Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/samtools/samtools_1.11-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/samtools-1.11-1q9qaiff1/samtools_1.11-1_amd64.buildinfo Get source package info: samtools=1.11-1 Source URL: http://snapshot.notset.fr/mr/package/samtools/1.11-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 autoconf-archive=20190106-2.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-7 bash-completion=1:2.11-2 binutils=2.35.1-1 binutils-common=2.35.1-1 binutils-x86-64-linux-gnu=2.35.1-1 bsdextrautils=2.36-3+b1 bsdutils=1:2.36-3+b1 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-12 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0-1 g++=4:10.2.0-1 g++-10=10.2.0-12 gcc=4:10.2.0-1 gcc-10=10.2.0-12 gcc-10-base=10.2.0-12 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-12 libatomic1=10.2.0-12 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.35.1-1 libblkid1=2.36-3+b1 libbrotli1=1.0.9-2 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-3 libc-dev-bin=2.31-3 libc6=2.31-3 libc6-dev=2.31-3 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-12 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-1 libctf0=2.35.1-1 libcurl3-gnutls=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.254 libdebhelper-perl=13.2.1 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.181-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-12 libgcc-s1=10.2.0-12 libgcrypt20=1.8.6-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.0-2 libgmp10=2:6.2.0+dfsg-6 libgnutls30=3.6.15-4 libgomp1=10.2.0-12 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libhogweed6=3.6-2 libhts-dev=1.11-1 libhts3=1.11-1 libicu67=67.1-4 libidn2-0=2.3.0-1 libio-pty-perl=1:1.12-1 libisl22=0.22.1-1 libitm1=10.2.0-12 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libldap-2.4-2=2.4.53+dfsg-1 liblsan0=10.2.0-12 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20200918-1 libncurses5-dev=6.2+20200918-1 libncurses6=6.2+20200918-1 libncursesw6=6.2+20200918-1 libnettle8=3.6-2 libnghttp2-14=1.41.0-3 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.30=5.30.3-4 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.1 libquadmath0=10.2.0-12 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.4-1 libselinux1=3.1-2 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1g-1 libstdc++-10-dev=10.2.0-12 libstdc++6=10.2.0-12 libsub-override-perl=0.09-2 libsystemd0=246.6-1 libtasn1-6=4.16.0-2 libtinfo6=6.2+20200918-1 libtool=2.4.6-14 libtsan0=10.2.0-12 libubsan1=10.2.0-12 libuchardet0=0.0.7-1 libudev1=246.6-1 libunistring2=0.9.10-4 libuuid1=2.36-3+b1 libxml2=2.9.10+dfsg-6 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.8.10-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 pkg-config=0.29.2-1 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tabix=1.11-1 tar=1.30+dfsg-7 util-linux=2.36-3+b1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201005T084025Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200930T204132Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d samtools=1.11-1 && mkdir -p /build/samtools-6MTViu && dpkg-source --no-check -x /*.dsc /build/samtools-6MTViu/samtools-1.11 && chown -R builduser:builduser /build/samtools-6MTViu" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/samtools-6MTViu/samtools-1.11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1601563342" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/samtools-6MTViu /tmp/samtools-1.11-1q9qaiff1 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200930T204132Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.5R0yZNlkEV as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.5R0yZNlkEV Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200930T204132Z unstable/main amd64 libfakeroot amd64 1.25.1-1 [46.8 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200930T204132Z unstable/main amd64 fakeroot amd64 1.25.1-1 [86.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1062 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4582 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.1-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.1-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.1-1_amd64.deb ... Unpacking fakeroot (1.25.1-1) ... Setting up libfakeroot:amd64 (1.25.1-1) ... Setting up fakeroot (1.25.1-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-3) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201005T084025Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200930T204132Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.5R0yZNlkEV Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201005T084025Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20200930T204132Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201005T084025Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201005T084025Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201005T084025Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201005T084025Z unstable/main amd64 Packages [11.4 MB] Fetched 34.1 MB in 29s (1184 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.5R0yZNlkEV I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d samtools=1.11-1 && mkdir -p /build/samtools-6MTViu && dpkg-source --no-check -x /*.dsc /build/samtools-6MTViu/samtools-1.11 && chown -R builduser:builduser /build/samtools-6MTViu"' exec /tmp/mmdebstrap.5R0yZNlkEV Reading package lists... NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools.git Please use: git clone https://salsa.debian.org/med-team/samtools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4539 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main samtools 1.11-1 (dsc) [2248 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main samtools 1.11-1 (tar) [4516 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main samtools 1.11-1 (diff) [20.1 kB] Fetched 4539 kB in 4s (1253 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'samtools_1.11-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting samtools in /build/samtools-6MTViu/samtools-1.11 dpkg-source: info: unpacking samtools_1.11.orig.tar.gz dpkg-source: info: unpacking samtools_1.11-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/samtools-6MTViu/samtools-1.11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1601563342" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.5R0yZNlkEV dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.11-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from samtools-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/samtools-6MTViu/samtools-1.11' rm -f config.mk touch config.mk dh_auto_clean -- install -d /build/samtools-6MTViu/samtools-1.11/debian/.debhelper/generated/_source/home make -j4 distclean make[2]: Entering directory '/build/samtools-6MTViu/samtools-1.11' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS rm -rf autom4te.cache make[2]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' make[1]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/samtools-6MTViu/samtools-1.11' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level autoconf configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system install -d /build/samtools-6MTViu/samtools-1.11/debian/.debhelper/generated/_source/home ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /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... