I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 29 16:55:24 +14 2021 I: pbuilder-time-stamp: 1627527324 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_1.11-1.dsc] I: copying [./samtools_1.11.orig.tar.gz] I: copying [./samtools_1.11-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.ZTDcevGl/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 2 04:52:01 2020 +14 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_1.11-1.dsc dpkg-source: info: extracting samtools in samtools-1.11 dpkg-source: info: unpacking samtools_1.11.orig.tar.gz dpkg-source: info: unpacking samtools_1.11-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/12083/tmp/hooks/D01_modify_environment starting debug: Running on virt64c. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/12083/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/12083/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=03fafc15b39643608fd1779e36218e26 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=12083 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Rsa8oGtFuV/pbuilderrc_IoUZ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Rsa8oGtFuV/b2 --logfile b2/build.log --extrapackages usrmerge samtools_1.11-1.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-2 (2021-07-20) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash -rwxr-xr-x 1 root root 75880 Sep 23 2020 date -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd -rwxr-xr-x 1 root root 59912 Sep 23 2020 df -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir -rwxr-xr-x 1 root root 55012 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln -rwxr-xr-x 1 root root 35068 Feb 8 2020 login -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 29 16:55 sh -> bash lrwxrwxrwx 1 root root 4 Jul 26 23:26 sh.distrib -> dash -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch -rwxr-xr-x 1 root root 22496 Sep 23 2020 true -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/12083/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.11), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.11); 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. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libhts-dev{a} libhts3{a} libicu67{a} libio-pty-perl{a} libldap-2.4-2{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} libsub-override-perl{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: bzip2-doc ca-certificates curl libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 27.0 MB of archives. After unpacking 86.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-7 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf autoconf-archive all 20190106-2.1 [746 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf bash-completion all 1:2.11-2 [234 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libbz2-dev armhf 1.0.8-4 [29.2 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+b1 [306 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3+b1 [402 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libdeflate-dev armhf 1.7-1 [39.9 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2 [220 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf libhts-dev armhf 1.11-4 [3819 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf libio-pty-perl armhf 1:1.15-2 [36.2 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf libncurses-dev armhf 6.2+20201114-2 [308 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf libncurses5-dev armhf 6.2+20201114-2 [936 B] Get: 56 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf tabix armhf 1.11-4 [306 kB] Fetched 27.0 MB in 2s (13.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_armhf.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package autoconf-archive. Preparing to unpack .../05-autoconf-archive_20190106-2.1_all.deb ... Unpacking autoconf-archive (20190106-2.1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package bash-completion. Preparing to unpack .../07-bash-completion_1%3a2.11-2_all.deb ... Unpacking bash-completion (1:2.11-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../09-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../12-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../22-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../23-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../24-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../25-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../26-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../27-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../28-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-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 .../31-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../33-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../34-libbz2-dev_1.0.8-4_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-4) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../35-libsasl2-modules-db_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../36-libsasl2-2_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../37-libldap-2.4-2_2.4.57+dfsg-3_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../38-libnghttp2-14_1.43.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.43.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../39-libpsl5_0.21.0-1.2_armhf.deb ... Unpacking libpsl5:armhf (0.21.0-1.2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../40-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../41-libssh2-1_1.9.0-2_armhf.deb ... Unpacking libssh2-1:armhf (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../42-libcurl3-gnutls_7.74.0-1.3+b1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../43-libcurl4-gnutls-dev_7.74.0-1.3+b1_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../44-libdeflate0_1.7-1_armhf.deb ... Unpacking libdeflate0:armhf (1.7-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../45-libdeflate-dev_1.7-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.7-1) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../46-libglib2.0-0_2.66.8-1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.66.8-1) ... Selecting previously unselected package libhts3:armhf. Preparing to unpack .../47-libhts3_1.11-4_armhf.deb ... Unpacking libhts3:armhf (1.11-4) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../48-liblzma-dev_5.2.5-2_armhf.deb ... Unpacking liblzma-dev:armhf (5.2.5-2) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../49-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../50-libhts-dev_1.11-4_armhf.deb ... Unpacking libhts-dev:armhf (1.11-4) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../51-libio-pty-perl_1%3a1.15-2_armhf.deb ... Unpacking libio-pty-perl (1:1.15-2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../52-libncurses6_6.2+20201114-2_armhf.deb ... Unpacking libncurses6:armhf (6.2+20201114-2) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../53-libncurses-dev_6.2+20201114-2_armhf.deb ... Unpacking libncurses-dev:armhf (6.2+20201114-2) ... Selecting previously unselected package libncurses5-dev:armhf. Preparing to unpack .../54-libncurses5-dev_6.2+20201114-2_armhf.deb ... Unpacking libncurses5-dev:armhf (6.2+20201114-2) ... Selecting previously unselected package pkg-config. Preparing to unpack .../55-pkg-config_0.29.2-1_armhf.deb ... Unpacking pkg-config (0.29.2-1) ... Selecting previously unselected package tabix. Preparing to unpack .../56-tabix_1.11-4_armhf.deb ... Unpacking tabix (1.11-4) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up libpsl5:armhf (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7) ... Setting up libio-pty-perl (1:1.15-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:armhf (1.0.9-2+b2) ... Setting up libnghttp2-14:armhf (1.43.