0s autopkgtest [18:59:42]: starting date and time: 2025-03-15 18:59:42+0000 0s autopkgtest [18:59:42]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:59:42]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9ng3kfdw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade samtools --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-20.secgroup --name adt-plucky-s390x-samtools-20250315-185942-juju-7f2275-prod-proposed-migration-environment-15-3a1d6f84-e60a-4e2a-9742-5395949624cb --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 90s autopkgtest [19:01:12]: testbed dpkg architecture: s390x 90s autopkgtest [19:01:12]: testbed apt version: 2.9.33 90s autopkgtest [19:01:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 90s autopkgtest [19:01:12]: testbed release detected to be: None 91s autopkgtest [19:01:13]: updating testbed package index (apt update) 91s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 92s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 92s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 92s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 92s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 92s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 92s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 92s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 93s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 93s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 93s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 93s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 93s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 93s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 93s Fetched 1073 kB in 2s (680 kB/s) 94s Reading package lists... 94s + lsb_release --codename --short 94s + RELEASE=plucky 94s + cat 94s + [ plucky != trusty ] 94s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 95s Calculating upgrade... 95s The following packages were automatically installed and are no longer required: 95s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 95s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 95s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 95s linux-tools-6.11.0-8-generic 95s Use 'sudo apt autoremove' to remove them. 95s The following packages will be upgraded: 95s pinentry-curses python3-jinja2 strace 95s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 652 kB of archives. 95s After this operation, 27.6 kB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 95s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 96s Fetched 652 kB in 1s (737 kB/s) 96s (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 ... 81428 files and directories currently installed.) 96s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 96s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 96s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 96s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 96s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 96s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 96s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 96s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 97s Setting up strace (6.13+ds-1ubuntu1) ... 97s Processing triggers for man-db (2.13.0-1) ... 97s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 97s + /usr/lib/apt/apt-helper analyze-pattern ?true 97s + uname -r 97s + sed s/\./\\./g 97s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 97s + apt list ?obsolete 97s + tail -n+2 97s + cut -d/ -f1 97s + grep -v ^linux-.*6\.14\.0-10-generic.* 97s + obsolete_pkgs=linux-headers-6.11.0-8-generic 97s linux-headers-6.11.0-8 97s linux-modules-6.11.0-8-generic 97s linux-tools-6.11.0-8-generic 97s linux-tools-6.11.0-8 97s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s Solving dependencies... 98s The following packages will be REMOVED: 98s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 98s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 98s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 98s linux-tools-6.11.0-8-generic* 98s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 98s After this operation, 167 MB disk space will be freed. 98s (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 ... 81428 files and directories currently installed.) 98s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 98s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 98s Removing libpython3.12t64:s390x (3.12.9-1) ... 98s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 98s Removing libnsl2:s390x (1.3.0-3build3) ... 98s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 98s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 98s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 99s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 99s Processing triggers for libc-bin (2.41-1ubuntu1) ... 99s (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 ... 56328 files and directories currently installed.) 99s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 99s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 100s + grep -q trusty /etc/lsb-release 100s + [ ! -d /usr/share/doc/unattended-upgrades ] 100s + [ ! -d /usr/share/doc/lxd ] 100s + [ ! -d /usr/share/doc/lxd-client ] 100s + [ ! -d /usr/share/doc/snapd ] 100s + type iptables 100s + cat 100s + chmod 755 /etc/rc.local 100s + . /etc/rc.local 100s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 100s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 100s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 100s + uname -m 100s + [ s390x = ppc64le ] 100s + [ -d /run/systemd/system ] 100s + systemd-detect-virt --quiet --vm 100s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 100s + cat 100s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 100s + echo COMPRESS=lz4 100s autopkgtest [19:01:22]: upgrading testbed (apt dist-upgrade and autopurge) 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 100s Starting 2 pkgProblemResolver with broken count: 0 100s Done 100s Entering ResolveByKeep 101s 101s Calculating upgrade... 