I: pbuilder: network access will be disabled during build I: Current time: Wed May 24 00:04:58 +14 2023 I: pbuilder-time-stamp: 1684836298 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [samtools_1.16.1-1.dsc] I: copying [./samtools_1.16.1.orig.tar.gz] I: copying [./samtools_1.16.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Sep 30 23:55:42 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./samtools_1.16.1-1.dsc: no acceptable signature found dpkg-source: info: extracting samtools in samtools-1.16.1 dpkg-source: info: unpacking samtools_1.16.1.orig.tar.gz dpkg-source: info: unpacking samtools_1.16.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch dpkg-source: info: applying samtools-fasta-q-whatis.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30201/tmp/hooks/D01_modify_environment starting debug: Running on virt32a. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 24 00:06 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/30201/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/30201/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.15(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 parallel=4 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=c9ba4320257f4a82bf7aa6e9f9ca203c 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=30201 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HZLk05aI/pbuilderrc_FFGX --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HZLk05aI/b2 --logfile b2/build.log --extrapackages usrmerge samtools_1.16.1-1.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://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash -rwxr-xr-x 1 root root 133220 Sep 21 2022 date -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd -rwxr-xr-x 1 root root 68104 Sep 21 2022 df -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 67548 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 24 00:06 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch -rwxr-xr-x 1 root root 67548 Sep 21 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/30201/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 (>= 1.14~), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix, liblzma-dev, libbz2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19329 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 (>= 1.14~); 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; 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} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 24.8 MB of archives. After unpacking 90.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf bash-completion all 1:2.11-6 [234 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 23 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 25 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libbz2-dev armhf 1.0.8-5+b1 [28.1 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-9 [343 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libcurl4-gnutls-dev armhf 7.88.1-9 [448 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libio-pty-perl armhf 1:1.17-1 [34.5 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libncurses6 armhf 6.4-4 [81.1 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libncurses-dev armhf 6.4-4 [311 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libncurses5-dev armhf 6.4-4 [932 B] Get: 55 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf tabix armhf 1.16+ds-3 [388 kB] Fetched 24.8 MB in 3s (8914 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) Preparing to unpack .../00-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package bash-completion. Preparing to unpack .../02-bash-completion_1%3a2.11-6_all.deb ... Unpacking bash-completion (1:2.11-6) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../04-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-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 .../21-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../24-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../26-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-12_armhf.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../32-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../33-libbz2-dev_1.0.8-5+b1_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-5+b1) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../34-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../35-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../36-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../37-libnghttp2-14_1.52.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../38-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../39-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 .../40-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../41-libcurl3-gnutls_7.88.1-9_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.88.1-9) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../42-libcurl4-gnutls-dev_7.88.1-9_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (7.88.1-9) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../43-libdeflate0_1.14-1_armhf.deb ... Unpacking libdeflate0:armhf (1.14-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../44-libdeflate-dev_1.14-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.14-1) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../45-libhtscodecs2_1.3.0-4_armhf.deb ... Unpacking libhtscodecs2:armhf (1.3.0-4) ... Selecting previously unselected package libhts3:armhf. Preparing to unpack .../46-libhts3_1.16+ds-3_armhf.deb ... Unpacking libhts3:armhf (1.16+ds-3) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../47-liblzma-dev_5.4.1-0.2_armhf.deb ... Unpacking liblzma-dev:armhf (5.4.1-0.2) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../48-zlib1g-dev_1%3a1.2.13.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../49-libhts-dev_1.16+ds-3_armhf.deb ... Unpacking libhts-dev:armhf (1.16+ds-3) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../50-libio-pty-perl_1%3a1.17-1_armhf.deb ... Unpacking libio-pty-perl (1:1.17-1) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../51-libncurses6_6.4-4_armhf.deb ... Unpacking libncurses6:armhf (6.4-4) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../52-libncurses-dev_6.4-4_armhf.deb ... Unpacking libncurses-dev:armhf (6.4-4) ... Selecting previously unselected package libncurses5-dev:armhf. Preparing to unpack .../53-libncurses5-dev_6.4-4_armhf.deb ... Unpacking libncurses5-dev:armhf (6.4-4) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../54-libpkgconf3_1.8.1-1_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../55-pkgconf-bin_1.8.1-1_armhf.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../56-pkgconf_1.8.1-1_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-1) ... Selecting previously unselected package pkg-config:armhf. Preparing to unpack .../57-pkg-config_1.8.1-1_armhf.deb ... Unpacking pkg-config:armhf (1.8.1-1) ... Selecting previously unselected package tabix. Preparing to unpack .../58-tabix_1.16+ds-3_armhf.deb ... Unpacking tabix (1.16+ds-3) ... Setting up libhtscodecs2:armhf (1.3.0-4) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libpsl5:armhf (0.21.2-1) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libio-pty-perl (1:1.17-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up autoconf-archive (20220903-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up bash-completion (1:2.11-6) ... Setting up libncurses6:armhf (6.4-4) ... Setting up autopoint (0.21-12) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:armhf (5.4.1-0.2) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up libdeflate-dev:armhf (1.14-1) ... Setting up tabix (1.16+ds-3) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up libbz2-dev:armhf (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libncurses-dev:armhf (6.4-4) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up pkgconf:armhf (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libncurses5-dev:armhf (6.4-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:armhf (7.88.1-9) ... Setting up libcurl4-gnutls-dev:armhf (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:armhf (1.16+ds-3) ... Setting up libhts-dev:armhf (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/30201/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/30201/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/samtools-1.16.1/ && 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_1.16.1-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.16.1-1 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-1.16.