Z:20-40 (CRAM input) .. ok 158: Region ref1 (BAM input) .. ok 159: Count ref1 (BAM input) .. ok 160: Region ref1 (CRAM input) .. ok 161: Count ref1 (CRAM input) .. ok 162: Region ref1:15 (BAM input) .. ok 163: Count ref1:15 (BAM input) .. ok 164: Region ref1:15 (CRAM input) .. ok 165: Count ref1:15 (CRAM input) .. ok 166: Region ref1:15-45 (BAM input) .. ok 167: Count ref1:15-45 (BAM input) .. ok 168: Region ref1:15-45 (CRAM input) .. ok 169: Count ref1:15-45 (CRAM input) .. ok 170: Region ref1:15-45 ref2 (BAM input) .. ok 171: Count ref1:15-45 ref2 (BAM input) .. ok 172: Region ref1:15-45 ref2 (CRAM input) .. ok 173: Count ref1:15-45 ref2 (CRAM input) .. ok 174: Region ref1:15-45 ref2:16 (BAM input) .. ok 175: Count ref1:15-45 ref2:16 (BAM input) .. ok 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 186: Region -f 128 ref1 (BAM input) .. ok 187: Count -f 128 ref1 (BAM input) .. ok 188: Region -f 128 ref1 (CRAM input) .. ok 189: Count -f 128 ref1 (CRAM input) .. ok 190: Region -q 50 ref1:15-45 (BAM input) .. ok 191: Count -q 50 ref1:15-45 (BAM input) .. ok 192: Region -q 50 ref1:15-45 (CRAM input) .. ok 193: Count -q 50 ref1:15-45 (CRAM input) .. ok 194: Region -r grp2 ref1:15-45 (BAM input) .. ok 195: Count -r grp2 ref1:15-45 (BAM input) .. ok 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok 198: Region * (BAM input) .. ok 199: Count * (BAM input) .. ok 200: Region * (CRAM input) .. ok 201: Count * (CRAM input) .. ok 202: Region -L /build/samtools-1.9/test/dat/view.002.01.bed (BAM input).. ok 203: Count -L /build/samtools-1.9/test/dat/view.002.01.bed (BAM input).. ok 204: Region -L /build/samtools-1.9/test/dat/view.002.01.bed (CRAM input).. ok 205: Count -L /build/samtools-1.9/test/dat/view.002.01.bed (CRAM input).. ok 206: Region -L /build/samtools-1.9/test/dat/view.002.02.bed (BAM input).. ok 207: Count -L /build/samtools-1.9/test/dat/view.002.02.bed (BAM input).. ok 208: Region -L /build/samtools-1.9/test/dat/view.002.02.bed (CRAM input).. ok 209: Count -L /build/samtools-1.9/test/dat/view.002.02.bed (CRAM input).. ok 210: Region -L /build/samtools-1.9/test/dat/view.001.01.bed (BAM input).. ok 211: Count -L /build/samtools-1.9/test/dat/view.001.01.bed (BAM input).. ok 212: Region -L /build/samtools-1.9/test/dat/view.001.01.bed (CRAM input).. ok 213: Count -L /build/samtools-1.9/test/dat/view.001.01.bed (CRAM input).. ok 214: Region -L /build/samtools-1.9/test/dat/view.001.02.bed (BAM input).. ok 215: Count -L /build/samtools-1.9/test/dat/view.001.02.bed (BAM input).. ok 216: Region -L /build/samtools-1.9/test/dat/view.001.02.bed (CRAM input).. ok 217: Count -L /build/samtools-1.9/test/dat/view.001.02.bed (CRAM input).. ok 218: Region -L /build/samtools-1.9/test/dat/view.002.01.bed Z (BAM input).. ok 219: Count -L /build/samtools-1.9/test/dat/view.002.01.bed Z (BAM input).. ok 220: Region -L /build/samtools-1.9/test/dat/view.002.01.bed Z (CRAM input).. ok 221: Count -L /build/samtools-1.9/test/dat/view.002.01.bed Z (CRAM input).. ok 222: Region -L /build/samtools-1.9/test/dat/view.002.01.bed Z:30 (BAM input).. ok 223: Count -L /build/samtools-1.9/test/dat/view.002.01.bed Z:30 (BAM input).. ok 224: Region -L /build/samtools-1.9/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 225: Count -L /build/samtools-1.9/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 226: Region -L /build/samtools-1.9/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 227: Count -L /build/samtools-1.9/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 228: Region -L /build/samtools-1.9/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 229: Count -L /build/samtools-1.9/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 230: Region -L /build/samtools-1.9/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 231: Count -L /build/samtools-1.9/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 232: Region -L /build/samtools-1.9/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 233: Count -L /build/samtools-1.9/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 234: Region -L /build/samtools-1.9/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 235: Count -L /build/samtools-1.9/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 236: Region -L /build/samtools-1.9/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 237: Count -L /build/samtools-1.9/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 238: Region -L /build/samtools-1.9/test/dat/view.001.01.bed ref2 (BAM input).. ok 239: Count -L /build/samtools-1.9/test/dat/view.001.01.bed ref2 (BAM input).. ok 240: Region -L /build/samtools-1.9/test/dat/view.001.01.bed ref2 (CRAM input).. ok 241: Count -L /build/samtools-1.9/test/dat/view.001.01.bed ref2 (CRAM input).. ok 242: Region -L /build/samtools-1.9/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 243: Count -L /build/samtools-1.9/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 244: Region -L /build/samtools-1.9/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 245: Count -L /build/samtools-1.9/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 246: Region -L /build/samtools-1.9/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 247: Count -L /build/samtools-1.9/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 248: Region -L /build/samtools-1.9/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 249: Count -L /build/samtools-1.9/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 250: Region -L /build/samtools-1.9/test/dat/view.001.01.bed -f 128 (BAM input).. ok 251: Count -L /build/samtools-1.9/test/dat/view.001.01.bed -f 128 (BAM input).. ok 252: Region -L /build/samtools-1.9/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 253: Count -L /build/samtools-1.9/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 254: Region -L /build/samtools-1.9/test/dat/view.001.01.bed -q 5 (BAM input).. ok 255: Count -L /build/samtools-1.9/test/dat/view.001.01.bed -q 5 (BAM input).. ok 256: Region -L /build/samtools-1.9/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 257: Count -L /build/samtools-1.9/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 258: Region -L /build/samtools-1.9/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 259: Count -L /build/samtools-1.9/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 260: Region -L /build/samtools-1.9/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 261: Count -L /build/samtools-1.9/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 262: Make BAM with no M5/UR tags .. ok 263: Add @SQ with -t (SAM -> SAM) .. ok 264: Add @SQ with -T (SAM -> SAM) .. ok 265: Add @SQ with -t (BAM -> SAM) .. ok 266: Add @SQ with -T (BAM -> SAM) .. ok 267: Add @SQ with -t (SAM -> BAM) .. ok 268: Add @SQ with -T (SAM -> BAM) .. ok 269: Add @SQ with -t (BAM -> BAM) .. ok 270: Add @SQ with -T (BAM -> BAM) .. ok 271: Add @SQ with -t (SAM -> CRAM) .. ok 272: Add @SQ with -T (SAM -> CRAM) .. ok 273: Add @SQ with -t (BAM -> CRAM) .. ok 274: Add @SQ with -T (BAM -> CRAM) .. ok 275: Make CRAM with no UR field .. ok 276: Decoding CRAM with no UR field via -T .. ok 277: CIGAR B-operator removal .. ok 278: Big SAM -> BAM .. ok 279: Big SAM -> BAM (2 threads) .. ok 280: Big SAM -> BAM (4 threads) .. ok 281: Big SAM -> CRAM .. ok 282: Big SAM -> CRAM (2 threads) .. ok 283: Big SAM -> CRAM (4 threads) .. ok 284: Subsample 0.2 (SAM input) ............ ok 285: Subsample 0.5 (SAM input) ............ ok 286: Subsample 0.8 (SAM input) ............ ok 287: Subsample 0.2 (BAM input) ............ ok 288: Subsample 0.5 (BAM input) ............ ok 289: Subsample 0.8 (BAM input) ............ ok 290: Subsample 0.2 (CRAM input) ............ ok 291: Subsample 0.5 (CRAM input) ............ ok 292: Subsample 0.8 (CRAM input) ............ ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_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/samtools-1.9/samtools fastq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-1.9/test/bc.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.9/test/bc.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.9/test/bc.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-1.9/test/bc_split.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -N -t -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -N -t -T MD,ia -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -N -t -i -T MD,ia -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-1.9/test/i.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.703.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/samtools-1.9/samtools fastq -@ 2 -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-1.9/test/bc.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.9/test/bc.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.9/test/bc.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-1.9/test/bc_split.