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up libdeflate0:armhf (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up autoconf-archive (20190106-2.1) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up bash-completion (1:2.11-2) ... Setting up libncurses6:armhf (6.2+20201114-2) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:armhf (5.2.5-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:armhf (1.9.0-2) ... Setting up libdeflate-dev:armhf (1.7-1) ... Setting up tabix (1.11-4) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up libbz2-dev:armhf (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libncurses-dev:armhf (6.2+20201114-2) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libncurses5-dev:armhf (6.2+20201114-2) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:armhf (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:armhf (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... 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... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (377 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 23613 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Name or service not known I: Running cd /build/samtools-1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../samtools_1.11-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.11-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from samtools-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/samtools-1.11' rm -f config.mk touch config.mk dh_auto_clean -- install -d /build/samtools-1.11/debian/.debhelper/generated/_source/home make -j4 distclean make[2]: Entering directory '/build/samtools-1.11' 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-1.11' make[1]: Leaving directory '/build/samtools-1.11' 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 binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: 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:64: the top level configure.ac:64: 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:64: the top level configure.ac:64: 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:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/samtools-1.11' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal configure.ac:64: 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:64: the top level autoconf configure.ac:64: 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:64: the top level dh_auto_configure -- --with-htslib=system install -d /build/samtools-1.11/debian/.debhelper/generated/_source/home ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether 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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/samtools-1.11' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/samtools-1.11' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -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-1.11' gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.11"' > version.h gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -fdebug-prefix-map=/build/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/samtools-1.11' make[1]: Leaving directory '/build/samtools-1.11' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/samtools-1.11' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j4 test VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/samtools-1.11' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} /usr/bin/bgzip -c -b 65272 -s 5 /tmp/xWaIZqXfN5/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/xWaIZqXfN5/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/xWaIZqXfN5/bgzip.dat.gz .. ok /build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/samtools-1.11/samtools faidx /tmp/xWaIZqXfN5/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq 3:11-13 .. ok .. ok /build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq.gz 3:11-13 .. ok .. ok /build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq 2:998-1003 .. ok .. ok /build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq 1:100-104 .. ok .. ok /build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq.gz 1:100-104 .. ok .. ok /build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq 1:99998-100007 .. ok .. ok /build/samtools-1.11/samtools fqidx /tmp/xWaIZqXfN5/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/samtools-1.11/test/dat/dict.fa .. ok test_dict: /build/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/xWaIZqXfN5/dict.fa.gz .. ok test_dict: cat /build/samtools-1.11/test/dat/dict.fa | /build/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/samtools-1.11/samtools dict -AH < /build/samtools-1.11/test/dat/dict.alias.fa .. ok test_index: /build/samtools-1.11/samtools view /tmp/xWaIZqXfN5/large_chrom.bam ref2 .. ok test_index: /build/samtools-1.11/samtools view /tmp/xWaIZqXfN5/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-1.11/samtools index /build/samtools-1.11/test/dat/test_input_1_a.bam && cat /build/samtools-1.11/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-1.11/samtools view -X /build/samtools-1.11/test/dat/test_input_1_b.bam /tmp/xWaIZqXfN5/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-1.11/samtools merge -O sam - -X -cp -R ref2 /build/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/xWaIZqXfN5/test_input_1_b.bam.bai .. ok test_index: /build/samtools-1.11/samtools index -c /build/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/xWaIZqXfN5/auto_indexed.csi && cat /tmp/xWaIZqXfN5/auto_indexed.csi .. ok test_index: /build/samtools-1.11/samtools index /build/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/xWaIZqXfN5/auto_indexed.crai && cat /tmp/xWaIZqXfN5/auto_indexed.crai .. ok test_index: /build/samtools-1.11/samtools index -c /build/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/xWaIZqXfN5/auto_indexed.csi && cat /tmp/xWaIZqXfN5/auto_indexed.csi .. ok test_index: /build/samtools-1.11/samtools view -@ 2 /tmp/xWaIZqXfN5/large_chrom.bam ref2 .. ok test_index: /build/samtools-1.11/samtools view -@ 2 /tmp/xWaIZqXfN5/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-1.11/samtools index -@ 2 /build/samtools-1.11/test/dat/test_input_1_a.bam && cat /build/samtools-1.11/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-1.11/samtools view -@ 2 -X /build/samtools-1.11/test/dat/test_input_1_b.bam /tmp/xWaIZqXfN5/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-1.11/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/xWaIZqXfN5/test_input_1_b.bam.bai .. ok test_index: /build/samtools-1.11/samtools index -@ 2 -c /build/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/xWaIZqXfN5/auto_indexed.csi && cat /tmp/xWaIZqXfN5/auto_indexed.csi .. ok test_index: /build/samtools-1.11/samtools index -@ 2 /build/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/xWaIZqXfN5/auto_indexed.crai && cat /tmp/xWaIZqXfN5/auto_indexed.crai .. ok test_index: /build/samtools-1.11/samtools index -@ 2 -c /build/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/xWaIZqXfN5/auto_indexed.csi && cat /tmp/xWaIZqXfN5/auto_indexed.csi .