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/samtools-1.16.1' rm -f config.mk touch config.mk dh_auto_clean -- make -j4 distclean make[2]: Entering directory '/build/samtools-1.16.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* cd test/reference && rm -f mpileup.*.fai rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS rm -rf autom4te.cache make[2]: Leaving directory '/build/samtools-1.16.1' make[1]: Leaving directory '/build/samtools-1.16.1' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/samtools-1.16.1' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for 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-1.16.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/samtools-1.16.1' 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 -ffile-prefix-map=/build/samtools-1.16.1=. -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-1.16.1' gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 "1.16.1"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h sed -i -e 's@/build/samtools-1.16.1@«BUILDPATH»@g' version.h gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -ffile-prefix-map=/build/samtools-1.16.1=. -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 -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -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_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/samtools-1.16.1' make[1]: Leaving directory '/build/samtools-1.16.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/samtools-1.16.1' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/samtools-1.16.1' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} test_reference: /build/samtools-1.16.1/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-1.16.1/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-1.16.1/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-1.16.1/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-1.16.1/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-1.16.1/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-1.16.1/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-1.16.1/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/8XFqOIQ9QB/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/8XFqOIQ9QB/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/8XFqOIQ9QB/bgzip.dat.gz .. ok /build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/samtools-1.16.1/samtools faidx /tmp/8XFqOIQ9QB/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq 3:11-13 .. ok .. ok /build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq.gz 3:11-13 .. ok .. ok /build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq 2:998-1003 .. ok .. ok /build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq 1:100-104 .. ok .. ok /build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq.gz 1:100-104 .. ok .. ok /build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq 1:99998-100007 .. ok .. ok /build/samtools-1.16.1/samtools fqidx /tmp/8XFqOIQ9QB/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/samtools-1.16.1/test/dat/dict.fa .. ok test_dict: /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/8XFqOIQ9QB/dict.fa.gz .. ok test_dict: cat /build/samtools-1.16.1/test/dat/dict.fa | /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/samtools-1.16.1/samtools dict -AH < /build/samtools-1.16.1/test/dat/dict.alias.fa .. ok test_dict: /build/samtools-1.16.1/samtools dict -H -l /build/samtools-1.16.1/test/dat/dict.alt < /build/samtools-1.16.1/test/dat/dict.alias.fa .. ok test_index: /build/samtools-1.16.1/samtools view /tmp/8XFqOIQ9QB/large_chrom.bam ref2 .. ok test_index: /build/samtools-1.16.1/samtools view /tmp/8XFqOIQ9QB/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-1.16.1/samtools index /build/samtools-1.16.1/test/dat/test_input_1_a.bam && cat /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/8XFqOIQ9QB/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-1.16.1/samtools merge -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/8XFqOIQ9QB/test_input_1_b.bam.bai .. ok test_index: /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/8XFqOIQ9QB/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/samtools-1.16.1/samtools index /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam .. ok test_index: /build/samtools-1.16.1/samtools index -M /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam && cat /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/8XFqOIQ9QB/auto_indexed.csi && cat /tmp/8XFqOIQ9QB/auto_indexed.csi .. ok test_index: /build/samtools-1.16.1/samtools index /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/8XFqOIQ9QB/auto_indexed.crai && cat /tmp/8XFqOIQ9QB/auto_indexed.crai .. ok test_index: /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/8XFqOIQ9QB/auto_indexed.csi && cat /tmp/8XFqOIQ9QB/auto_indexed.csi .. ok test_index: /build/samtools-1.16.1/samtools view -@ 2 /tmp/8XFqOIQ9QB/large_chrom.bam ref2 .. ok test_index: /build/samtools-1.16.1/samtools view -@ 2 /tmp/8XFqOIQ9QB/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-1.16.1/samtools index -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam && cat /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/8XFqOIQ9QB/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-1.16.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/8XFqOIQ9QB/test_input_1_b.bam.bai .. ok test_index: /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/8XFqOIQ9QB/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/samtools-1.16.1/samtools index -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam .. ok test_index: /build/samtools-1.16.1/samtools index -@ 2 -M /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam && cat /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/8XFqOIQ9QB/auto_indexed.csi && cat /tmp/8XFqOIQ9QB/auto_indexed.csi .. ok test_index: /build/samtools-1.16.1/samtools index -@ 2 /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/8XFqOIQ9QB/auto_indexed.crai && cat /tmp/8XFqOIQ9QB/auto_indexed.crai .. ok test_index: /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/8XFqOIQ9QB/auto_indexed.csi && cat /tmp/8XFqOIQ9QB/auto_indexed.csi .. ok test_mpileup: /build/samtools-1.16.1/samtools mpileup -b /tmp/8XFqOIQ9QB/mpileup.bam.list -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.16.1/samtools mpileup -b /tmp/8XFqOIQ9QB/mpileup.cram.list -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.16.1/samtools mpileup -b /tmp/8XFqOIQ9QB/mpileup.bam.urllist -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.16.1/samtools mpileup -b /tmp/8XFqOIQ9QB/mpileup.cram.urllist -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/8XFqOIQ9QB/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/8XFqOIQ9QB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/8XFqOIQ9QB/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/samtools-1.16.1/samtools mpileup /build/samtools-1.16.1/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate 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 consensus .. ok test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools import .. ok test_usage_subcommand: samtools reference .