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 -N -t -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 -N -t -T MD,ia -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 -N -t -i -T MD,ia -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-1.9/test/i.fq -s /build/samtools-1.9/test/s.fq -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.9/samtools fastq -@ 2 -1 /build/samtools-1.9/test/1.fq -2 /build/samtools-1.9/test/2.fq /build/samtools-1.9/test/dat/bam2fq.703.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/samtools-1.9/samtools stats -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -r /build/samtools-1.9/test/stat/test.fa -i 0 /build/samtools-1.9/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -S RG -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -S RG -r /build/samtools-1.9/test/stat/test.fa /build/samtools-1.9/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -t /build/samtools-1.9/test/stat/11.stats.targets /build/samtools-1.9/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats /build/samtools-1.9/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -g 4 -t /build/samtools-1.9/test/stat/11.stats.targets /build/samtools-1.9/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats -g 4 /build/samtools-1.9/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats /build/samtools-1.9/test/stat/12_overlaps.bam -t /build/samtools-1.9/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats /build/samtools-1.9/test/stat/12_overlaps.bam -p -t /build/samtools-1.9/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats /build/samtools-1.9/test/stat/12_overlaps.bam -t /build/samtools-1.9/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.9/samtools stats /build/samtools-1.9/test/stat/12_overlaps.bam -p -t /build/samtools-1.9/test/stat/12_2reads.bed | tail -n+4 .. ok test_merge: /build/samtools-1.9/samtools merge -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a.sam /build/samtools-1.9/test/dat/test_input_1_b.sam /build/samtools-1.9/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.9/samtools merge -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a.bam /build/samtools-1.9/test/dat/test_input_1_b.bam /build/samtools-1.9/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-1.9/samtools merge -s 1 -O sam -b /tmp/VV6jbpNvW5 - /build/samtools-1.9/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-1.9/samtools merge -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-1.9/samtools merge -r -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a.sam /build/samtools-1.9/test/dat/test_input_1_b.sam /build/samtools-1.9/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.9/samtools merge -cp -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a.sam /build/samtools-1.9/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-1.9/samtools merge -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a_regex.sam /build/samtools-1.9/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-1.9/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/vwAFHEfE6l/merge.tag.1.bam /tmp/vwAFHEfE6l/merge.tag.2.bam .. ok test_merge: /build/samtools-1.9/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/vwAFHEfE6l/merge.tag.3.bam /tmp/vwAFHEfE6l/merge.tag.4.bam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a.sam /build/samtools-1.9/test/dat/test_input_1_b.sam /build/samtools-1.9/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a.bam /build/samtools-1.9/test/dat/test_input_1_b.bam /build/samtools-1.9/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -s 1 -O sam -b /tmp/t8UAISCSB1 - /build/samtools-1.9/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -r -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a.sam /build/samtools-1.9/test/dat/test_input_1_b.sam /build/samtools-1.9/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -cp -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a.sam /build/samtools-1.9/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.9/test/dat/test_input_1_a_regex.sam /build/samtools-1.9/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/vwAFHEfE6l/merge.tag.1.bam /tmp/vwAFHEfE6l/merge.tag.2.bam .. ok test_merge: /build/samtools-1.9/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/vwAFHEfE6l/merge.tag.3.bam /tmp/vwAFHEfE6l/merge.tag.4.bam .. ok test_sort: /build/samtools-1.9/samtools sort /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sortout .. ok test_sort: /build/samtools-1.9/samtools sort -f /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sortout.bam .. ok test_sort: /build/samtools-1.9/samtools sort -o /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sorttmp .. ok test_sort: /build/samtools-1.9/samtools sort -m 192M /build/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -m 192M -n /build/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -m 192M -t RG /build/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -m 192M -n -t RG /build/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -m 192M -t AS /build/samtools-1.9/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -m 192M -t FI /build/samtools-1.9/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sortout .