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -b /tmp/xWaIZqXfN5/mpileup.bam.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -b /tmp/xWaIZqXfN5/mpileup.cram.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -b /tmp/xWaIZqXfN5/mpileup.bam.urllist -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -b /tmp/xWaIZqXfN5/mpileup.cram.urllist -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -uvDV -b /tmp/xWaIZqXfN5/mpileup.bam.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -uvDV -b /tmp/xWaIZqXfN5/mpileup.cram.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/xWaIZqXfN5/mpileup.cram.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/xWaIZqXfN5/mpileup.cram.list -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xWaIZqXfN5/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/xWaIZqXfN5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xWaIZqXfN5/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/samtools-1.11/samtools mpileup /build/samtools-1.11/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, 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 ampliconclip 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 coverage .. ok 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 ampliconstats .. 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/xWaIZqXfN5/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/xWaIZqXfN5/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/xWaIZqXfN5/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/xWaIZqXfN5/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/xWaIZqXfN5/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/xWaIZqXfN5/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/xWaIZqXfN5/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/xWaIZqXfN5/view.001.fogn (CRAM input).. ok 67: Filter -d BC:TGCA (SAM input) .. ok 68: Count -d BC:TGCA (SAM input) .. ok 69: Filter -d BC:TGCA (BAM input) .. ok 70: Count -d BC:TGCA (BAM input) .. ok 71: Filter -d BC:TGCA (CRAM input) .. ok 72: Count -d BC:TGCA (CRAM input) .. ok 73: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc (SAM input) .. ok 74: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc (SAM input) .. ok 75: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc (BAM input) .. ok 76: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc (BAM input) .. ok 77: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input) .. ok 78: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input) .. ok 79: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (SAM input).. ok 80: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (SAM input).. ok 81: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (BAM input).. ok 82: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (BAM input).. ok 83: Filter -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (CRAM input).. ok 84: Count -D BC:/tmp/xWaIZqXfN5/view.001.fobc -d BC:TGCA (CRAM input).. ok 85: Filter -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (SAM input).. ok 86: Count -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (SAM input).. ok 87: Filter -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (BAM input).. ok 88: Count -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (BAM input).. ok 89: Filter -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input).. ok 90: Count -d BC:TGCA -D BC:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input).. ok 91: Filter -D RG:/tmp/xWaIZqXfN5/view.001.fogn (SAM input) .. ok 92: Count -D RG:/tmp/xWaIZqXfN5/view.001.fogn (SAM input) .. ok 93: Filter -D RG:/tmp/xWaIZqXfN5/view.001.fogn (BAM input) .. ok 94: Count -D RG:/tmp/xWaIZqXfN5/view.001.fogn (BAM input) .. ok 95: Filter -D RG:/tmp/xWaIZqXfN5/view.001.fogn (CRAM input) .. ok 96: Count -D RG:/tmp/xWaIZqXfN5/view.001.fogn (CRAM input) .. ok 97: Filter -d NE:TGCA (SAM input) .. ok 98: Count -d NE:TGCA (SAM input) .. ok 99: Filter -d NE:TGCA (BAM input) .. ok 100: Count -d NE:TGCA (BAM input) .. ok 101: Filter -d NE:TGCA (CRAM input) .. ok 102: Count -d NE:TGCA (CRAM input) .. ok 103: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test103.sam -h -d TGCA /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure 104: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.11/samtools view -c -d TGCA /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure 105: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test105.sam -h -d TGCA /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure 106: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.11/samtools view -c -d TGCA /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure 107: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test107.sam -h -d TGCA /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure 108: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.11/samtools view -c -d TGCA /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure 109: Filter -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test109.sam -h -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure 110: Count -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: /build/samtools-1.11/samtools view -c -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure 111: Filter -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test111.sam -h -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure 112: Count -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: /build/samtools-1.11/samtools view -c -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure 113: Filter -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test113.sam -h -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure 114: Count -D BClong:/tmp/xWaIZqXfN5/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/xWaIZqXfN5/view.001.fobc" Failed command: /build/samtools-1.11/samtools view -c -D BClong:/tmp/xWaIZqXfN5/view.001.fobc /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure 115: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure 116: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/view.001.sam --no-PG .. expected failure 117: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure 118: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/view.test001.bam --no-PG .. expected failure 119: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.11/samtools view -o /tmp/xWaIZqXfN5/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure 120: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/xWaIZqXfN5/view.test006.cram --no-PG .. expected failure 121: Filter -l Library 2 (SAM input) .. ok 122: Count -l Library 2 (SAM input) .. ok 123: Filter -l Library 2 (BAM input) .. ok 124: Count -l Library 2 (BAM input) .. ok 125: Filter -l Library 2 (CRAM input) .. ok 126: Count -l Library 2 (CRAM input) .. ok 127: Filter -l Library 3 (SAM input) .. ok 128: Count -l Library 3 (SAM input) .. ok 129: Filter -l Library 3 (BAM input) .. ok 130: Count -l Library 3 (BAM input) .. ok 131: Filter -l Library 3 (CRAM input) .. ok 132: Count -l Library 3 (CRAM input) .. ok 133: Filter -q 50 (SAM