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth .. ok test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags .. ok test_usage_subcommand: samtools head .. ok test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools samples Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/8XFqOIQ9QB/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/8XFqOIQ9QB/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/8XFqOIQ9QB/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/8XFqOIQ9QB/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/8XFqOIQ9QB/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/8XFqOIQ9QB/view.001.forn (SAM input) .. ok 68: Count -N /tmp/8XFqOIQ9QB/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/8XFqOIQ9QB/view.001.forn (BAM input) .. ok 70: Count -N /tmp/8XFqOIQ9QB/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/8XFqOIQ9QB/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/8XFqOIQ9QB/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/8XFqOIQ9QB/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/8XFqOIQ9QB/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test115.sam -h -d TGCA /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test117.sam -h -d TGCA /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test119.sam -h -d TGCA /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test121.sam -h -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test123.sam -h -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test125.sam -h -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/8XFqOIQ9QB/view.001.fobc" Failed command: /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/8XFqOIQ9QB/view.001.fobc /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.16.1/samtools view -o /tmp/8XFqOIQ9QB/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/8XFqOIQ9QB/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa,ha (SAM input) .. ok 188: Count -x fa,ha (SAM input) .. ok 189: Filter -x fa,ha (BAM input) .. ok 190: Count -x fa,ha (BAM input) .. ok 191: Filter -x fa,ha (CRAM input) .. ok 192: Count -x fa,ha (CRAM input) .. ok 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 205: Filter -x fa -r grp2 (SAM input) .. ok 206: Count -x fa -r grp2 (SAM input) .. ok 207: Filter -x fa -r grp2 (BAM input) .. ok 208: Count -x fa -r grp2 (BAM input) .. ok 209: Filter -x fa -r grp2 (CRAM input) .. ok 210: Count -x fa -r grp2 (CRAM input) .. ok 211: Filter -x RG -r grp2 (SAM input) .. ok 212: Count -x RG -r grp2 (SAM input) .. ok 213: Filter -x RG -r grp2 (BAM input) .. ok 214: Count -x RG -r grp2 (BAM input) .. ok 215: Filter -x RG -r grp2 (CRAM input) .. ok 216: Count -x RG -r grp2 (CRAM input) .. ok 217: Filter -m 10 (SAM input) .. ok 218: Count -m 10 (SAM input) .. ok 219: Filter -m 10 (BAM input) .. ok 220: Count -m 10 (BAM input) .. ok 221: Filter -m 10 (CRAM input) .. ok 222: Count -m 10 (CRAM input) .. ok 223: Filter -m 11 (SAM input) .. ok 224: Count -m 11 (SAM input) .. ok 225: Filter -m 11 (BAM input) .. ok 226: Count -m 11 (BAM input) .. ok 227: Filter -m 11 (CRAM input) .. ok 228: Count -m 11 (CRAM input) .. ok 229: Filter -m 15 (SAM input) .. ok 230: Count -m 15 (SAM input) .. ok 231: Filter -m 15 (BAM input) .. ok 232: Count -m 15 (BAM input) .. ok 233: Filter -m 15 (CRAM input) .. ok 234: Count -m 15 (CRAM input) .. ok 235: Filter -m 16 (SAM input) .. ok 236: Count -m 16 (SAM input) .. ok 237: Filter -m 16 (BAM input) .. ok 238: Count -m 16 (BAM input) .. ok 239: Filter -m 16 (CRAM input) .. ok 240: Count -m 16 (CRAM input) .. ok 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247: Filter -e [BC] (SAM input) .. ok 248: Count -e [BC] (SAM input) .. ok 249: Filter -e [BC] (BAM input) .. ok 250: Count -e [BC] (BAM input) .. ok 251: Filter -e [BC] (CRAM input) .. ok 252: Count -e [BC] (CRAM input) .. ok 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 259: Filter -e mapq >= 50 (SAM input) .. ok 260: Count -e mapq >= 50 (SAM input) .. ok 261: Filter -e mapq >= 50 (BAM input) .. ok 262: Count -e mapq >= 50 (BAM input) .. ok 263: Filter -e mapq >= 50 (CRAM input) .. ok 264: Count -e mapq >= 50 (CRAM input) .. ok 265: Filter -e mapq >= 99 (SAM input) .. ok 266: Count -e mapq >= 99 (SAM input) .. ok 267: Filter -e mapq >= 99 (BAM input) .. ok 268: Count -e mapq >= 99 (BAM input) .. ok 269: Filter -e mapq >= 99 (CRAM input) .. ok 270: Count -e mapq >= 99 (CRAM input) .. ok 271: Filter -e mapq >= 100 (SAM input) .. ok 272: Count -e mapq >= 100 (SAM input) .. ok 273: Filter -e mapq >= 100 (BAM input) .. ok 274: Count -e mapq >= 100 (BAM input) .. ok 275: Filter -e mapq >= 100 (CRAM input) .. ok 276: Count -e mapq >= 100 (CRAM input) .. ok 277: 1bp reads file SAM -> BAM -> SAM .. ok 278: 1bp reads file SAM -> CRAM -> SAM .. ok 278: Region Z (BAM input) .. ok 279: Count Z (BAM input) .. ok 280: Region Z (CRAM input) .. ok 281: Count Z (CRAM input) .. ok 282: Region Z:30 (BAM input) .. ok 283: Count Z:30 (BAM input) .. ok 284: Region Z:30 (CRAM input) .. ok 285: Count Z:30 (CRAM input) .. ok 286: Region Z:20-40 (BAM input) .. ok 287: Count Z:20-40 (BAM input) .. ok 288: Region Z:20-40 (CRAM input) .. ok 289: Count Z:20-40 (CRAM input) .. ok 290: Region ref1 (BAM input) .. ok 291: Count ref1 (BAM input) .. ok 292: Region ref1 (CRAM input) .. ok 293: Count ref1 (CRAM input) .. ok 294: Region ref1:15 (BAM input) .. ok 295: Count ref1:15 (BAM input) .. ok 296: Region ref1:15 (CRAM input) .. ok 297: Count ref1:15 (CRAM input) .. ok 298: Region ref1:15-45 (BAM input) .. ok 299: Count ref1:15-45 (BAM input) .. ok 300: Region ref1:15-45 (CRAM input) .. ok 301: Count ref1:15-45 (CRAM input) .. ok 302: Region ref1:15-45 ref2 (BAM input) .. ok 303: Count ref1:15-45 ref2 (BAM input) .. ok 304: Region ref1:15-45 ref2 (CRAM input) .. ok 305: Count ref1:15-45 ref2 (CRAM input) .. ok 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 318: Region -f 128 ref1 (BAM input) .. ok 319: Count -f 128 ref1 (BAM input) .. ok 320: Region -f 128 ref1 (CRAM input) .. ok 321: Count -f 128 ref1 (CRAM input) .. ok 322: Region -q 50 ref1:15-45 (BAM input) .. ok 323: Count -q 50 ref1:15-45 (BAM input) .. ok 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 330: Region * (BAM input) .. ok 331: Count * (BAM input) .. ok 332: Region * (CRAM input) .. ok 333: Count * (CRAM input) .. ok 334: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /build/samtools-1.16.1/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /build/samtools-1.16.1/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /build/samtools-1.16.1/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /build/samtools-1.16.1/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /build/samtools-1.16.1/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /build/samtools-1.16.1/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /build/samtools-1.16.1/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /build/samtools-1.16.1/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z (BAM input).. ok 351: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z (BAM input).. ok 352: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z (CRAM input).. ok 353: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z (CRAM input).. ok 354: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 355: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 356: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 357: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 358: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 359: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 360: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 361: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 362: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 363: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 364: Region -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 365: Count -L /build/samtools-1.16.