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 -f /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sortout.bam .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 -o /build/samtools-1.9/test/dat/test_input_1_a.bam /tmp/vwAFHEfE6l/sorttmp .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 -m 192M /build/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 -m 192M -n /build/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 -m 192M -t RG /build/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 -m 192M -n -t RG /build/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 -m 192M -t AS /build/samtools-1.9/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.9/samtools sort -@ 2 -m 192M -t FI /build/samtools-1.9/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /build/samtools-1.9/samtools collate --output-fmt=sam -O /build/samtools-1.9/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.9/samtools collate -o /build/samtools-1.9/test/collate/collate1.tmp.sam /build/samtools-1.9/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.9/samtools collate -o /build/samtools-1.9/test/collate/collate2.tmp.sam /build/samtools-1.9/test/dat/test_input_1_d.sam /build/samtools-1.9/test/collate/collate2.tmp .. ok test_collate: /build/samtools-1.9/samtools collate --output-fmt=sam /build/samtools-1.9/test/dat/test_input_1_d.sam /build/samtools-1.9/test/collate/collate3.tmp .. ok test_collate: /build/samtools-1.9/samtools collate --output-fmt=sam -f /build/samtools-1.9/test/collate/fast_collate.sam -o /build/samtools-1.9/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-1.9/samtools collate --output-fmt=sam -f -r 4 /build/samtools-1.9/test/collate/fast_collate.sam -o /build/samtools-1.9/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/samtools-1.9/samtools collate -@ 2 --output-fmt=sam -O /build/samtools-1.9/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.9/samtools collate -@ 2 -o /build/samtools-1.9/test/collate/collate1.tmp.sam /build/samtools-1.9/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.9/samtools collate -@ 2 -o /build/samtools-1.9/test/collate/collate2.tmp.sam /build/samtools-1.9/test/dat/test_input_1_d.sam /build/samtools-1.9/test/collate/collate2.tmp .. ok test_collate: /build/samtools-1.9/samtools collate -@ 2 --output-fmt=sam /build/samtools-1.9/test/dat/test_input_1_d.sam /build/samtools-1.9/test/collate/collate3.tmp .. ok test_collate: /build/samtools-1.9/samtools collate -@ 2 --output-fmt=sam -f /build/samtools-1.9/test/collate/fast_collate.sam -o /build/samtools-1.9/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-1.9/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/samtools-1.9/test/collate/fast_collate.sam -o /build/samtools-1.9/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -O sam /build/samtools-1.9/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-1.9/samtools fixmate -O sam /build/samtools-1.9/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -O sam /build/samtools-1.9/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -O sam /build/samtools-1.9/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -cO sam /build/samtools-1.9/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -cO sam /build/samtools-1.9/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -O sam /build/samtools-1.9/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -@ 2 -O sam /build/samtools-1.9/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-1.9/samtools fixmate -@ 2 -O sam /build/samtools-1.9/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -@ 2 -O sam /build/samtools-1.9/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -@ 2 -O sam /build/samtools-1.9/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -@ 2 -cO sam /build/samtools-1.9/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -@ 2 -cO sam /build/samtools-1.9/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-1.9/samtools fixmate -@ 2 -O sam /build/samtools-1.9/test/fixmate/7_two_read_mapped.sam - .. ok /build/samtools-1.9/samtools calmd -uAr /build/samtools-1.9/test/dat/mpileup.1.sam /build/samtools-1.9/test/dat/mpileup.ref.fa .. ok /build/samtools-1.9/samtools calmd -@ 2 -uAr /build/samtools-1.9/test/dat/mpileup.1.sam /build/samtools-1.9/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/samtools-1.9/samtools idxstats /build/samtools-1.9/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/samtools-1.9/samtools idxstats /build/samtools-1.9/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/samtools-1.9/samtools idxstats /build/samtools-1.9/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck /build/samtools-1.9/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/samtools-1.9/samtools quickcheck -v /build/samtools-1.9/test/quickcheck/1.quickcheck.badeof.bam /build/samtools-1.9/test/quickcheck/2.quickcheck.badheader.bam /build/samtools-1.9/test/quickcheck/3.quickcheck.ok.bam /build/samtools-1.9/test/quickcheck/4.quickcheck.ok.bam /build/samtools-1.9/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/samtools-1.9/test/quickcheck/6.quickcheck.cram21.ok.cram /build/samtools-1.9/test/quickcheck/7.quickcheck.cram30.ok.cram /build/samtools-1.9/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/samtools-1.9/test/quickcheck/9.quickcheck.cram30.truncated.cram | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/samtools-1.9/samtools reheader /build/samtools-1.9/test/reheader/hdr.sam /build/samtools-1.9/test/dat/view.001.tmp.bam | /build/samtools-1.9/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.9/samtools reheader /build/samtools-1.9/test/reheader/hdr.sam /build/samtools-1.9/test/dat/view.001.tmp.v21.cram | /build/samtools-1.9/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.9/samtools reheader /build/samtools-1.9/test/reheader/hdr.sam /build/samtools-1.9/test/dat/view.001.tmp.v30.cram | /build/samtools-1.9/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.9/samtools reheader --in-place /build/samtools-1.9/test/reheader/hdr.sam /build/samtools-1.9/test/dat/view.001.tmp.v21.cram && /build/samtools-1.9/samtools view -h /build/samtools-1.9/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.9/samtools reheader --in-place /build/samtools-1.9/test/reheader/hdr.sam /build/samtools-1.9/test/dat/view.001.tmp.v30.cram && /build/samtools-1.9/samtools view -h /build/samtools-1.9/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -O sam -m overwrite_all /build/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -O sam -m orphan_only /build/samtools-1.9/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -O sam -R '1#7' /build/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-1.9/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-1.9/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/samtools-1.9/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -@ 2 -O sam -R '1#7' /build/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-1.9/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.9/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-1.9/test/addrprg/4_fixup_norg.sam .. ok test_markdup: /build/samtools-1.9/samtools markdup -O sam /build/samtools-1.9/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-1.9/samtools markdup -O sam /build/samtools-1.9/test/markdup/2_bad_order.sam - ERR: [markdup] error: bad coordinate order. .. expected failure test_markdup: /build/samtools-1.9/samtools markdup -O sam /build/samtools-1.9/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /build/samtools-1.9/samtools markdup -O sam /build/samtools-1.9/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /build/samtools-1.9/samtools markdup -O sam /build/samtools-1.9/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-1.9/samtools markdup -O sam -r /build/samtools-1.9/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-1.9/samtools markdup -S -O sam /build/samtools-1.9/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-1.9/samtools markdup -@ 2 -O sam /build/samtools-1.9/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-1.9/samtools markdup -@ 2 -O sam /build/samtools-1.9/test/markdup/2_bad_order.sam - ERR: [markdup] error: bad coordinate order. .. expected failure test_markdup: /build/samtools-1.9/samtools markdup -@ 2 -O sam /build/samtools-1.9/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /build/samtools-1.9/samtools markdup -@ 2 -O sam /build/samtools-1.9/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /build/samtools-1.9/samtools markdup -@ 2 -O sam /build/samtools-1.9/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-1.9/samtools markdup -@ 2 -O sam -r /build/samtools-1.9/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-1.9/samtools markdup -@ 2 -S -O sam /build/samtools-1.9/test/markdup/7_mark_supp_dup.sam - .. ok test_bedcov: /build/samtools-1.9/samtools bedcov /build/samtools-1.9/test/bedcov/bedcov.bed /build/samtools-1.9/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-1.9/samtools bedcov -j /build/samtools-1.9/test/bedcov/bedcov.bed /build/samtools-1.9/test/bedcov/bedcov.bam .. ok Number of tests: total .. 