input) .. ok 134: Count -q 50 (SAM input) .. ok 135: Filter -q 50 (BAM input) .. ok 136: Count -q 50 (BAM input) .. ok 137: Filter -q 50 (CRAM input) .. ok 138: Count -q 50 (CRAM input) .. ok 139: Filter -q 99 (SAM input) .. ok 140: Count -q 99 (SAM input) .. ok 141: Filter -q 99 (BAM input) .. ok 142: Count -q 99 (BAM input) .. ok 143: Filter -q 99 (CRAM input) .. ok 144: Count -q 99 (CRAM input) .. ok 145: Filter -q 100 (SAM input) .. ok 146: Count -q 100 (SAM input) .. ok 147: Filter -q 100 (BAM input) .. ok 148: Count -q 100 (BAM input) .. ok 149: Filter -q 100 (CRAM input) .. ok 150: Count -q 100 (CRAM input) .. ok 151: Filter -x fa (SAM input) .. ok 152: Count -x fa (SAM input) .. ok 153: Filter -x fa (BAM input) .. ok 154: Count -x fa (BAM input) .. ok 155: Filter -x fa (CRAM input) .. ok 156: Count -x fa (CRAM input) .. ok 157: Filter -x fa -x ha (SAM input) .. ok 158: Count -x fa -x ha (SAM input) .. ok 159: Filter -x fa -x ha (BAM input) .. ok 160: Count -x fa -x ha (BAM input) .. ok 161: Filter -x fa -x ha (CRAM input) .. ok 162: Count -x fa -x ha (CRAM input) .. ok 163: Filter -x fa -r grp2 (SAM input) .. ok 164: Count -x fa -r grp2 (SAM input) .. ok 165: Filter -x fa -r grp2 (BAM input) .. ok 166: Count -x fa -r grp2 (BAM input) .. ok 167: Filter -x fa -r grp2 (CRAM input) .. ok 168: Count -x fa -r grp2 (CRAM input) .. ok 169: Filter -x RG -r grp2 (SAM input) .. ok 170: Count -x RG -r grp2 (SAM input) .. ok 171: Filter -x RG -r grp2 (BAM input) .. ok 172: Count -x RG -r grp2 (BAM input) .. ok 173: Filter -x RG -r grp2 (CRAM input) .. ok 174: Count -x RG -r grp2 (CRAM input) .. ok 175: Filter -m 10 (SAM input) .. ok 176: Count -m 10 (SAM input) .. ok 177: Filter -m 10 (BAM input) .. ok 178: Count -m 10 (BAM input) .. ok 179: Filter -m 10 (CRAM input) .. ok 180: Count -m 10 (CRAM input) .. ok 181: Filter -m 11 (SAM input) .. ok 182: Count -m 11 (SAM input) .. ok 183: Filter -m 11 (BAM input) .. ok 184: Count -m 11 (BAM input) .. ok 185: Filter -m 11 (CRAM input) .. ok 186: Count -m 11 (CRAM input) .. ok 187: Filter -m 15 (SAM input) .. ok 188: Count -m 15 (SAM input) .. ok 189: Filter -m 15 (BAM input) .. ok 190: Count -m 15 (BAM input) .. ok 191: Filter -m 15 (CRAM input) .. ok 192: Count -m 15 (CRAM input) .. ok 193: Filter -m 16 (SAM input) .. ok 194: Count -m 16 (SAM input) .. ok 195: Filter -m 16 (BAM input) .. ok 196: Count -m 16 (BAM input) .. ok 197: Filter -m 16 (CRAM input) .. ok 198: Count -m 16 (CRAM input) .. ok 199: 1bp reads file SAM -> BAM -> SAM .. ok 200: 1bp reads file SAM -> CRAM -> SAM .. ok 200: Region Z (BAM input) .. ok 201: Count Z (BAM input) .. ok 202: Region Z (CRAM input) .. ok 203: Count Z (CRAM input) .. ok 204: Region Z:30 (BAM input) .. ok 205: Count Z:30 (BAM input) .. ok 206: Region Z:30 (CRAM input) .. ok 207: Count Z:30 (CRAM input) .. ok 208: Region Z:20-40 (BAM input) .. ok 209: Count Z:20-40 (BAM input) .. ok 210: Region Z:20-40 (CRAM input) .. ok 211: Count Z:20-40 (CRAM input) .. ok 212: Region ref1 (BAM input) .. ok 213: Count ref1 (BAM input) .. ok 214: Region ref1 (CRAM input) .. ok 215: Count ref1 (CRAM input) .. ok 216: Region ref1:15 (BAM input) .. ok 217: Count ref1:15 (BAM input) .. ok 218: Region ref1:15 (CRAM input) .. ok 219: Count ref1:15 (CRAM input) .. ok 220: Region ref1:15-45 (BAM input) .. ok 221: Count ref1:15-45 (BAM input) .. ok 222: Region ref1:15-45 (CRAM input) .. ok 223: Count ref1:15-45 (CRAM input) .. ok 224: Region ref1:15-45 ref2 (BAM input) .. ok 225: Count ref1:15-45 ref2 (BAM input) .. ok 226: Region ref1:15-45 ref2 (CRAM input) .. ok 227: Count ref1:15-45 ref2 (CRAM input) .. ok 228: Region ref1:15-45 ref2:16 (BAM input) .. ok 229: Count ref1:15-45 ref2:16 (BAM input) .. ok 230: Region ref1:15-45 ref2:16 (CRAM input) .. ok 231: Count ref1:15-45 ref2:16 (CRAM input) .. ok 232: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 233: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 234: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 235: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 236: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 237: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 238: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 239: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 240: Region -f 128 ref1 (BAM input) .. ok 241: Count -f 128 ref1 (BAM input) .. ok 242: Region -f 128 ref1 (CRAM input) .. ok 243: Count -f 128 ref1 (CRAM input) .. ok 244: Region -q 50 ref1:15-45 (BAM input) .. ok 245: Count -q 50 ref1:15-45 (BAM input) .. ok 246: Region -q 50 ref1:15-45 (CRAM input) .. ok 247: Count -q 50 ref1:15-45 (CRAM input) .. ok 248: Region -r grp2 ref1:15-45 (BAM input) .. ok 249: Count -r grp2 ref1:15-45 (BAM input) .. ok 250: Region -r grp2 ref1:15-45 (CRAM input) .. ok 251: Count -r grp2 ref1:15-45 (CRAM input) .. ok 252: Region * (BAM input) .. ok 253: Count * (BAM input) .. ok 254: Region * (CRAM input) .. ok 255: Count * (CRAM input) .. ok 256: Region -L /build/samtools-1.11/test/dat/view.002.01.bed (BAM input).. ok 257: Count -L /build/samtools-1.11/test/dat/view.002.01.bed (BAM input).. ok 258: Region -L /build/samtools-1.11/test/dat/view.002.01.bed (CRAM input).. ok 259: Count -L /build/samtools-1.11/test/dat/view.002.01.bed (CRAM input).. ok 260: Region -L /build/samtools-1.11/test/dat/view.002.02.bed (BAM input).. ok 261: Count -L /build/samtools-1.11/test/dat/view.002.02.bed (BAM input).. ok 262: Region -L /build/samtools-1.11/test/dat/view.002.02.bed (CRAM input).. ok 263: Count -L /build/samtools-1.11/test/dat/view.002.02.bed (CRAM input).. ok 264: Region -L /build/samtools-1.11/test/dat/view.001.01.bed (BAM input).. ok 265: Count -L /build/samtools-1.11/test/dat/view.001.01.bed (BAM input).. ok 266: Region -L /build/samtools-1.11/test/dat/view.001.01.bed (CRAM input).. ok 267: Count -L /build/samtools-1.11/test/dat/view.001.01.bed (CRAM input).. ok 268: Region -L /build/samtools-1.11/test/dat/view.001.02.bed (BAM input).. ok 269: Count -L /build/samtools-1.11/test/dat/view.001.02.bed (BAM input).. ok 270: Region -L /build/samtools-1.11/test/dat/view.001.02.bed (CRAM input).. ok 271: Count -L /build/samtools-1.11/test/dat/view.001.02.bed (CRAM input).. ok 272: Region -L /build/samtools-1.11/test/dat/view.002.01.bed Z (BAM input).. ok 273: Count -L /build/samtools-1.11/test/dat/view.002.01.bed Z (BAM input).. ok 274: Region -L /build/samtools-1.11/test/dat/view.002.01.bed Z (CRAM input).. ok 275: Count -L /build/samtools-1.11/test/dat/view.002.01.bed Z (CRAM input).. ok 276: Region -L /build/samtools-1.11/test/dat/view.002.01.bed Z:30 (BAM input).. ok 277: Count -L /build/samtools-1.11/test/dat/view.002.01.bed Z:30 (BAM input).. ok 278: Region -L /build/samtools-1.11/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 279: Count -L /build/samtools-1.11/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 280: Region -L /build/samtools-1.11/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 281: Count -L /build/samtools-1.11/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 282: Region -L /build/samtools-1.11/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 283: Count -L /build/samtools-1.11/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 284: Region -L /build/samtools-1.11/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 