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 366: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 367: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 368: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 369: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 370: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 371: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 372: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 373: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 374: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 375: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 376: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 377: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 378: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 379: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 380: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 381: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 382: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 383: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 384: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 385: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 386: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 387: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 388: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 389: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 390: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 391: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 392: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 393: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 394: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 395: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 396: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 397: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 398: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 399: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 400: Region -L /build/samtools-1.16.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 401: Count -L /build/samtools-1.16.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 402: Make BAM with no M5/UR tags .. ok 403: Add @SQ with -t (SAM -> SAM) .. ok 404: Add @SQ with -T (SAM -> SAM) .. ok 405: Add @SQ with -t (BAM -> SAM) .. ok 406: Add @SQ with -T (BAM -> SAM) .. ok 407: Add @SQ with -t (SAM -> BAM) .. ok 408: Add @SQ with -T (SAM -> BAM) .. ok 409: Add @SQ with -t (BAM -> BAM) .. ok 410: Add @SQ with -T (BAM -> BAM) .. ok 411: Add @SQ with -t (SAM -> CRAM) .. ok 412: Add @SQ with -T (SAM -> CRAM) .. ok 413: Add @SQ with -t (BAM -> CRAM) .. ok 414: Add @SQ with -T (BAM -> CRAM) .. ok 415: Make CRAM with no UR field .. ok 416: Decoding CRAM with no UR field via -T .. ok 417: CIGAR B-operator removal .. ok 418: Big SAM -> BAM .. ok 419: Big SAM -> BAM (2 threads) .. ok 420: Big SAM -> BAM (4 threads) .. ok 421: Big SAM -> CRAM .. ok 422: Big SAM -> CRAM (2 threads) .. ok 423: Big SAM -> CRAM (4 threads) .. ok 424: Subsample 0.2 (SAM input) ............ ok 425: Subsample 0.5 (SAM input) ............ ok 426: Subsample 0.8 (SAM input) ............ ok 427: Subsample 0.2 (BAM input) ............ ok 428: Subsample 0.5 (BAM input) ............ ok 429: Subsample 0.8 (BAM input) ............ ok 430: Subsample 0.2 (CRAM input) ............ ok 431: Subsample 0.5 (CRAM input) ............ ok 432: Subsample 0.8 (CRAM input) ............ ok 433: SAM add PG .. ok 434: Unset dup flag, remove dt and do tags .. ok 435: Unmap dup flagged reads. .. ok 436: Unmap dup flagged reads. .. ok 437: fetch pairs .. ok 438: fetch pairs .. ok 439: fetch pairs .. ok test_head: /build/samtools-1.16.1/samtools head /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -h 0 /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -h 1 /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -h 5 /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -h 29 /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -h 30 /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -n 0 /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -n 1 /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -n 5 /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_head: /build/samtools-1.16.1/samtools head -h 5 -n 5 < /build/samtools-1.16.1/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_import: /build/samtools-1.16.1/samtools import -0 test/bam2fq/1.1.fq.expected | /build/samtools-1.16.1/samtools fastq -0 /build/samtools-1.16.1/test/0.fq .. ok test_import: /build/samtools-1.16.1/samtools import -s test/bam2fq/1.1.fq.expected | /build/samtools-1.16.1/samtools fastq -0 /build/samtools-1.16.1/test/0.fq .. ok test_import: /build/samtools-1.16.1/samtools import -s test/bam2fq/5.s.fq.expected | /build/samtools-1.16.1/samtools fastq -s /build/samtools-1.16.1/test/s.fq .. ok test_import: /build/samtools-1.16.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/samtools-1.16.1/samtools fastq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq .. ok test_import: /build/samtools-1.16.1/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/samtools-1.16.1/samtools fastq -N -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq .. ok test_import: /build/samtools-1.16.1/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/samtools-1.16.1/samtools fastq -i --index-format 'i*i*' -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq .. ok test_import: /build/samtools-1.16.1/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/samtools-1.16.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq .. ok test_import: /build/samtools-1.16.1/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/samtools-1.16.1/samtools fastq -N -T RG,BC,QT -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq .. ok test_import: /build/samtools-1.16.1/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/samtools-1.16.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq .. ok test_import: /build/samtools-1.16.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /build/samtools-1.16.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /build/samtools-1.16.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /build/samtools-1.16.1/samtools import test/import/2.interleaved.fq -T "" .. ok test_import: /build/samtools-1.16.1/samtools import test/import/3.interleaved.fq -i .. ok test_import: /build/samtools-1.16.1/samtools import test/import/4.aux.fq -T "*" .. ok test_import: /build/samtools-1.16.1/samtools import test/import/4.aux.fq -T "" .. ok test_import: /build/samtools-1.16.1/samtools import test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /build/samtools-1.16.1/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /build/samtools-1.16.1/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-1.16.1/test/bc.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.16.1/test/bc.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.16.1/test/bc.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-1.16.1/test/bc_split.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -N -t -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -N -t -T MD,ia -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-1.16.1/test/i.