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for 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-6MTViu/samtools-1.11' rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/samtools-6MTViu/samtools-1.11' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/samtools-6MTViu/samtools-1.11' gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.11"' > version.h gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -g -O2 -fdebug-prefix-map=/build/samtools-6MTViu/samtools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/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/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' make[1]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/samtools-6MTViu/samtools-1.11' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j4 test VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/samtools-6MTViu/samtools-1.11' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} /usr/bin/bgzip -c -b 65272 -s 5 /tmp/m3JQGmVFLF/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/m3JQGmVFLF/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/m3JQGmVFLF/bgzip.dat.gz .. ok /build/samtools-6MTViu/samtools-1.11/samtools faidx /tmp/m3JQGmVFLF/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/samtools-6MTViu/samtools-1.11/samtools faidx /tmp/m3JQGmVFLF/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/samtools-6MTViu/samtools-1.11/samtools faidx /tmp/m3JQGmVFLF/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/samtools-6MTViu/samtools-1.11/samtools faidx /tmp/m3JQGmVFLF/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/samtools-6MTViu/samtools-1.11/samtools faidx /tmp/m3JQGmVFLF/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/samtools-6MTViu/samtools-1.11/samtools faidx /tmp/m3JQGmVFLF/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/samtools-6MTViu/samtools-1.11/samtools faidx /tmp/m3JQGmVFLF/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/samtools-6MTViu/samtools-1.11/samtools faidx /tmp/m3JQGmVFLF/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/samtools-6MTViu/samtools-1.11/samtools fqidx /tmp/m3JQGmVFLF/fqidx.fq 3:11-13 .. ok .. ok /build/samtools-6MTViu/samtools-1.11/samtools fqidx /tmp/m3JQGmVFLF/fqidx.fq.gz 3:11-13 .. ok .. ok /build/samtools-6MTViu/samtools-1.11/samtools fqidx /tmp/m3JQGmVFLF/fqidx.fq 2:998-1003 .. ok .. ok /build/samtools-6MTViu/samtools-1.11/samtools fqidx /tmp/m3JQGmVFLF/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/samtools-6MTViu/samtools-1.11/samtools fqidx /tmp/m3JQGmVFLF/fqidx.fq 1:100-104 .. ok .. ok /build/samtools-6MTViu/samtools-1.11/samtools fqidx /tmp/m3JQGmVFLF/fqidx.fq.gz 1:100-104 .. ok .. ok /build/samtools-6MTViu/samtools-1.11/samtools fqidx /tmp/m3JQGmVFLF/fqidx.fq 1:99998-100007 .. ok .. ok /build/samtools-6MTViu/samtools-1.11/samtools fqidx /tmp/m3JQGmVFLF/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/samtools-6MTViu/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/samtools-6MTViu/samtools-1.11/test/dat/dict.fa .. ok test_dict: /build/samtools-6MTViu/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/m3JQGmVFLF/dict.fa.gz .. ok test_dict: cat /build/samtools-6MTViu/samtools-1.11/test/dat/dict.fa | /build/samtools-6MTViu/samtools-1.11/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/samtools-6MTViu/samtools-1.11/samtools dict -AH < /build/samtools-6MTViu/samtools-1.11/test/dat/dict.alias.fa .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools view /tmp/m3JQGmVFLF/large_chrom.bam ref2 .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools view /tmp/m3JQGmVFLF/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools index /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam && cat /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools view -X /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.bam /tmp/m3JQGmVFLF/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools merge -O sam - -X -cp -R ref2 /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/m3JQGmVFLF/test_input_1_b.bam.bai .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools index -c /build/samtools-6MTViu/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/m3JQGmVFLF/auto_indexed.csi && cat /tmp/m3JQGmVFLF/auto_indexed.csi .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools index /build/samtools-6MTViu/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/m3JQGmVFLF/auto_indexed.crai && cat /tmp/m3JQGmVFLF/auto_indexed.crai .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools index -c /build/samtools-6MTViu/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/m3JQGmVFLF/auto_indexed.csi && cat /tmp/m3JQGmVFLF/auto_indexed.csi .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools view -@ 2 /tmp/m3JQGmVFLF/large_chrom.bam ref2 .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools view -@ 2 /tmp/m3JQGmVFLF/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools index -@ 2 /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam && cat /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools view -@ 2 -X /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.bam /tmp/m3JQGmVFLF/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam.bai /tmp/m3JQGmVFLF/test_input_1_b.bam.bai .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools index -@ 2 -c /build/samtools-6MTViu/samtools-1.11/test/dat/auto_indexed.tmp.bam /tmp/m3JQGmVFLF/auto_indexed.csi && cat /tmp/m3JQGmVFLF/auto_indexed.csi .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools index -@ 2 /build/samtools-6MTViu/samtools-1.11/test/dat/auto_indexed.tmp.cram /tmp/m3JQGmVFLF/auto_indexed.crai && cat /tmp/m3JQGmVFLF/auto_indexed.crai .. ok test_index: /build/samtools-6MTViu/samtools-1.11/samtools index -@ 2 -c /build/samtools-6MTViu/samtools-1.11/test/dat/auto_indexed.tmp.sam /tmp/m3JQGmVFLF/auto_indexed.csi && cat /tmp/m3JQGmVFLF/auto_indexed.csi .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -b /tmp/m3JQGmVFLF/mpileup.bam.list -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -b /tmp/m3JQGmVFLF/mpileup.cram.list -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -b /tmp/m3JQGmVFLF/mpileup.bam.urllist -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -b /tmp/m3JQGmVFLF/mpileup.cram.urllist -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -uvDV -b /tmp/m3JQGmVFLF/mpileup.bam.list -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -uvDV -b /tmp/m3JQGmVFLF/mpileup.cram.list -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/m3JQGmVFLF/mpileup.cram.list -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/m3JQGmVFLF/mpileup.cram.list -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:1050-1060 /tmp/m3JQGmVFLF/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup -B --ff 0x14 -f /tmp/m3JQGmVFLF/mpileup.ref.fa.gz -r17:1050-1060 /tmp/m3JQGmVFLF/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/samtools-6MTViu/samtools-1.11/samtools mpileup /build/samtools-6MTViu/samtools-1.11/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, tview, view, depad .