565 passed .. 541 failed .. 0 expected failure .. 24 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 && ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -Q0 -x -f c1.fa c1#pad1.bam EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -Q0 -x -f c1.fa c1#pad2.bam EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 153 Unexpected passes: 0 Expected failures: 3 Unexpected failures: 0 => PASS cd test/mpileup && ./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: 43 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args make[2]: Leaving directory '/build/samtools-1.9' make[1]: Leaving directory '/build/samtools-1.9' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot 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/samtools-1.9' dh_auto_install -- \ prefix=/usr install -d /build/samtools-1.9/debian/tmp make -j16 install DESTDIR=/build/samtools-1.9/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-1.9' mkdir -p -m 755 /build/samtools-1.9/debian/tmp/usr/bin /build/samtools-1.9/debian/tmp/usr/bin /build/samtools-1.9/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-1.9/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /build/samtools-1.9/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /build/samtools-1.9/debian/tmp/usr/bin install -p -m 644 samtools.1 misc/wgsim.1 /build/samtools-1.9/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/samtools-1.9' make clean make[2]: Entering directory '/build/samtools-1.9' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a 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/samtools-1.9' make[1]: Leaving directory '/build/samtools-1.9' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/samtools-1.9' dh_install install -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -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// cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ install -d debian/.debhelper/generated/samtools install -d debian/samtools-test/usr/share/samtools cp --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/ install -d debian/.debhelper/generated/samtools-test # 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 make[1]: Leaving directory '/build/samtools-1.9' dh_installdocs install -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 chown -R 0:0 debian/samtools/usr/share/doc 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 -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/samtools-1.9' dh_installchangelogs NEWS install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog install -p -m0644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian install -p -m0644 debian/NEWS debian/samtools-test/usr/share/doc/samtools-test/NEWS.Debian install -p -m0644 NEWS debian/samtools-test/usr/share/doc/samtools-test/changelog make[1]: Leaving directory '/build/samtools-1.9' dh_installexamples install -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 dh_installman man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/samtools.pl.1 > debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/ace2sam.1 > debian/samtools/usr/share/man/man1/ace2sam.1.dh-new man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/wgsim.1 > debian/samtools/usr/share/man/man1/wgsim.1.dh-new man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/samtools.1 > debian/samtools/usr/share/man/man1/samtools.1.dh-new mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/wgsim.1 dh_lintian install -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl (grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > debian/samtools.substvars.new mv debian/samtools.substvars.new debian/samtools.substvars (grep -a -s -v perl:Depends debian/samtools-test.substvars; echo perl:Depends=perl:any) > debian/samtools-test.substvars.new mv debian/samtools-test.substvars.new debian/samtools-test.substvars dh_link dh_strip_nondeterminism Using 1550767817 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1550767817 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/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.