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/samtools-1.16.1/test/i.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -i --index-format 'i*i*' -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -N -1 /build/samtools-1.16.1/test/o.fq -2 /build/samtools-1.16.1/test/o.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fasta -N -1 /build/samtools-1.16.1/test/o.fa -2 /build/samtools-1.16.1/test/o.fa /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -N -o /build/samtools-1.16.1/test/o.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -N -s /tmp/8XFqOIQ9QB/bam2fq.discard.s.fq -0 /tmp/8XFqOIQ9QB/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/samtools-1.16.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq --index-format 'i8n1i8' --i1 /build/samtools-1.16.1/test/i1.fq --i2 /build/samtools-1.16.1/test/i2.fq -0 /build/samtools-1.16.1/test/0.fq /build/samtools-1.16.1/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -N -T '*' /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -N -T '' /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -N -t -T '*' /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-1.16.1/test/bc.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.16.1/test/bc.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-1.16.1/test/bc.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-1.16.1/test/bc_split.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -N -t -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -N -t -T MD,ia -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-1.16.1/test/i.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/samtools-1.16.1/test/i.fq -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/samtools-1.16.1/test/s.fq -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -1 /build/samtools-1.16.1/test/1.fq -2 /build/samtools-1.16.1/test/2.fq /build/samtools-1.16.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -N -1 /build/samtools-1.16.1/test/o.fq -2 /build/samtools-1.16.1/test/o.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fasta -@ 2 -N -1 /build/samtools-1.16.1/test/o.fa -2 /build/samtools-1.16.1/test/o.fa /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -N -o /build/samtools-1.16.1/test/o.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -N -s /tmp/8XFqOIQ9QB/bam2fq.discard.s.fq -0 /tmp/8XFqOIQ9QB/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/samtools-1.16.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/samtools-1.16.1/test/i1.fq --i2 /build/samtools-1.16.1/test/i2.fq -0 /build/samtools-1.16.1/test/0.fq /build/samtools-1.16.1/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -N -T '*' /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -N -T '' /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-1.16.1/samtools fastq -@ 2 -N -t -T '*' /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /build/samtools-1.16.1/samtools stats -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -r /build/samtools-1.16.1/test/stat/test.fa -i 0 /build/samtools-1.16.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -S RG -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -S RG -r /build/samtools-1.16.1/test/stat/test.fa /build/samtools-1.16.1/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -t /build/samtools-1.16.1/test/stat/11.stats.targets /build/samtools-1.16.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -g 4 -t /build/samtools-1.16.1/test/stat/11.stats.targets /build/samtools-1.16.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -g 4 /build/samtools-1.16.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/12_overlaps.bam -t /build/samtools-1.16.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/12_overlaps.bam -p -t /build/samtools-1.16.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/12_overlaps.bam -t /build/samtools-1.16.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/12_overlaps.bam -p -t /build/samtools-1.16.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/samtools-1.16.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/samtools-1.16.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-1.16.1/samtools stats /build/samtools-1.16.1/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/samtools-1.16.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-1.16.1/samtools stats -I s1 /build/samtools-1.16.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -I grp2 /build/samtools-1.16.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -I grp3 /build/samtools-1.16.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/samtools-1.16.1/samtools stats -I Sample /build/samtools-1.16.1/test/stat/11_target.bam | tail -n+4 .. ok test_merge: /build/samtools-1.16.1/samtools merge -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a.sam /build/samtools-1.16.1/test/dat/test_input_1_b.sam /build/samtools-1.16.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -s 1 -O sam -b /tmp/fs2QL3qQos - /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -r -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a.sam /build/samtools-1.16.1/test/dat/test_input_1_b.sam /build/samtools-1.16.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -cp -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a.sam /build/samtools-1.16.1/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a_regex.sam /build/samtools-1.16.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -o - -s 1 -O sam /build/samtools-1.16.1/test/dat/test_input_1_a.sam /build/samtools-1.16.1/test/dat/test_input_1_b.sam /build/samtools-1.16.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/8XFqOIQ9QB/merge.tag.1.bam /tmp/8XFqOIQ9QB/merge.tag.2.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/8XFqOIQ9QB/merge.tag.3.bam /tmp/8XFqOIQ9QB/merge.tag.4.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge --no-PG -O SAM - /build/samtools-1.16.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/8XFqOIQ9QB/merge.bed.1.bam /tmp/8XFqOIQ9QB/merge.bed.2.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge --no-PG -r -O SAM - /build/samtools-1.16.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a.sam /build/samtools-1.16.1/test/dat/test_input_1_b.sam /build/samtools-1.16.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/EzqekvVRy4 - /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -r -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a.sam /build/samtools-1.16.1/test/dat/test_input_1_b.sam /build/samtools-1.16.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -cp -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a.sam /build/samtools-1.16.1/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam - /build/samtools-1.16.1/test/dat/test_input_1_a_regex.sam /build/samtools-1.16.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -o - -s 1 -O sam /build/samtools-1.16.1/test/dat/test_input_1_a.sam /build/samtools-1.16.1/test/dat/test_input_1_b.sam /build/samtools-1.16.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/8XFqOIQ9QB/merge.tag.1.bam /tmp/8XFqOIQ9QB/merge.tag.2.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/8XFqOIQ9QB/merge.tag.3.bam /tmp/8XFqOIQ9QB/merge.tag.4.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 --no-PG -O SAM - /build/samtools-1.16.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/8XFqOIQ9QB/merge.bed.1.bam /tmp/8XFqOIQ9QB/merge.bed.2.bam .. ok test_merge: /build/samtools-1.16.1/samtools merge -@ 2 --no-PG -r -O SAM - /build/samtools-1.16.1/test/merge/test_no_pg_rg_co.sam .. ok test_sort: /build/samtools-1.16.1/samtools sort /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sortout .. ok test_sort: /build/samtools-1.16.1/samtools sort -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sortout.bam .. ok test_sort: /build/samtools-1.16.1/samtools sort -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sorttmp .. ok test_sort: /build/samtools-1.16.1/samtools sort -m 10M /build/samtools-1.16.