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/m3JQGmVFLF/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/m3JQGmVFLF/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/m3JQGmVFLF/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/m3JQGmVFLF/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/m3JQGmVFLF/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/m3JQGmVFLF/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/m3JQGmVFLF/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/m3JQGmVFLF/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/m3JQGmVFLF/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/m3JQGmVFLF/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/m3JQGmVFLF/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/m3JQGmVFLF/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/m3JQGmVFLF/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/m3JQGmVFLF/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/m3JQGmVFLF/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/m3JQGmVFLF/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/m3JQGmVFLF/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/m3JQGmVFLF/view.001.fogn (CRAM input).. ok 67: Filter -d BC:TGCA (SAM input) .. ok 68: Count -d BC:TGCA (SAM input) .. ok 69: Filter -d BC:TGCA (BAM input) .. ok 70: Count -d BC:TGCA (BAM input) .. ok 71: Filter -d BC:TGCA (CRAM input) .. ok 72: Count -d BC:TGCA (CRAM input) .. ok 73: Filter -D BC:/tmp/m3JQGmVFLF/view.001.fobc (SAM input) .. ok 74: Count -D BC:/tmp/m3JQGmVFLF/view.001.fobc (SAM input) .. ok 75: Filter -D BC:/tmp/m3JQGmVFLF/view.001.fobc (BAM input) .. ok 76: Count -D BC:/tmp/m3JQGmVFLF/view.001.fobc (BAM input) .. ok 77: Filter -D BC:/tmp/m3JQGmVFLF/view.001.fobc (CRAM input) .. ok 78: Count -D BC:/tmp/m3JQGmVFLF/view.001.fobc (CRAM input) .. ok 79: Filter -D BC:/tmp/m3JQGmVFLF/view.001.fobc -d BC:TGCA (SAM input).. ok 80: Count -D BC:/tmp/m3JQGmVFLF/view.001.fobc -d BC:TGCA (SAM input).. ok 81: Filter -D BC:/tmp/m3JQGmVFLF/view.001.fobc -d BC:TGCA (BAM input).. ok 82: Count -D BC:/tmp/m3JQGmVFLF/view.001.fobc -d BC:TGCA (BAM input).. ok 83: Filter -D BC:/tmp/m3JQGmVFLF/view.001.fobc -d BC:TGCA (CRAM input).. ok 84: Count -D BC:/tmp/m3JQGmVFLF/view.001.fobc -d BC:TGCA (CRAM input).. ok 85: Filter -d BC:TGCA -D BC:/tmp/m3JQGmVFLF/view.001.fobc (SAM input).. ok 86: Count -d BC:TGCA -D BC:/tmp/m3JQGmVFLF/view.001.fobc (SAM input).. ok 87: Filter -d BC:TGCA -D BC:/tmp/m3JQGmVFLF/view.001.fobc (BAM input).. ok 88: Count -d BC:TGCA -D BC:/tmp/m3JQGmVFLF/view.001.fobc (BAM input).. ok 89: Filter -d BC:TGCA -D BC:/tmp/m3JQGmVFLF/view.001.fobc (CRAM input).. ok 90: Count -d BC:TGCA -D BC:/tmp/m3JQGmVFLF/view.001.fobc (CRAM input).. ok 91: Filter -D RG:/tmp/m3JQGmVFLF/view.001.fogn (SAM input) .. ok 92: Count -D RG:/tmp/m3JQGmVFLF/view.001.fogn (SAM input) .. ok 93: Filter -D RG:/tmp/m3JQGmVFLF/view.001.fogn (BAM input) .. ok 94: Count -D RG:/tmp/m3JQGmVFLF/view.001.fogn (BAM input) .. ok 95: Filter -D RG:/tmp/m3JQGmVFLF/view.001.fogn (CRAM input) .. ok 96: Count -D RG:/tmp/m3JQGmVFLF/view.001.fogn (CRAM input) .. ok 97: Filter -d NE:TGCA (SAM input) .. ok 98: Count -d NE:TGCA (SAM input) .. ok 99: Filter -d NE:TGCA (BAM input) .. ok 100: Count -d NE:TGCA (BAM input) .. ok 101: Filter -d NE:TGCA (CRAM input) .. ok 102: Count -d NE:TGCA (CRAM input) .. ok 103: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test103.sam -h -d TGCA /tmp/m3JQGmVFLF/view.001.sam --no-PG .. expected failure 104: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -d TGCA /tmp/m3JQGmVFLF/view.001.sam --no-PG .. expected failure 105: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test105.sam -h -d TGCA /tmp/m3JQGmVFLF/view.test001.bam --no-PG .. expected failure 106: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -d TGCA /tmp/m3JQGmVFLF/view.test001.bam --no-PG .. expected failure 107: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test107.sam -h -d TGCA /tmp/m3JQGmVFLF/view.test006.cram --no-PG .. expected failure 108: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -d TGCA /tmp/m3JQGmVFLF/view.test006.cram --no-PG .. expected failure 109: Filter -D BClong:/tmp/m3JQGmVFLF/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/m3JQGmVFLF/view.001.fobc": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test109.sam -h -D BClong:/tmp/m3JQGmVFLF/view.001.fobc /tmp/m3JQGmVFLF/view.001.sam --no-PG .. expected failure 110: Count -D BClong:/tmp/m3JQGmVFLF/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/m3JQGmVFLF/view.001.fobc": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -D BClong:/tmp/m3JQGmVFLF/view.001.fobc /tmp/m3JQGmVFLF/view.001.sam --no-PG .. expected failure 111: Filter -D BClong:/tmp/m3JQGmVFLF/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/m3JQGmVFLF/view.001.fobc": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test111.sam -h -D BClong:/tmp/m3JQGmVFLF/view.001.fobc /tmp/m3JQGmVFLF/view.test001.bam --no-PG .. expected failure 112: Count -D BClong:/tmp/m3JQGmVFLF/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/m3JQGmVFLF/view.001.fobc": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -D BClong:/tmp/m3JQGmVFLF/view.001.fobc /tmp/m3JQGmVFLF/view.test001.bam --no-PG .. expected failure 113: Filter -D BClong:/tmp/m3JQGmVFLF/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/m3JQGmVFLF/view.001.fobc": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test113.sam -h -D BClong:/tmp/m3JQGmVFLF/view.001.fobc /tmp/m3JQGmVFLF/view.test006.cram --no-PG .. expected failure 114: Count -D BClong:/tmp/m3JQGmVFLF/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/m3JQGmVFLF/view.001.fobc": No such file or directory Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -D BClong:/tmp/m3JQGmVFLF/view.001.fobc /tmp/m3JQGmVFLF/view.test006.cram --no-PG .. expected failure 115: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/m3JQGmVFLF/view.001.sam --no-PG .. expected failure 116: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/m3JQGmVFLF/view.001.sam --no-PG .. expected failure 117: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/m3JQGmVFLF/view.test001.bam --no-PG .. expected failure 118: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/m3JQGmVFLF/view.test001.bam --no-PG .. expected failure 119: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -o /tmp/m3JQGmVFLF/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/m3JQGmVFLF/view.test006.cram --no-PG .. expected failure 120: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /build/samtools-6MTViu/samtools-1.11/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/m3JQGmVFLF/view.test006.cram --no-PG .. expected failure 121: Filter -l Library 2 (SAM input) .. ok 122: Count -l Library 2 (SAM input) .. ok 123: Filter -l Library 2 (BAM input) .. ok 124: Count -l Library 2 (BAM input) .. ok 125: Filter -l Library 2 (CRAM input) .. ok 126: Count -l Library 2 (CRAM