285: Count -L /build/samtools-1.11/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 286: Region -L /build/samtools-1.11/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 287: Count -L /build/samtools-1.11/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 288: Region -L /build/samtools-1.11/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 289: Count -L /build/samtools-1.11/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 290: Region -L /build/samtools-1.11/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 291: Count -L /build/samtools-1.11/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 292: Region -L /build/samtools-1.11/test/dat/view.001.01.bed ref2 (BAM input).. ok 293: Count -L /build/samtools-1.11/test/dat/view.001.01.bed ref2 (BAM input).. ok 294: Region -L /build/samtools-1.11/test/dat/view.001.01.bed ref2 (CRAM input).. ok 295: Count -L /build/samtools-1.11/test/dat/view.001.01.bed ref2 (CRAM input).. ok 296: Region -L /build/samtools-1.11/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 297: Count -L /build/samtools-1.11/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 298: Region -L /build/samtools-1.11/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 299: Count -L /build/samtools-1.11/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 300: Region -L /build/samtools-1.11/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 301: Count -L /build/samtools-1.11/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 302: Region -L /build/samtools-1.11/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 303: Count -L /build/samtools-1.11/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 304: Region -L /build/samtools-1.11/test/dat/view.001.01.bed -f 128 (BAM input).. ok 305: Count -L /build/samtools-1.11/test/dat/view.001.01.bed -f 128 (BAM input).. ok 306: Region -L /build/samtools-1.11/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 307: Count -L /build/samtools-1.11/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 308: Region -L /build/samtools-1.11/test/dat/view.001.01.bed -q 5 (BAM input).. ok 309: Count -L /build/samtools-1.11/test/dat/view.001.01.bed -q 5 (BAM input).. ok 310: Region -L /build/samtools-1.11/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 311: Count -L /build/samtools-1.11/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 312: Region -L /build/samtools-1.11/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 313: Count -L /build/samtools-1.11/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 314: Region -L /build/samtools-1.11/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 315: Count -L /build/samtools-1.11/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 316: Make BAM with no M5/UR tags .. ok 317: Add @SQ with -t (SAM -> SAM) .. ok 318: Add @SQ with -T (SAM -> SAM) .. ok 319: Add @SQ with -t (BAM -> SAM) .. ok 320: Add @SQ with -T (BAM -> SAM) .. ok 321: Add @SQ with -t (SAM -> BAM) .. ok 322: Add @SQ with -T (SAM -> BAM) .. ok 323: Add @SQ with -t (BAM -> BAM) .. ok 324: Add @SQ with -T (BAM -> BAM) .. ok 325: Add @SQ with -t (SAM -> CRAM) .. ok 326: Add @SQ with -T (SAM -> CRAM) .. ok 327: Add @SQ with -t (BAM -> CRAM) .. ok 328: Add @SQ with -T (BAM -> CRAM) .. ok 329: Make CRAM with no UR field .. ok 330: Decoding CRAM with no UR field via -T .. ok 331: CIGAR B-operator removal .. ok 332: Big SAM -> BAM .. ok 333: Big SAM -> BAM (2 threads) .. ok 334: Big SAM -> BAM (4 threads) .. ok 335: Big SAM -> CRAM .. ok 336: Big SAM -> CRAM (2 threads) .. ok 337: Big SAM -> CRAM (4 threads) .. ok 338: Subsample 0.2 (SAM input) ............ ok 339: Subsample 0.5 (SAM input) ............ ok 340: Subsample 0.8 (SAM input) ............ ok 341: Subsample 0.2 (BAM input) ............ ok 342: Subsample 0.5 (BAM input) ............ ok 343: Subsample 0.8 (BAM input) ............ ok 344: Subsample 0.2 (CRAM input) ............ ok 345: Subsample 0.5 (CRAM input) ............ ok 346: Subsample 0.8 (CRAM input) ............ ok 347: SAM add PG .. 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-1.11/samtools fastq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-1.11/test/bc.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.11/test/bc.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.11/test/bc.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-1.11/test/bc_split.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -N -t -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -N -t -T MD,ia -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-1.11/test/i.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/samtools-1.11/test/i.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -i --index-format 'i*i*' -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -N -1 /build/samtools-1.11/test/o.fq -2 /build/samtools-1.11/test/o.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -N -o /build/samtools-1.11/test/o.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -N -s /tmp/xWaIZqXfN5/bam2fq.discard.s.fq -0 /tmp/xWaIZqXfN5/bam2fq.discard.0.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/samtools-1.11/test/dat/bam2fq.013.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-1.11/samtools fastq -@ 2 -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-1.11/test/bc.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.11/test/bc.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.11/test/bc.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-1.11/test/bc_split.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -N -t -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -N -t -T MD,ia -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-1.11/test/i.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/samtools-1.11/test/i.fq -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/samtools-1.11/test/s.fq -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -1 /build/samtools-1.11/test/1.fq -2 /build/samtools-1.11/test/2.fq /build/samtools-1.11/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -N -1 /build/samtools-1.11/test/o.fq -2 /build/samtools-1.11/test/o.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -N -o /build/samtools-1.11/test/o.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -N -s /tmp/xWaIZqXfN5/bam2fq.discard.s.fq -0 /tmp/xWaIZqXfN5/bam2fq.discard.0.fq /build/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.11/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/samtools-1.11/test/dat/bam2fq.013.