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -n -m 10M /build/samtools-1.16.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -t RG -m 10M /build/samtools-1.16.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -n -t RG -m 10M /build/samtools-1.16.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -t AS -m 10M /build/samtools-1.16.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -t FI -m 10M /build/samtools-1.16.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort --template-coordinate -m 10M /build/samtools-1.16.1/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sortout .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sortout.bam .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/8XFqOIQ9QB/sorttmp .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 -m 10M /build/samtools-1.16.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 -n -m 10M /build/samtools-1.16.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 -t RG -m 10M /build/samtools-1.16.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 -n -t RG -m 10M /build/samtools-1.16.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 -t AS -m 10M /build/samtools-1.16.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 -t FI -m 10M /build/samtools-1.16.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-1.16.1/samtools sort -@ 2 --template-coordinate -m 10M /build/samtools-1.16.1/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_collate: /build/samtools-1.16.1/samtools collate --output-fmt=sam -O /build/samtools-1.16.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.16.1/samtools collate -o /build/samtools-1.16.1/test/collate/collate1.tmp.sam /build/samtools-1.16.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.16.1/samtools collate -o /build/samtools-1.16.1/test/collate/collate2.tmp.sam /build/samtools-1.16.1/test/dat/test_input_1_d.sam /build/samtools-1.16.1/test/collate/collate2.tmp .. ok test_collate: /build/samtools-1.16.1/samtools collate --output-fmt=sam /build/samtools-1.16.1/test/dat/test_input_1_d.sam /build/samtools-1.16.1/test/collate/collate3.tmp .. ok test_collate: /build/samtools-1.16.1/samtools collate --output-fmt=sam -f /build/samtools-1.16.1/test/collate/fast_collate.sam -o /build/samtools-1.16.1/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-1.16.1/samtools collate --output-fmt=sam -f -r 4 /build/samtools-1.16.1/test/collate/fast_collate.sam -o /build/samtools-1.16.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/samtools-1.16.1/samtools collate -@ 2 --output-fmt=sam -O /build/samtools-1.16.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.16.1/samtools collate -@ 2 -o /build/samtools-1.16.1/test/collate/collate1.tmp.sam /build/samtools-1.16.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-1.16.1/samtools collate -@ 2 -o /build/samtools-1.16.1/test/collate/collate2.tmp.sam /build/samtools-1.16.1/test/dat/test_input_1_d.sam /build/samtools-1.16.1/test/collate/collate2.tmp .. ok test_collate: /build/samtools-1.16.1/samtools collate -@ 2 --output-fmt=sam /build/samtools-1.16.1/test/dat/test_input_1_d.sam /build/samtools-1.16.1/test/collate/collate3.tmp .. ok test_collate: /build/samtools-1.16.1/samtools collate -@ 2 --output-fmt=sam -f /build/samtools-1.16.1/test/collate/fast_collate.sam -o /build/samtools-1.16.1/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-1.16.1/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/samtools-1.16.1/test/collate/fast_collate.sam -o /build/samtools-1.16.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -O sam /build/samtools-1.16.1/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-1.16.1/samtools fixmate -O sam /build/samtools-1.16.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -O sam /build/samtools-1.16.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -O sam /build/samtools-1.16.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -cO sam /build/samtools-1.16.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -cO sam /build/samtools-1.16.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -O sam /build/samtools-1.16.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -O sam /build/samtools-1.16.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -@ 2 -O sam /build/samtools-1.16.1/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-1.16.1/samtools fixmate -@ 2 -O sam /build/samtools-1.16.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -@ 2 -O sam /build/samtools-1.16.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -@ 2 -O sam /build/samtools-1.16.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -@ 2 -cO sam /build/samtools-1.16.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -@ 2 -cO sam /build/samtools-1.16.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -@ 2 -O sam /build/samtools-1.16.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-1.16.1/samtools fixmate -@ 2 -O sam /build/samtools-1.16.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok /build/samtools-1.16.1/samtools calmd -uAr /build/samtools-1.16.1/test/dat/mpileup.1.sam /build/samtools-1.16.1/test/dat/mpileup.ref.fa .. ok /build/samtools-1.16.1/samtools calmd -@ 2 -uAr /build/samtools-1.16.1/test/dat/mpileup.1.sam /build/samtools-1.16.1/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/samtools-1.16.1/samtools idxstats /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/samtools-1.16.1/samtools idxstats /build/samtools-1.16.1/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/samtools-1.16.1/samtools idxstats /build/samtools-1.16.1/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck /build/samtools-1.16.1/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck -v /build/samtools-1.16.1/test/quickcheck/1.quickcheck.badeof.bam /build/samtools-1.16.1/test/quickcheck/2.quickcheck.badheader.bam /build/samtools-1.16.1/test/quickcheck/3.quickcheck.ok.bam /build/samtools-1.16.1/test/quickcheck/4.quickcheck.ok.bam /build/samtools-1.16.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/samtools-1.16.1/test/quickcheck/6.quickcheck.cram21.ok.cram /build/samtools-1.16.1/test/quickcheck/7.quickcheck.cram30.ok.cram /build/samtools-1.16.1/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/samtools-1.16.1/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/samtools-1.16.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/samtools-1.16.1/samtools quickcheck -uv /build/samtools-1.16.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/samtools-1.16.1/samtools reheader /build/samtools-1.16.1/test/reheader/hdr.sam /build/samtools-1.16.1/test/dat/view.001.tmp.bam | /build/samtools-1.16.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.16.1/samtools reheader /build/samtools-1.16.1/test/reheader/hdr.sam /build/samtools-1.16.1/test/dat/view.001.tmp.v21.cram | /build/samtools-1.16.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.16.1/samtools reheader /build/samtools-1.16.1/test/reheader/hdr.sam /build/samtools-1.16.1/test/dat/view.001.tmp.v30.cram | /build/samtools-1.16.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.16.1/samtools reheader --in-place /build/samtools-1.16.1/test/reheader/hdr.sam /build/samtools-1.16.1/test/dat/view.001.tmp.v21.cram && /build/samtools-1.16.1/samtools view -h --no-PG /build/samtools-1.16.1/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.16.1/samtools reheader --in-place /build/samtools-1.16.1/test/reheader/hdr.sam /build/samtools-1.16.1/test/dat/view.001.tmp.v30.cram && /build/samtools-1.16.1/samtools view -h --no-PG /build/samtools-1.16.1/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.16.