input) .. ok 127: Filter -l Library 3 (SAM input) .. ok 128: Count -l Library 3 (SAM input) .. ok 129: Filter -l Library 3 (BAM input) .. ok 130: Count -l Library 3 (BAM input) .. ok 131: Filter -l Library 3 (CRAM input) .. ok 132: Count -l Library 3 (CRAM input) .. ok 133: Filter -q 50 (SAM input) .. ok 134: Count -q 50 (SAM input) .. ok 135: Filter -q 50 (BAM input) .. ok 136: Count -q 50 (BAM input) .. ok 137: Filter -q 50 (CRAM input) .. ok 138: Count -q 50 (CRAM input) .. ok 139: Filter -q 99 (SAM input) .. ok 140: Count -q 99 (SAM input) .. ok 141: Filter -q 99 (BAM input) .. ok 142: Count -q 99 (BAM input) .. ok 143: Filter -q 99 (CRAM input) .. ok 144: Count -q 99 (CRAM input) .. ok 145: Filter -q 100 (SAM input) .. ok 146: Count -q 100 (SAM input) .. ok 147: Filter -q 100 (BAM input) .. ok 148: Count -q 100 (BAM input) .. ok 149: Filter -q 100 (CRAM input) .. ok 150: Count -q 100 (CRAM input) .. ok 151: Filter -x fa (SAM input) .. ok 152: Count -x fa (SAM input) .. ok 153: Filter -x fa (BAM input) .. ok 154: Count -x fa (BAM input) .. ok 155: Filter -x fa (CRAM input) .. ok 156: Count -x fa (CRAM input) .. ok 157: Filter -x fa -x ha (SAM input) .. ok 158: Count -x fa -x ha (SAM input) .. ok 159: Filter -x fa -x ha (BAM input) .. ok 160: Count -x fa -x ha (BAM input) .. ok 161: Filter -x fa -x ha (CRAM input) .. ok 162: Count -x fa -x ha (CRAM input) .. ok 163: Filter -x fa -r grp2 (SAM input) .. ok 164: Count -x fa -r grp2 (SAM input) .. ok 165: Filter -x fa -r grp2 (BAM input) .. ok 166: Count -x fa -r grp2 (BAM input) .. ok 167: Filter -x fa -r grp2 (CRAM input) .. ok 168: Count -x fa -r grp2 (CRAM input) .. ok 169: Filter -x RG -r grp2 (SAM input) .. ok 170: Count -x RG -r grp2 (SAM input) .. ok 171: Filter -x RG -r grp2 (BAM input) .. ok 172: Count -x RG -r grp2 (BAM input) .. ok 173: Filter -x RG -r grp2 (CRAM input) .. ok 174: Count -x RG -r grp2 (CRAM input) .. ok 175: Filter -m 10 (SAM input) .. ok 176: Count -m 10 (SAM input) .. ok 177: Filter -m 10 (BAM input) .. ok 178: Count -m 10 (BAM input) .. ok 179: Filter -m 10 (CRAM input) .. ok 180: Count -m 10 (CRAM input) .. ok 181: Filter -m 11 (SAM input) .. ok 182: Count -m 11 (SAM input) .. ok 183: Filter -m 11 (BAM input) .. ok 184: Count -m 11 (BAM input) .. ok 185: Filter -m 11 (CRAM input) .. ok 186: Count -m 11 (CRAM input) .. ok 187: Filter -m 15 (SAM input) .. ok 188: Count -m 15 (SAM input) .. ok 189: Filter -m 15 (BAM input) .. ok 190: Count -m 15 (BAM input) .. ok 191: Filter -m 15 (CRAM input) .. ok 192: Count -m 15 (CRAM input) .. ok 193: Filter -m 16 (SAM input) .. ok 194: Count -m 16 (SAM input) .. ok 195: Filter -m 16 (BAM input) .. ok 196: Count -m 16 (BAM input) .. ok 197: Filter -m 16 (CRAM input) .. ok 198: Count -m 16 (CRAM input) .. ok 199: 1bp reads file SAM -> BAM -> SAM .. ok 200: 1bp reads file SAM -> CRAM -> SAM .. ok 200: Region Z (BAM input) .. ok 201: Count Z (BAM input) .. ok 202: Region Z (CRAM input) .. ok 203: Count Z (CRAM input) .. ok 204: Region Z:30 (BAM input) .. ok 205: Count Z:30 (BAM input) .. ok 206: Region Z:30 (CRAM input) .. ok 207: Count Z:30 (CRAM input) .. ok 208: Region Z:20-40 (BAM input) .. ok 209: Count Z:20-40 (BAM input) .. ok 210: Region Z:20-40 (CRAM input) .. ok 211: Count Z:20-40 (CRAM input) .. ok 212: Region ref1 (BAM input) .. ok 213: Count ref1 (BAM input) .. ok 214: Region ref1 (CRAM input) .. ok 215: Count ref1 (CRAM input) .. ok 216: Region ref1:15 (BAM input) .. ok 217: Count ref1:15 (BAM input) .. ok 218: Region ref1:15 (CRAM input) .. ok 219: Count ref1:15 (CRAM input) .. ok 220: Region ref1:15-45 (BAM input) .. ok 221: Count ref1:15-45 (BAM input) .. ok 222: Region ref1:15-45 (CRAM input) .. ok 223: Count ref1:15-45 (CRAM input) .. ok 224: Region ref1:15-45 ref2 (BAM input) .. ok 225: Count ref1:15-45 ref2 (BAM input) .. ok 226: Region ref1:15-45 ref2 (CRAM input) .. ok 227: Count ref1:15-45 ref2 (CRAM input) .. ok 228: Region ref1:15-45 ref2:16 (BAM input) .. ok 229: Count ref1:15-45 ref2:16 (BAM input) .. ok 230: Region ref1:15-45 ref2:16 (CRAM input) .. ok 231: Count ref1:15-45 ref2:16 (CRAM input) .. ok 232: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 233: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 234: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 235: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 236: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 237: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 238: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 239: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 240: Region -f 128 ref1 (BAM input) .. ok 241: Count -f 128 ref1 (BAM input) .. ok 242: Region -f 128 ref1 (CRAM input) .. ok 243: Count -f 128 ref1 (CRAM input) .. ok 244: Region -q 50 ref1:15-45 (BAM input) .. ok 245: Count -q 50 ref1:15-45 (BAM input) .. ok 246: Region -q 50 ref1:15-45 (CRAM input) .. ok 247: Count -q 50 ref1:15-45 (CRAM input) .. ok 248: Region -r grp2 ref1:15-45 (BAM input) .. ok 249: Count -r grp2 ref1:15-45 (BAM input) .. ok 250: Region -r grp2 ref1:15-45 (CRAM input) .. ok 251: Count -r grp2 ref1:15-45 (CRAM input) .. ok 252: Region * (BAM input) .. ok 253: Count * (BAM input) .. ok 254: Region * (CRAM input) .. ok 255: Count * (CRAM input) .. ok 256: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed (BAM input).. ok 257: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed (BAM input).. ok 258: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed (CRAM input).. ok 259: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed (CRAM input).. ok 260: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.02.bed (BAM input).. ok 261: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.02.bed (BAM input).. ok 262: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.02.bed (CRAM input).. ok 263: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.02.bed (CRAM input).. ok 264: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed (BAM input).. ok 265: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed (BAM input).. ok 266: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed (CRAM input).. ok 267: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed (CRAM input).. ok 268: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.02.bed (BAM input).. ok 269: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.02.bed (BAM input).. ok 270: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.02.bed (CRAM input).. ok 271: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.02.bed (CRAM input).. ok 272: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z (BAM input).. ok 273: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z (BAM input).. ok 274: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z (CRAM input).. ok 275: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z (CRAM input).. ok 276: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:30 (BAM input).. ok 277: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:30 (BAM input).. ok 278: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 279: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 