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-1.11/samtools stats -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -r /build/samtools-1.11/test/stat/test.fa -i 0 /build/samtools-1.11/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -S RG -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -S RG -r /build/samtools-1.11/test/stat/test.fa /build/samtools-1.11/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -t /build/samtools-1.11/test/stat/11.stats.targets /build/samtools-1.11/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -g 4 -t /build/samtools-1.11/test/stat/11.stats.targets /build/samtools-1.11/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats -g 4 /build/samtools-1.11/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/12_overlaps.bam -t /build/samtools-1.11/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/12_overlaps.bam -p -t /build/samtools-1.11/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/12_overlaps.bam -t /build/samtools-1.11/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/12_overlaps.bam -p -t /build/samtools-1.11/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/samtools-1.11/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/samtools-1.11/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-1.11/samtools stats /build/samtools-1.11/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/samtools-1.11/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_merge: /build/samtools-1.11/samtools merge -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-1.11/test/dat/test_input_1_b.sam /build/samtools-1.11/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.11/samtools merge -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-1.11/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-1.11/samtools merge -s 1 -O sam -b /tmp/dg9Xw1qrec - /build/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-1.11/samtools merge -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-1.11/samtools merge -r -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-1.11/test/dat/test_input_1_b.sam /build/samtools-1.11/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.11/samtools merge -cp -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-1.11/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-1.11/samtools merge -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a_regex.sam /build/samtools-1.11/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-1.11/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/xWaIZqXfN5/merge.tag.1.bam /tmp/xWaIZqXfN5/merge.tag.2.bam .. ok test_merge: /build/samtools-1.11/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/xWaIZqXfN5/merge.tag.3.bam /tmp/xWaIZqXfN5/merge.tag.4.bam .. ok test_merge: /build/samtools-1.11/samtools merge --no-PG -O SAM - /build/samtools-1.11/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-1.11/samtools merge --no-PG -O SAM -L /build/samtools-1.11/test/merge/merge.bed - /tmp/xWaIZqXfN5/merge.bed.1.bam /tmp/xWaIZqXfN5/merge.bed.2.bam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-1.11/test/dat/test_input_1_b.sam /build/samtools-1.11/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-1.11/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -s 1 -O sam -b /tmp/7EwXKV13fC - /build/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -r -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-1.11/test/dat/test_input_1_b.sam /build/samtools-1.11/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -cp -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-1.11/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.11/test/dat/test_input_1_a_regex.sam /build/samtools-1.11/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/xWaIZqXfN5/merge.tag.1.bam /tmp/xWaIZqXfN5/merge.tag.2.bam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/xWaIZqXfN5/merge.tag.3.bam /tmp/xWaIZqXfN5/merge.tag.4.bam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 --no-PG -O SAM - /build/samtools-1.11/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-1.11/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-1.11/test/merge/merge.bed - /tmp/xWaIZqXfN5/merge.bed.1.bam /tmp/xWaIZqXfN5/merge.bed.2.bam .. ok test_sort: /build/samtools-1.11/samtools sort /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sortout .. ok test_sort: /build/samtools-1.11/samtools sort -f /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sortout.bam .. ok test_sort: /build/samtools-1.11/samtools sort -o /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sorttmp .. ok test_sort: /build/samtools-1.11/samtools sort -m 10M /build/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -n -m 10M /build/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -t RG -m 10M /build/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -n -t RG -m 10M /build/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -t AS -m 10M /build/samtools-1.11/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -t FI -m 10M /build/samtools-1.11/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sortout .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 -f /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sortout.bam .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 -o /build/samtools-1.11/test/dat/test_input_1_a.bam /tmp/xWaIZqXfN5/sorttmp .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 -m 10M /build/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 -n -m 10M /build/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 -t RG -m 10M /build/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 -n -t RG -m 10M /build/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 -t AS -m 10M /build/samtools-1.11/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.11/samtools sort -@ 2 -t FI -m 10M /build/samtools-1.11/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /build/samtools-1.11/samtools collate --output-fmt=sam -O /build/samtools-1.11/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.11/samtools collate -o /build/samtools-1.11/test/collate/collate1.tmp.sam /build/samtools-1.11/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.11/samtools collate -o /build/samtools-1.11/test/collate/collate2.tmp.sam /build/samtools-1.11/test/dat/test_input_1_d.sam /build/samtools-1.11/test/collate/collate2.tmp .. ok test_collate: /build/samtools-1.11/samtools collate --output-fmt=sam /build/samtools-1.11/test/dat/test_input_1_d.sam /build/samtools-1.11/test/collate/collate3.tmp .. ok test_collate: /build/samtools-1.11/samtools collate --output-fmt=sam -f /build/samtools-1.11/test/collate/fast_collate.sam -o /build/samtools-1.11/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-1.11/samtools collate --output-fmt=sam -f -r 4 /build/samtools-1.11/test/collate/fast_collate.sam -o /build/samtools-1.11/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/samtools-1.11/samtools collate -@ 2 --output-fmt=sam -O /build/samtools-1.11/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.11/samtools collate -@ 2 -o /build/samtools-1.11/test/collate/collate1.tmp.sam /build/samtools-1.11/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.11/samtools collate -@ 2 -o /build/samtools-1.11/test/collate/collate2.tmp.sam /build/samtools-1.11/test/dat/test_input_1_d.sam /build/samtools-1.11/test/collate/collate2.tmp .. ok test_collate: /build/samtools-1.11/samtools collate -@ 2 --output-fmt=sam /build/samtools-1.11/test/dat/test_input_1_d.sam /build/samtools-1.11/test/collate/collate3.tmp .. ok test_collate: /build/samtools-1.11/samtools collate -@ 2 --output-fmt=sam -f /build/samtools-1.11/test/collate/fast_collate.sam -o /build/samtools-1.11/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-1.11/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/samtools-1.11/test/collate/fast_collate.sam -o /build/samtools-1.11/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -O sam /build/samtools-1.11/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-1.11/samtools fixmate -O sam /build/samtools-1.11/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -O sam /build/samtools-1.11/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -O sam /build/samtools-1.11/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -cO sam /build/samtools-1.11/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -cO sam /build/samtools-1.11/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -O sam /build/samtools-1.11/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -O sam /build/samtools-1.11/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-1.11/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-1.11/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-1.11/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-1.11/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -@ 2 -cO sam /build/samtools-1.11/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -@ 2 -cO sam /build/samtools-1.11/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-1.11/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-1.11/test/fixmate/8_isize_overflow_64bit.sam - .. ok /build/samtools-1.11/samtools calmd -uAr /build/samtools-1.11/test/dat/mpileup.1.sam /build/samtools-1.11/test/dat/mpileup.ref.fa .. ok /build/samtools-1.11/samtools calmd -@ 2 -uAr /build/samtools-1.11/test/dat/mpileup.1.sam /build/samtools-1.11/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/samtools-1.11/samtools idxstats /build/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/samtools-1.11/samtools idxstats /build/samtools-1.11/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/samtools-1.11/samtools idxstats /build/samtools-1.11/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck /build/samtools-1.11/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck -v /build/samtools-1.11/test/quickcheck/1.quickcheck.badeof.bam /build/samtools-1.11/test/quickcheck/2.quickcheck.badheader.bam /build/samtools-1.11/test/quickcheck/3.quickcheck.ok.bam /build/samtools-1.11/test/quickcheck/4.quickcheck.ok.bam /build/samtools-1.11/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/samtools-1.11/test/quickcheck/6.quickcheck.cram21.ok.cram /build/samtools-1.11/test/quickcheck/7.quickcheck.cram30.ok.cram /build/samtools-1.11/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/samtools-1.11/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/samtools-1.11/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/samtools-1.11/samtools quickcheck -uv /build/samtools-1.11/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/samtools-1.11/samtools reheader /build/samtools-1.11/test/reheader/hdr.sam /build/samtools-1.11/test/dat/view.001.tmp.bam | /build/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.11/samtools reheader /build/samtools-1.11/test/reheader/hdr.sam /build/samtools-1.11/test/dat/view.001.tmp.v21.cram | /build/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.11/samtools reheader /build/samtools-1.11/test/reheader/hdr.sam /build/samtools-1.11/test/dat/view.001.tmp.v30.cram | /build/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.11/samtools reheader --in-place /build/samtools-1.11/test/reheader/hdr.sam /build/samtools-1.11/test/dat/view.001.tmp.v21.cram && /build/samtools-1.11/samtools view -h --no-PG /build/samtools-1.11/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.11/samtools reheader --in-place /build/samtools-1.11/test/reheader/hdr.sam /build/samtools-1.11/test/dat/view.001.tmp.v30.cram && /build/samtools-1.11/samtools view -h --no-PG /build/samtools-1.11/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.11/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/samtools-1.11/test/dat/view.001.tmp.bam | /build/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.11/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/samtools-1.11/test/dat/view.001.tmp.v30.cram | /build/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -O sam -m overwrite_all /build/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -O sam -m orphan_only /build/samtools-1.11/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -O sam -R '1#9' /build/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-1.11/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-1.11/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/samtools-1.11/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-1.11/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.11/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-1.11/test/addrprg/4_fixup_norg.sam .. ok test_markdup: /build/samtools-1.11/samtools markdup -O sam --no-PG /build/samtools-1.11/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-1.11/samtools markdup -O sam --no-PG /build/samtools-1.11/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /build/samtools-1.11/samtools markdup -O sam --no-PG /build/samtools-1.11/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-1.11/samtools markdup -O sam --no-PG /build/samtools-1.11/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-1.11/samtools markdup -O sam --no-PG /build/samtools-1.11/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -O sam -r --no-PG /build/samtools-1.11/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -S -O sam --no-PG /build/samtools-1.11/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/samtools-1.11/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/samtools-1.11/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.11/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.11/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /build/samtools-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.11/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-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.11/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-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.11/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -@ 2 -O sam -r --no-PG /build/samtools-1.11/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -@ 2 -S -O sam --no-PG /build/samtools-1.11/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/samtools-1.11/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/samtools-1.11/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/samtools-1.11/test/markdup/9_optical_dup_qcfail.sam - .. ok test_bedcov: /build/samtools-1.11/samtools bedcov /build/samtools-1.11/test/bedcov/bedcov.bed /build/samtools-1.11/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-1.11/samtools bedcov -j /build/samtools-1.11/test/bedcov/bedcov.bed /build/samtools-1.11/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-1.11/samtools bedcov -g512 -G2048 /build/samtools-1.11/test/bedcov/bedcov_gG.bed /build/samtools-1.11/test/bedcov/bedcov.bam .. ok test_split: /build/samtools-1.11/samtools split --output-fmt sam -u /build/samtools-1.11/test/split/split.tmp.unk.sam -f /build/samtools-1.11/test/split/split.tmp.%!.%. /build/samtools-1.11/test/split/split.sam .. ok test_split: /build/samtools-1.11/samtools split -@ 2 --output-fmt sam -u /build/samtools-1.11/test/split/split.tmp.unk.sam -f /build/samtools-1.11/test/split/split.tmp.%!.