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/samtools-1.16.1/test/dat/view.001.tmp.bam | /build/samtools-1.16.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-1.16.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/samtools-1.16.1/test/dat/view.001.tmp.v30.cram | /build/samtools-1.16.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -O sam -m overwrite_all /build/samtools-1.16.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -O sam -m orphan_only /build/samtools-1.16.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -O sam -R '1#9' /build/samtools-1.16.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-1.16.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/samtools-1.16.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-1.16.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/samtools-1.16.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/samtools-1.16.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/samtools-1.16.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/samtools-1.16.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-1.16.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/samtools-1.16.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-1.16.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-1.16.1/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/samtools-1.16.1/test/addrprg/1_fixup.sam .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -O sam --no-PG /build/samtools-1.16.1/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-1.16.1/samtools markdup -O sam --no-PG /build/samtools-1.16.1/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /build/samtools-1.16.1/samtools markdup -O sam --no-PG /build/samtools-1.16.1/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-1.16.1/samtools markdup -O sam --no-PG /build/samtools-1.16.1/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-1.16.1/samtools markdup -O sam --no-PG /build/samtools-1.16.1/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -O sam -r --no-PG /build/samtools-1.16.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -O sam --no-PG /build/samtools-1.16.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/samtools-1.16.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/samtools-1.16.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/samtools-1.16.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/samtools-1.16.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/samtools-1.16.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/samtools-1.16.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/samtools-1.16.1/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/samtools-1.16.1/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/samtools-1.16.1/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /build/samtools-1.16.1/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /build/samtools-1.16.1/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.16.1/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.16.1/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.16.1/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-1.16.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.16.1/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-1.16.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-1.16.1/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -O sam -r --no-PG /build/samtools-1.16.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -O sam --no-PG /build/samtools-1.16.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/samtools-1.16.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/samtools-1.16.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/samtools-1.16.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/samtools-1.16.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/samtools-1.16.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/samtools-1.16.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/samtools-1.16.1/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/samtools-1.16.1/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/samtools-1.16.1/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /build/samtools-1.16.1/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/samtools-1.16.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /build/samtools-1.16.1/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_bedcov: /build/samtools-1.16.1/samtools bedcov /build/samtools-1.16.1/test/bedcov/bedcov.bed /build/samtools-1.16.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-1.16.1/samtools bedcov -j /build/samtools-1.16.1/test/bedcov/bedcov.bed /build/samtools-1.16.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-1.16.1/samtools bedcov -g512 -G2048 /build/samtools-1.16.1/test/bedcov/bedcov_gG.bed /build/samtools-1.16.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-1.16.1/samtools bedcov -c /build/samtools-1.16.1/test/bedcov/bedcov_gG.bed /build/samtools-1.16.1/test/bedcov/bedcov.bam .. ok test_split: /build/samtools-1.16.1/samtools split --output-fmt sam -u /build/samtools-1.16.1/test/split/split.tmp.unk.sam -f /build/samtools-1.16.1/test/split/split.tmp.%!.%. /build/samtools-1.16.1/test/split/split.sam .. ok test_split: /build/samtools-1.16.1/samtools split -@ 2 --output-fmt sam -u /build/samtools-1.16.1/test/split/split.tmp.unk.sam -f /build/samtools-1.16.1/test/split/split.tmp.%!.%. /build/samtools-1.16.1/test/split/split.sam .. ok test_large_positions: /build/samtools-1.16.1/samtools view -h --no-PG /tmp/8XFqOIQ9QB/longref.sam.gz .. ok test_large_positions: /build/samtools-1.16.1/samtools view -h --no-PG /tmp/8XFqOIQ9QB/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/samtools-1.16.1/samtools view -h --no-PG -L /build/samtools-1.16.1/test/large_pos/test.bed /tmp/8XFqOIQ9QB/longref.sam.gz .. ok test_large_positions: /build/samtools-1.16.1/samtools sort -O sam --no-PG -m 10M /build/samtools-1.16.1/test/large_pos/longref_name.sam .. ok test_large_positions: /build/samtools-1.16.1/samtools merge -O sam --no-PG - /build/samtools-1.16.1/test/large_pos/longref.sam /build/samtools-1.16.1/test/large_pos/longref2.sam .. ok test_large_positions: /build/samtools-1.16.1/samtools depth /build/samtools-1.16.1/test/large_pos/longref.sam .. ok test_large_positions: /build/samtools-1.16.1/samtools depth -b /build/samtools-1.16.1/test/large_pos/test.bed /build/samtools-1.16.1/test/large_pos/longref.sam .. ok test_large_positions: /build/samtools-1.16.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/8XFqOIQ9QB/longref.sam.gz .. ok test_large_positions: /build/samtools-1.16.1/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/samtools-1.16.1/samtools fixmate -O sam --no-PG - - | /build/samtools-1.16.1/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip --no-PG --output-fmt=sam -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-1.16.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconstats: /build/samtools-1.16.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/samtools-1.16.1/test/ampliconclip/ac_test.bed /build/samtools-1.16.1/test/ampliconclip/1_hard_clipped.expected.sam /build/samtools-1.16.1/test/ampliconclip/1_soft_clipped.expected.sam /build/samtools-1.16.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/samtools-1.16.1/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/samtools-1.16.1/samtools ampliconstats -@ 2 -c 0 /build/samtools-1.16.1/test/ampliconclip/multi_ref.bed /build/samtools-1.16.1/test/ampliconstats/mixed_clipped.sam | egrep -v 'Samtools version|Command line' .. ok Number of tests: total .. 881 passed .. 836 failed .. 0 expected failure .. 