280: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 281: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 282: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 283: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 284: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 285: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 286: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 287: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 288: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 289: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 290: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 291: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 292: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref2 (BAM input).. ok 293: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref2 (BAM input).. ok 294: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref2 (CRAM input).. ok 295: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref2 (CRAM input).. ok 296: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 297: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 298: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 299: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 300: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 301: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 302: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 303: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 304: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -f 128 (BAM input).. ok 305: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -f 128 (BAM input).. ok 306: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 307: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 308: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -q 5 (BAM input).. ok 309: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -q 5 (BAM input).. ok 310: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 311: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 312: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 313: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 314: Region -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 315: Count -L /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 316: Make BAM with no M5/UR tags .. ok 317: Add @SQ with -t (SAM -> SAM) .. ok 318: Add @SQ with -T (SAM -> SAM) .. ok 319: Add @SQ with -t (BAM -> SAM) .. ok 320: Add @SQ with -T (BAM -> SAM) .. ok 321: Add @SQ with -t (SAM -> BAM) .. ok 322: Add @SQ with -T (SAM -> BAM) .. ok 323: Add @SQ with -t (BAM -> BAM) .. ok 324: Add @SQ with -T (BAM -> BAM) .. ok 325: Add @SQ with -t (SAM -> CRAM) .. ok 326: Add @SQ with -T (SAM -> CRAM) .. ok 327: Add @SQ with -t (BAM -> CRAM) .. ok 328: Add @SQ with -T (BAM -> CRAM) .. ok 329: Make CRAM with no UR field .. ok 330: Decoding CRAM with no UR field via -T .. ok 331: CIGAR B-operator removal .. ok 332: Big SAM -> BAM .. ok 333: Big SAM -> BAM (2 threads) .. ok 334: Big SAM -> BAM (4 threads) .. ok 335: Big SAM -> CRAM .. ok 336: Big SAM -> CRAM (2 threads) .. ok 337: Big SAM -> CRAM (4 threads) .. ok 338: Subsample 0.2 (SAM input) ............ ok 339: Subsample 0.5 (SAM input) ............ ok 340: Subsample 0.8 (SAM input) ............ ok 341: Subsample 0.2 (BAM input) ............ ok 342: Subsample 0.5 (BAM input) ............ ok 343: Subsample 0.8 (BAM input) ............ ok 344: Subsample 0.2 (CRAM input) ............ ok 345: Subsample 0.5 (CRAM input) ............ ok 346: Subsample 0.8 (CRAM input) ............ ok 347: SAM add PG .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-6MTViu/samtools-1.11/test/bc.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-6MTViu/samtools-1.11/test/bc.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-6MTViu/samtools-1.11/test/bc.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-6MTViu/samtools-1.11/test/bc_split.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -N -t -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -N -t -T MD,ia -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-6MTViu/samtools-1.11/test/i.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/samtools-6MTViu/samtools-1.11/test/i.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -i --index-format 'i*i*' -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -N -1 /build/samtools-6MTViu/samtools-1.11/test/o.fq -2 /build/samtools-6MTViu/samtools-1.11/test/o.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -N -o /build/samtools-6MTViu/samtools-1.11/test/o.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -N -s /tmp/m3JQGmVFLF/bam2fq.discard.s.fq -0 /tmp/m3JQGmVFLF/bam2fq.discard.0.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.013.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-6MTViu/samtools-1.11/test/bc.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-6MTViu/samtools-1.11/test/bc.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-6MTViu/samtools-1.11/test/bc.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-6MTViu/samtools-1.11/test/bc_split.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -N -t -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -N -t -T MD,ia -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-6MTViu/samtools-1.11/test/i.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/samtools-6MTViu/samtools-1.11/test/i.fq -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/samtools-6MTViu/samtools-1.11/test/s.fq -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -1 /build/samtools-6MTViu/samtools-1.11/test/1.fq -2 /build/samtools-6MTViu/samtools-1.11/test/2.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -N -1 /build/samtools-6MTViu/samtools-1.11/test/o.fq -2 /build/samtools-6MTViu/samtools-1.11/test/o.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -N -o /build/samtools-6MTViu/samtools-1.11/test/o.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -N -s /tmp/m3JQGmVFLF/bam2fq.discard.s.fq -0 /tmp/m3JQGmVFLF/bam2fq.discard.0.fq /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-6MTViu/samtools-1.11/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/samtools-6MTViu/samtools-1.11/test/dat/bam2fq.013.