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/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/samtools-1.9' cd '/build/samtools-1.9' dh_fixperms find debian/samtools -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/samtools-test -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-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 dh_missing dh_dwz install -d debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -q -mdebian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug dh_strip install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3a/405faee9f6e0a664c1a6e8b9fa37e96bb0f198.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3a/405faee9f6e0a664c1a6e8b9fa37e96bb0f198.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3a/405faee9f6e0a664c1a6e8b9fa37e96bb0f198.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/3a/405faee9f6e0a664c1a6e8b9fa37e96bb0f198.debug debian/samtools/usr/bin/wgsim install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/87 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/87/ddd63f4dc243158b1aa3ca2bd71864ca7ac866.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/87/ddd63f4dc243158b1aa3ca2bd71864ca7ac866.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/87/ddd63f4dc243158b1aa3ca2bd71864ca7ac866.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/87/ddd63f4dc243158b1aa3ca2bd71864ca7ac866.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5b objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5b/619750b4fc10030fc6bc43571f702ea8361fb2.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5b/619750b4fc10030fc6bc43571f702ea8361fb2.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5b/619750b4fc10030fc6bc43571f702ea8361fb2.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/5b/619750b4fc10030fc6bc43571f702ea8361fb2.debug debian/samtools/usr/bin/md5fa install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/89 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/89/454b54e753286a6746d090e4f81b1bdea1d6c7.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/89/454b54e753286a6746d090e4f81b1bdea1d6c7.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/89/454b54e753286a6746d090e4f81b1bdea1d6c7.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/89/454b54e753286a6746d090e4f81b1bdea1d6c7.debug debian/samtools/usr/bin/maq2sam-short install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8b objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8b/af4955f18b4f18d61d18bccee5b12de33acfca.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8b/af4955f18b4f18d61d18bccee5b12de33acfca.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8b/af4955f18b4f18d61d18bccee5b12de33acfca.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/8b/af4955f18b4f18d61d18bccee5b12de33acfca.debug debian/samtools/usr/bin/maq2sam-long install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/d06c98646062c7fb2b1fe60d4f648772041729.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/d06c98646062c7fb2b1fe60d4f648772041729.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/d06c98646062c7fb2b1fe60d4f648772041729.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/65/d06c98646062c7fb2b1fe60d4f648772041729.debug debian/samtools/usr/bin/ace2sam install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/08732993602f9cf4182bead47bda115ac7eaa1.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/08732993602f9cf4182bead47bda115ac7eaa1.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/08732993602f9cf4182bead47bda115ac7eaa1.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/94/08732993602f9cf4182bead47bda115ac7eaa1.debug debian/samtools/usr/bin/samtools install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym dh_makeshlibs rm -f debian/samtools/DEBIAN/shlibs rm -f debian/samtools-test/DEBIAN/shlibs dh_shlibdeps install -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools 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/wgsim dh_installdeb install -d debian/samtools-test/DEBIAN dh_gencontrol 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 -Pdebian/samtools-test echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=3a405faee9f6e0a664c1a6e8b9fa37e96bb0f198 5b619750b4fc10030fc6bc43571f702ea8361fb2 65d06c98646062c7fb2b1fe60d4f648772041729 87ddd63f4dc243158b1aa3ca2bd71864ca7ac866 89454b54e753286a6746d090e4f81b1bdea1d6c7 