45 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 118 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 cd test/consensus && AWK="mawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 62 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/samtools-1.16.1' rm -fr -- /tmp/dh-xdg-rundir-6FcyVAKo make[1]: Leaving directory '/build/samtools-1.16.1' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/samtools.substvars debian/samtools-test.substvars rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/ debian/.debhelper/generated/samtools-test/ debian/samtools-test/ rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/samtools-1.16.1' dh_auto_install -- \ prefix=/usr install -m0755 -d /build/samtools-1.16.1/debian/tmp make -j4 install DESTDIR=/build/samtools-1.16.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-1.16.1' mkdir -p -m 755 /build/samtools-1.16.1/debian/tmp/usr/bin /build/samtools-1.16.1/debian/tmp/usr/bin /build/samtools-1.16.1/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-1.16.1/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /build/samtools-1.16.1/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /build/samtools-1.16.1/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/samtools-1.16.1/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/samtools-1.16.1' make clean make[2]: Entering directory '/build/samtools-1.16.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* cd test/reference && rm -f mpileup.*.fai rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview make[2]: Leaving directory '/build/samtools-1.16.1' make[1]: Leaving directory '/build/samtools-1.16.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/samtools-1.16.1' dh_install install -m0755 -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -m0755 -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -m0755 -d debian/samtools/usr/share/commonwl/ cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl// install -m0755 -d debian/samtools/usr/share/man/man1 cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ install -m0755 -d debian/samtools-test/usr/share/samtools cp --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/ # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done # Disable the executable bit on a dataset. if [ -d debian/samtools-test ] \ ; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \ ; fi make[1]: Leaving directory '/build/samtools-1.16.1' dh_installdocs install -m0755 -d debian/samtools/usr/share/doc/samtools install -m0755 -d debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools chmod -R u\+rw,go=rX debian/samtools/usr/share/doc install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test install -p -m0644 debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/samtools-1.16.1' dh_installchangelogs NEWS install -m0755 -d debian/samtools/usr/share/doc/samtools install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian install -p -m0644 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-1.16.1' dh_installexamples install -m0755 -d debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules execute_before_dh_installman make[1]: Entering directory '/build/samtools-1.16.1' # Fix whatis entries for subcommands; "samtools subcommand \- desc." # will confuse the lexer, but "samtools-subcommand \- desc." will work. sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \ debian/*/usr/share/man/man*/*.* # .EX expects a indentation width. sed -i 's/^.EX$/.EX 8/' debian/*/usr/share/man/man*/*.* make[1]: Leaving directory '/build/samtools-1.16.1' dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-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-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-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 dh_lintian install -m0755 -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl mv debian/samtools.substvars.new debian/samtools.substvars mv debian/samtools-test.substvars.new debian/samtools-test.substvars dh_link rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 dh_strip_nondeterminism Using 1664531159 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1664531159 as canonical time Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/samtools-test cd debian/samtools chmod a-x usr/share/doc/samtools-test/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/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/samtools-1.16.1' cd '/build/samtools-1.16.1' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/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/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 648619 new size 668919 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/0c9f8b18516ddadeb3fae409c686dd15349b85.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/0c9f8b18516ddadeb3fae409c686dd15349b85.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/b9/0c9f8b18516ddadeb3fae409c686dd15349b85.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/43f12265461daabff57ae0cf66c1ea1e4a55cb.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/43f12265461daabff57ae0cf66c1ea1e4a55cb.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/1a/43f12265461daabff57ae0cf66c1ea1e4a55cb.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/91e5484c9355d90d02970995a6164e308ed888.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/91e5484c9355d90d02970995a6164e308ed888.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/30/91e5484c9355d90d02970995a6164e308ed888.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.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/ce/b85fae99f451f6138c77d223a1567d2e57a3d7.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb/9b32252da618b6afd8e35576bc3483a19dee0e.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bb/9b32252da618b6afd8e35576bc3483a19dee0e.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/bb/9b32252da618b6afd8e35576bc3483a19dee0e.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.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/ed/83258f6ad143594b7b4d3baa2cc70919dbe539.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/35/b7d9e605225c7d471050eea7e9e90aa8dc9fb3.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools dh_installdeb install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN dh_gencontrol install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -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=1a43f12265461daabff57ae0cf66c1ea1e4a55cb 3091e5484c9355d90d02970995a6164e308ed888 35b7d9e605225c7d471050eea7e9e90aa8dc9fb3 b90c9f8b18516ddadeb3fae409c686dd15349b85 bb9b32252da618b6afd8e35576bc3483a19dee0e ceb85fae99f451f6138c77d223a1567d2e57a3d7 ed83258f6ad143594b7b4d3baa2cc70919dbe539" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/samtools-test/DEBIAN echo misc:Depends= >> debian/samtools-test.substvars echo misc:Pre-Depends= >> debian/samtools-test.substvars dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -Pdebian/samtools-test 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 ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.16.1-1_armhf.deb'. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools' in '../samtools_1.16.1-1_armhf.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.16.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.16.1-1_armhf.buildinfo dpkg-genchanges --build=binary -O../samtools_1.16.1-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.16.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/30201/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/30201/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/30201 and its subdirectories I: Current time: Wed May 24 00:25:41 +14 2023 I: pbuilder-time-stamp: 1684837541