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa -i 0 /build/samtools-6MTViu/samtools-1.11/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -S RG -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -S RG -r /build/samtools-6MTViu/samtools-1.11/test/stat/test.fa /build/samtools-6MTViu/samtools-1.11/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -t /build/samtools-6MTViu/samtools-1.11/test/stat/11.stats.targets /build/samtools-6MTViu/samtools-1.11/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -g 4 -t /build/samtools-6MTViu/samtools-1.11/test/stat/11.stats.targets /build/samtools-6MTViu/samtools-1.11/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats -g 4 /build/samtools-6MTViu/samtools-1.11/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/12_overlaps.bam -t /build/samtools-6MTViu/samtools-1.11/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/12_overlaps.bam -p -t /build/samtools-6MTViu/samtools-1.11/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/12_overlaps.bam -t /build/samtools-6MTViu/samtools-1.11/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/12_overlaps.bam -p -t /build/samtools-6MTViu/samtools-1.11/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/samtools-6MTViu/samtools-1.11/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/samtools-6MTViu/samtools-1.11/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-6MTViu/samtools-1.11/samtools stats /build/samtools-6MTViu/samtools-1.11/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/samtools-6MTViu/samtools-1.11/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -s 1 -O sam -b /tmp/E9QnECIvXr - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -r -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -cp -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a_regex.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/m3JQGmVFLF/merge.tag.1.bam /tmp/m3JQGmVFLF/merge.tag.2.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/m3JQGmVFLF/merge.tag.3.bam /tmp/m3JQGmVFLF/merge.tag.4.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge --no-PG -O SAM - /build/samtools-6MTViu/samtools-1.11/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge --no-PG -O SAM -L /build/samtools-6MTViu/samtools-1.11/test/merge/merge.bed - /tmp/m3JQGmVFLF/merge.bed.1.bam /tmp/m3JQGmVFLF/merge.bed.2.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.bam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -s 1 -O sam -b /tmp/aETX9ffTxc - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -r -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -cp -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -s 1 -O sam - /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a_regex.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/m3JQGmVFLF/merge.tag.1.bam /tmp/m3JQGmVFLF/merge.tag.2.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/m3JQGmVFLF/merge.tag.3.bam /tmp/m3JQGmVFLF/merge.tag.4.bam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 --no-PG -O SAM - /build/samtools-6MTViu/samtools-1.11/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-6MTViu/samtools-1.11/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-6MTViu/samtools-1.11/test/merge/merge.bed - /tmp/m3JQGmVFLF/merge.bed.1.bam /tmp/m3JQGmVFLF/merge.bed.2.bam .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /tmp/m3JQGmVFLF/sortout .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -f /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /tmp/m3JQGmVFLF/sortout.bam .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -o /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /tmp/m3JQGmVFLF/sorttmp .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -n -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -t RG -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -n -t RG -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -t AS -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -t FI -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /tmp/m3JQGmVFLF/sortout .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 -f /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /tmp/m3JQGmVFLF/sortout.bam .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 -o /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam /tmp/m3JQGmVFLF/sorttmp .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 -n -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 -t RG -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 -n -t RG -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 -t AS -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-6MTViu/samtools-1.11/samtools sort -@ 2 -t FI -m 10M /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate --output-fmt=sam -O /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate -o /build/samtools-6MTViu/samtools-1.11/test/collate/collate1.tmp.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate -o /build/samtools-6MTViu/samtools-1.11/test/collate/collate2.tmp.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam /build/samtools-6MTViu/samtools-1.11/test/collate/collate2.tmp .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate --output-fmt=sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam /build/samtools-6MTViu/samtools-1.11/test/collate/collate3.tmp .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate --output-fmt=sam -f /build/samtools-6MTViu/samtools-1.11/test/collate/fast_collate.sam -o /build/samtools-6MTViu/samtools-1.11/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate --output-fmt=sam -f -r 4 /build/samtools-6MTViu/samtools-1.11/test/collate/fast_collate.sam -o /build/samtools-6MTViu/samtools-1.11/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate -@ 2 --output-fmt=sam -O /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate -@ 2 -o /build/samtools-6MTViu/samtools-1.11/test/collate/collate1.tmp.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate -@ 2 -o /build/samtools-6MTViu/samtools-1.11/test/collate/collate2.tmp.sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam /build/samtools-6MTViu/samtools-1.11/test/collate/collate2.tmp .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate -@ 2 --output-fmt=sam /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_d.sam /build/samtools-6MTViu/samtools-1.11/test/collate/collate3.tmp .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate -@ 2 --output-fmt=sam -f /build/samtools-6MTViu/samtools-1.11/test/collate/fast_collate.sam -o /build/samtools-6MTViu/samtools-1.11/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-6MTViu/samtools-1.11/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/samtools-6MTViu/samtools-1.11/test/collate/fast_collate.sam -o /build/samtools-6MTViu/samtools-1.11/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -cO sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -cO sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -@ 2 -cO sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -@ 2 -cO sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-6MTViu/samtools-1.11/samtools fixmate -@ 2 -O sam /build/samtools-6MTViu/samtools-1.11/test/fixmate/8_isize_overflow_64bit.sam - .. ok /build/samtools-6MTViu/samtools-1.11/samtools calmd -uAr /build/samtools-6MTViu/samtools-1.11/test/dat/mpileup.1.sam /build/samtools-6MTViu/samtools-1.11/test/dat/mpileup.ref.fa .. ok /build/samtools-6MTViu/samtools-1.11/samtools calmd -@ 2 -uAr /build/samtools-6MTViu/samtools-1.11/test/dat/mpileup.1.sam /build/samtools-6MTViu/samtools-1.11/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/samtools-6MTViu/samtools-1.11/samtools idxstats /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/samtools-6MTViu/samtools-1.11/samtools idxstats /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/samtools-6MTViu/samtools-1.11/samtools idxstats /build/samtools-6MTViu/samtools-1.11/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck /build/samtools-6MTViu/samtools-1.11/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck -v /build/samtools-6MTViu/samtools-1.11/test/quickcheck/1.quickcheck.badeof.bam /build/samtools-6MTViu/samtools-1.11/test/quickcheck/2.quickcheck.badheader.bam /build/samtools-6MTViu/samtools-1.11/test/quickcheck/3.quickcheck.ok.bam /build/samtools-6MTViu/samtools-1.11/test/quickcheck/4.quickcheck.ok.bam /build/samtools-6MTViu/samtools-1.11/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/samtools-6MTViu/samtools-1.11/test/quickcheck/6.quickcheck.cram21.ok.cram /build/samtools-6MTViu/samtools-1.11/test/quickcheck/7.quickcheck.cram30.ok.cram /build/samtools-6MTViu/samtools-1.11/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/samtools-6MTViu/samtools-1.11/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/samtools-6MTViu/samtools-1.11/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/samtools-6MTViu/samtools-1.11/samtools quickcheck -uv /build/samtools-6MTViu/samtools-1.11/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/samtools-6MTViu/samtools-1.11/samtools reheader /build/samtools-6MTViu/samtools-1.11/test/reheader/hdr.sam /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.bam | /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-6MTViu/samtools-1.11/samtools reheader /build/samtools-6MTViu/samtools-1.11/test/reheader/hdr.sam /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.v21.cram | /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-6MTViu/samtools-1.11/samtools reheader /build/samtools-6MTViu/samtools-1.11/test/reheader/hdr.sam /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.v30.cram | /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-6MTViu/samtools-1.11/samtools reheader --in-place /build/samtools-6MTViu/samtools-1.11/test/reheader/hdr.sam /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.v21.cram && /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-6MTViu/samtools-1.11/samtools reheader --in-place /build/samtools-6MTViu/samtools-1.11/test/reheader/hdr.sam /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.v30.cram && /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-6MTViu/samtools-1.11/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.bam | /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-6MTViu/samtools-1.11/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/samtools-6MTViu/samtools-1.11/test/dat/view.001.tmp.v30.cram | /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -O sam -m overwrite_all /build/samtools-6MTViu/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -O sam -m orphan_only /build/samtools-6MTViu/samtools-1.11/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -O sam -R '1#9' /build/samtools-6MTViu/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-6MTViu/samtools-1.11/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/samtools-6MTViu/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-6MTViu/samtools-1.11/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/samtools-6MTViu/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/samtools-6MTViu/samtools-1.11/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/samtools-6MTViu/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-6MTViu/samtools-1.11/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/samtools-6MTViu/samtools-1.11/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-6MTViu/samtools-1.11/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-6MTViu/samtools-1.11/test/addrprg/4_fixup_norg.sam .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -O sam -r --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -S -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -O sam -r --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -S -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/samtools-6MTViu/samtools-1.11/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/samtools-6MTViu/samtools-1.11/test/markdup/9_optical_dup_qcfail.sam - .. ok test_bedcov: /build/samtools-6MTViu/samtools-1.11/samtools bedcov /build/samtools-6MTViu/samtools-1.11/test/bedcov/bedcov.bed /build/samtools-6MTViu/samtools-1.11/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-6MTViu/samtools-1.11/samtools bedcov -j /build/samtools-6MTViu/samtools-1.11/test/bedcov/bedcov.bed /build/samtools-6MTViu/samtools-1.11/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-6MTViu/samtools-1.11/samtools bedcov -g512 -G2048 /build/samtools-6MTViu/samtools-1.11/test/bedcov/bedcov_gG.bed /build/samtools-6MTViu/samtools-1.11/test/bedcov/bedcov.bam .. ok test_split: /build/samtools-6MTViu/samtools-1.11/samtools split --output-fmt sam -u /build/samtools-6MTViu/samtools-1.11/test/split/split.tmp.unk.sam -f /build/samtools-6MTViu/samtools-1.11/test/split/split.tmp.%!.%. /build/samtools-6MTViu/samtools-1.11/test/split/split.sam .. ok test_split: /build/samtools-6MTViu/samtools-1.11/samtools split -@ 2 --output-fmt sam -u /build/samtools-6MTViu/samtools-1.11/test/split/split.tmp.unk.sam -f /build/samtools-6MTViu/samtools-1.11/test/split/split.tmp.%!.%. /build/samtools-6MTViu/samtools-1.11/test/split/split.sam .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG /tmp/m3JQGmVFLF/longref.sam.gz .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG /tmp/m3JQGmVFLF/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools view -h --no-PG -L /build/samtools-6MTViu/samtools-1.11/test/large_pos/test.bed /tmp/m3JQGmVFLF/longref.sam.gz .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools sort -O sam --no-PG -m 10M /build/samtools-6MTViu/samtools-1.11/test/large_pos/longref_name.sam .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools merge -O sam --no-PG - /build/samtools-6MTViu/samtools-1.11/test/large_pos/longref.sam /build/samtools-6MTViu/samtools-1.11/test/large_pos/longref2.sam .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools depth /build/samtools-6MTViu/samtools-1.11/test/large_pos/longref.sam .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools depth -b /build/samtools-6MTViu/samtools-1.11/test/large_pos/test.bed /build/samtools-6MTViu/samtools-1.11/test/large_pos/longref.sam .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/m3JQGmVFLF/longref.sam.gz .. ok test_large_positions: /build/samtools-6MTViu/samtools-1.11/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/samtools-6MTViu/samtools-1.11/samtools fixmate -O sam --no-PG - - | /build/samtools-6MTViu/samtools-1.11/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip --no-PG --output-fmt=sam -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-6MTViu/samtools-1.11/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconstats: /build/samtools-6MTViu/samtools-1.11/samtools ampliconstats -@ 2 -t 50 -d 1,20,100 /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/ac_test.bed /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_hard_clipped.expected.sam /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_soft_clipped.expected.sam /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/samtools-6MTViu/samtools-1.11/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' | tee /tmp/out.txt .. ok Number of tests: total .. 700 passed .. 654 failed .. 