8baf4955f18b4f18d61d18bccee5b12de33acfca 9408732993602f9cf4182bead47bda115ac7eaa1" -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 chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools -UMulti-Arch dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control chown 0:0 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control chown 0:0 -- debian/samtools/DEBIAN/control dh_md5sums cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums chown 0:0 -- debian/samtools/DEBIAN/md5sums cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums chown 0:0 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/samtools .. dpkg-deb --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --build debian/samtools-test .. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.9-4_amd64.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.9-4_all.deb'. dpkg-deb: building package 'samtools' in '../samtools_1.9-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../samtools_1.9-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1882377 and its subdirectories I: Current time: Tue Jan 17 01:13:41 -12 2023 I: pbuilder-time-stamp: 1673961221 Wed Dec 15 06:50:40 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Wed Dec 15 06:50:40 UTC 2021 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Wed Dec 15 06:57:20 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Wed Dec 15 06:57:20 UTC 2021 I: samtools_1.9-4_amd64.changes: Format: 1.8 Date: Thu, 21 Feb 2019 17:50:17 +0100 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: amd64 all Version: 1.9-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats samtools-test - test files for the samtools package Closes: 922861 Changes: samtools (1.9-4) unstable; urgency=medium . [ Michael R. Crusoe ] * Mark samtools-test as Multi-Arch: foreign. . [ Andreas Tille ] * Update debian/README.Debian, install upstream NEWS as upstream changelog, install upstream README as doc, more complete debian/NEWS.Debian Closes: #922861 * Drop reduntant information in debian/reference. It is maintained in debian/upstream/metadata now. Checksums-Sha1: 7984fd745645d7583c164391c3053649071813a6 743960 samtools-dbgsym_1.9-4_amd64.deb cc18197ca2ad6353fbd1c656cef5036a8ff3e992 2060284 samtools-test_1.9-4_all.deb aa71683dcc06d3d4282b1da498415c0d96eef832 6084 samtools_1.9-4_amd64.buildinfo 9069cf1c30fbc47e4a8aac820c74ef46e4179cb2 442600 samtools_1.9-4_amd64.deb Checksums-Sha256: 15f9ca10d7872ed240348ec9069c20f2e7d18417eb764362b30a6a6501044bc9 743960 samtools-dbgsym_1.9-4_amd64.deb 0dfac41526b1eade84c80db1f1641ec83f1ee118ba5ea43a1b1c7ce40e756e71 2060284 samtools-test_1.9-4_all.deb ecd53c8b1b53590bc66d17de8c86495837c86f7e2780c5f2285f0a020dfac3ab 6084 samtools_1.9-4_amd64.buildinfo ebe2596cd65489686e0e336c872eeb6b92ee833c97f584a341777257fa78b988 442600 samtools_1.9-4_amd64.deb Files: 77c04b2814b41c68bab9f3201cb5aa0c 743960 debug optional samtools-dbgsym_1.9-4_amd64.deb 8eef0eba14c3f8ac42f2fb8824e13a53 2060284 science optional samtools-test_1.9-4_all.deb 8918a8ad41868eacfbc8e91d14c0387e 6084 science optional samtools_1.9-4_amd64.buildinfo 55d4e4f5b096ed8106697f54b86a285e 442600 science optional samtools_1.9-4_amd64.deb Wed Dec 15 06:57:21 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/samtools_1.9-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/samtools_1.9-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/samtools_1.9-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/b1/samtools_1.9-4_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.cjLObFpaCN/b2/samtools_1.9-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.295s) 0.295s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.062s) 0.061s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Wed Dec 15 06:57:22 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Wed Dec 15 06:57:22 UTC 2021 I: samtools from buster built successfully and reproducibly on amd64. Wed Dec 15 06:57:24 UTC 2021 I: Submitting .buildinfo files to external archives: Wed Dec 15 06:57:24 UTC 2021 I: Submitting 8.0K b1/samtools_1.9-4_amd64.buildinfo.asc Wed Dec 15 06:57:25 UTC 2021 I: Submitting 8.0K b2/samtools_1.9-4_amd64.buildinfo.asc Wed Dec 15 06:57:25 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Dec 15 06:57:26 UTC 2021 I: Done submitting .buildinfo files. Wed Dec 15 06:57:26 UTC 2021 I: Removing signed samtools_1.9-4_amd64.buildinfo.asc files: removed './b1/samtools_1.9-4_amd64.buildinfo.asc' removed './b2/samtools_1.9-4_amd64.buildinfo.asc'