%. /build/samtools-1.11/test/split/split.sam .. ok test_large_positions: /build/samtools-1.11/samtools view -h --no-PG /tmp/xWaIZqXfN5/longref.sam.gz .. ok test_large_positions: /build/samtools-1.11/samtools view -h --no-PG /tmp/xWaIZqXfN5/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/samtools-1.11/samtools view -h --no-PG -L /build/samtools-1.11/test/large_pos/test.bed /tmp/xWaIZqXfN5/longref.sam.gz .. ok test_large_positions: /build/samtools-1.11/samtools sort -O sam --no-PG -m 10M /build/samtools-1.11/test/large_pos/longref_name.sam .. ok test_large_positions: /build/samtools-1.11/samtools merge -O sam --no-PG - /build/samtools-1.11/test/large_pos/longref.sam /build/samtools-1.11/test/large_pos/longref2.sam .. ok test_large_positions: /build/samtools-1.11/samtools depth /build/samtools-1.11/test/large_pos/longref.sam .. ok test_large_positions: /build/samtools-1.11/samtools depth -b /build/samtools-1.11/test/large_pos/test.bed /build/samtools-1.11/test/large_pos/longref.sam .. ok test_large_positions: /build/samtools-1.11/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/xWaIZqXfN5/longref.sam.gz .. ok test_large_positions: /build/samtools-1.11/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/samtools-1.11/samtools fixmate -O sam --no-PG - - | /build/samtools-1.11/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip --no-PG --output-fmt=sam -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconstats: /build/samtools-1.11/samtools ampliconstats -@ 2 -t 50 -d 1,20,100 /build/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-1.11/test/ampliconclip/1_hard_clipped.expected.sam /build/samtools-1.11/test/ampliconclip/1_soft_clipped.expected.sam /build/samtools-1.11/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/samtools-1.11/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' | tee /tmp/out.txt .. ok Number of tests: total .. 700 passed .. 654 failed .. 0 expected failure .. 46 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 163 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ./regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 47 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/samtools-1.11' rm -fr -- /tmp/dh-xdg-rundir-zkrLiXgy make[1]: Leaving directory '/build/samtools-1.11' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/samtools.substvars debian/samtools-test.substvars rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/ debian/.debhelper/generated/samtools-test/ debian/samtools-test/ rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/samtools-1.11' dh_auto_install -- \ prefix=/usr install -d /build/samtools-1.11/debian/tmp make -j4 install DESTDIR=/build/samtools-1.11/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-1.11' mkdir -p -m 755 /build/samtools-1.11/debian/tmp/usr/bin /build/samtools-1.11/debian/tmp/usr/bin /build/samtools-1.11/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-1.11/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /build/samtools-1.11/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/wgsim_eval.pl misc/zoom2sam.pl misc/plot-ampliconstats /build/samtools-1.11/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/samtools-1.11/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/samtools-1.11' make clean make[2]: Entering directory '/build/samtools-1.11' 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-1.11' make[1]: Leaving directory '/build/samtools-1.11' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/samtools-1.11' 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-1.11' 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 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-1.11' 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-1.11' 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 rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 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 rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 dh_strip_nondeterminism Using 1601563342 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1601563342 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 gzip -9nf 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-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/samtools-1.11' cd '/build/samtools-1.11' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a install -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 586252 new size 607065 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/57 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/57/bb9880f18ecf7667ce5534ef530a6bf35e1a6a.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/57/bb9880f18ecf7667ce5534ef530a6bf35e1a6a.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/57/bb9880f18ecf7667ce5534ef530a6bf35e1a6a.debug debian/samtools/usr/bin/wgsim install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/e8bcfeca4939d768b51d712defa0da18dad300.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/e8bcfeca4939d768b51d712defa0da18dad300.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/1c/e8bcfeca4939d768b51d712defa0da18dad300.debug debian/samtools/usr/bin/ace2sam install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bc objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bc/f849a1727409ffe3ad7d810b11f4f03f9d27b5.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bc/f849a1727409ffe3ad7d810b11f4f03f9d27b5.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/bc/f849a1727409ffe3ad7d810b11f4f03f9d27b5.debug debian/samtools/usr/bin/md5fa install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.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/0b/7c9879235c025a48c0b5df5b53a7e1e12b2e3e.debug debian/samtools/usr/bin/maq2sam-long install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/25677a2ac9ec55e3028473c9ce4813820da8e4.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/25677a2ac9ec55e3028473c9ce4813820da8e4.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/91/25677a2ac9ec55e3028473c9ce4813820da8e4.debug debian/samtools/usr/bin/samtools objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/925ea5765600fca317e280a0b6eb655a9e71d4.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/925ea5765600fca317e280a0b6eb655a9e71d4.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/91/925ea5765600fca317e280a0b6eb655a9e71d4.debug debian/samtools/usr/bin/maq2sam-short install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.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/28/30243c9cbcb20002b282bf848cefc9d9aef8fd.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite 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 -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=0b7c9879235c025a48c0b5df5b53a7e1e12b2e3e 1ce8bcfeca4939d768b51d712defa0da18dad300 2830243c9cbcb20002b282bf848cefc9d9aef8fd 57bb9880f18ecf7667ce5534ef530a6bf35e1a6a 9125677a2ac9ec55e3028473c9ce4813820da8e4 91925ea5765600fca317e280a0b6eb655a9e71d4 bcf849a1727409ffe3ad7d810b11f4f03f9d27b5" -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools' in '../samtools_1.11-1_armhf.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.11-1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.11-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../samtools_1.11-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/12083/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/12083/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/12083 and its subdirectories I: Current time: Thu Jul 29 17:01:22 +14 2021 I: pbuilder-time-stamp: 1627527682