0 expected failure .. 46 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 163 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ./regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 47 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' rm -fr -- /tmp/dh-xdg-rundir-cEbPzNBb make[1]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a rm -f -- debian/samtools.substvars rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/ rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/samtools-6MTViu/samtools-1.11' dh_auto_install -- \ prefix=/usr install -d /build/samtools-6MTViu/samtools-1.11/debian/tmp make -j4 install DESTDIR=/build/samtools-6MTViu/samtools-1.11/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-6MTViu/samtools-1.11' mkdir -p -m 755 /build/samtools-6MTViu/samtools-1.11/debian/tmp/usr/bin /build/samtools-6MTViu/samtools-1.11/debian/tmp/usr/bin /build/samtools-6MTViu/samtools-1.11/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-6MTViu/samtools-1.11/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /build/samtools-6MTViu/samtools-1.11/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl misc/plot-ampliconstats /build/samtools-6MTViu/samtools-1.11/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/samtools-6MTViu/samtools-1.11/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' make clean make[2]: Entering directory '/build/samtools-6MTViu/samtools-1.11' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview make[2]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' make[1]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' rm -f debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/samtools-6MTViu/samtools-1.11' dh_install install -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -d debian/samtools/usr/share/commonwl/ cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl// cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ install -d debian/.debhelper/generated/samtools install -d debian/.debhelper/generated/samtools-test # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' dh_installdocs -a install -d debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools chmod -R u\+rw,go=rX debian/samtools/usr/share/doc install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright rm -f debian/samtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/samtools-6MTViu/samtools-1.11' dh_installchangelogs NEWS install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/build/samtools-6MTViu/samtools-1.11' dh_installexamples -a install -d debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples dh_installman -a rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 dh_lintian -a install -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl -a (grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > debian/samtools.substvars.new mv debian/samtools.substvars.new debian/samtools.substvars dh_link -a 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 -a Using 1601563342 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip dh_compress -a cd debian/samtools chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/samtools-6MTViu/samtools-1.11' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms -a find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -a dh_dwz -a -a install -d debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 661274 new size 684381 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug dh_strip -a -a install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0d/53510caa0ce0353b6f554f37c48183e17761a0.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0d/53510caa0ce0353b6f554f37c48183e17761a0.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/0d/53510caa0ce0353b6f554f37c48183e17761a0.debug debian/samtools/usr/bin/samtools install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9/03f2af31c20a62a99aa11dd145a5e0de871d0f.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d9/03f2af31c20a62a99aa11dd145a5e0de871d0f.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/d9/03f2af31c20a62a99aa11dd145a5e0de871d0f.debug debian/samtools/usr/bin/wgsim install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02/fbfa3afca4d2b4715fa22e11727e8758a1223d.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02/fbfa3afca4d2b4715fa22e11727e8758a1223d.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/02/fbfa3afca4d2b4715fa22e11727e8758a1223d.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43/3a3f7f4f242c122f7562b1d174fd0b2b6a11c9.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43/3a3f7f4f242c122f7562b1d174fd0b2b6a11c9.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/43/3a3f7f4f242c122f7562b1d174fd0b2b6a11c9.debug debian/samtools/usr/bin/md5fa install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/7d06a66a1745cedf8eb5dbdfcadb4e700c0e54.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/7d06a66a1745cedf8eb5dbdfcadb4e700c0e54.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/80/7d06a66a1745cedf8eb5dbdfcadb4e700c0e54.debug debian/samtools/usr/bin/ace2sam install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f1 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f1/cb8f84930ec768ae7e8c7e7f4a933f5179e146.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f1/cb8f84930ec768ae7e8c7e7f4a933f5179e146.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/f1/cb8f84930ec768ae7e8c7e7f4a933f5179e146.debug debian/samtools/usr/bin/maq2sam-long install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/e46ded8645e45d4656734522d589aa02309659.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/e46ded8645e45d4656734522d589aa02309659.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/bd/e46ded8645e45d4656734522d589aa02309659.debug debian/samtools/usr/bin/maq2sam-short install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym dh_makeshlibs -a -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a -a install -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=02fbfa3afca4d2b4715fa22e11727e8758a1223d 0d53510caa0ce0353b6f554f37c48183e17761a0 433a3f7f4f242c122f7562b1d174fd0b2b6a11c9 807d06a66a1745cedf8eb5dbdfcadb4e700c0e54 bde46ded8645e45d4656734522d589aa02309659 d903f2af31c20a62a99aa11dd145a5e0de871d0f f1cb8f84930ec768ae7e8c7e7f4a933f5179e146" -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums -a cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb: building package 'samtools' in '../samtools_1.11-1_amd64.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.11-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../samtools_1.11-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/samtools-6MTViu /tmp/samtools-1.11-1q9qaiff1 I: cleaning package lists and apt cache... W: deleting files in /tmp: out.txt I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.5R0yZNlkEV... I: success in 532.1626 seconds md5: samtools-dbgsym_1.11-1_amd64.deb: OK md5: samtools_1.11-1_amd64.deb: OK sha1: samtools-dbgsym_1.11-1_amd64.deb: OK sha1: samtools_1.11-1_amd64.deb: OK sha256: samtools-dbgsym_1.11-1_amd64.deb: OK sha256: samtools_1.11-1_amd64.deb: OK Checksums: OK