101s The following packages will be upgraded: 101s libc-bin libc-dev-bin libc6 libc6-dev locales 101s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 9512 kB of archives. 101s After this operation, 8192 B of additional disk space will be used. 101s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 103s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 105s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 105s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 108s Preconfiguring packages ... 108s Fetched 9512 kB in 7s (1292 kB/s) 108s (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 ... 56326 files and directories currently installed.) 108s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 108s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 109s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 109s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Setting up libc6:s390x (2.41-1ubuntu2) ... 109s (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 ... 56326 files and directories currently installed.) 109s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 109s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Setting up libc-bin (2.41-1ubuntu2) ... 109s (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 ... 56326 files and directories currently installed.) 109s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 109s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Setting up locales (2.41-1ubuntu2) ... 110s Generating locales (this might take a while)... 111s en_US.UTF-8... done 111s Generation complete. 111s Setting up libc-dev-bin (2.41-1ubuntu2) ... 111s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 111s Processing triggers for man-db (2.13.0-1) ... 112s Processing triggers for systemd (257.3-1ubuntu3) ... 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 113s Solving dependencies... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [19:01:35]: rebooting testbed after setup commands that affected boot 134s autopkgtest [19:01:56]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 137s autopkgtest [19:01:59]: @@@@@@@@@@@@@@@@@@@@ apt-source samtools 144s Get:1 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (dsc) [2281 B] 144s Get:2 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (tar) [5683 kB] 144s Get:3 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (diff) [22.1 kB] 144s gpgv: Signature made Thu Feb 6 21:19:50 2025 UTC 144s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 144s gpgv: issuer "emollier@debian.org" 144s gpgv: Can't check signature: No public key 144s dpkg-source: warning: cannot verify inline signature for ./samtools_1.21-1.dsc: no acceptable signature found 144s autopkgtest [19:02:06]: testing package samtools version 1.21-1 144s autopkgtest [19:02:06]: build not needed 145s autopkgtest [19:02:07]: test run-unit-test: preparing testbed 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Starting pkgProblemResolver with broken count: 0 146s Starting 2 pkgProblemResolver with broken count: 0 146s Done 146s The following NEW packages will be installed: 146s libdeflate0 libhts3t64 libhtscodecs2 samtools samtools-test tabix 146s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 4208 kB of archives. 146s After this operation, 23.1 MB of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 147s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 147s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 147s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x samtools s390x 1.21-1 [633 kB] 147s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x samtools-test all 1.21-1 [2413 kB] 149s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x tabix s390x 1.21+ds-1 [546 kB] 150s Fetched 4208 kB in 3s (1311 kB/s) 150s Selecting previously unselected package libdeflate0:s390x. 150s (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 ... 56326 files and directories currently installed.) 150s Preparing to unpack .../0-libdeflate0_1.23-1_s390x.deb ... 150s Unpacking libdeflate0:s390x (1.23-1) ... 150s Selecting previously unselected package libhtscodecs2:s390x. 150s Preparing to unpack .../1-libhtscodecs2_1.6.1-2_s390x.deb ... 150s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 150s Selecting previously unselected package libhts3t64:s390x. 150s Preparing to unpack .../2-libhts3t64_1.21+ds-1_s390x.deb ... 150s Unpacking libhts3t64:s390x (1.21+ds-1) ... 150s Selecting previously unselected package samtools. 150s Preparing to unpack .../3-samtools_1.21-1_s390x.deb ... 150s Unpacking samtools (1.21-1) ... 150s Selecting previously unselected package samtools-test. 150s Preparing to unpack .../4-samtools-test_1.21-1_all.deb ... 150s Unpacking samtools-test (1.21-1) ... 150s Selecting previously unselected package tabix. 150s Preparing to unpack .../5-tabix_1.21+ds-1_s390x.deb ... 150s Unpacking tabix (1.21+ds-1) ... 150s Setting up libhtscodecs2:s390x (1.6.1-2) ... 150s Setting up libdeflate0:s390x (1.23-1) ... 150s Setting up libhts3t64:s390x (1.21+ds-1) ... 150s Setting up samtools-test (1.21-1) ... 150s Setting up tabix (1.21+ds-1) ... 150s Setting up samtools (1.21-1) ... 150s Processing triggers for man-db (2.13.0-1) ... 151s Processing triggers for libc-bin (2.41-1ubuntu2) ... 152s autopkgtest [19:02:14]: test run-unit-test: [----------------------- 152s test_reference: 152s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reference test/reference/mpileup.1.tmp.cram 152s .. ok 152s 152s test_reference: 152s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reference -e test/reference/mpileup.1.tmp.cram 152s .. ok 152s 152s test_reference: 152s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 152s .. ok 152s 152s test_reference: 152s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 152s .. ok 152s 152s test_reference: 152s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram 152s .. ok 152s 152s test_reference: 152s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram 152s .. ok 152s 152s test_reference: 152s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 152s .. ok 152s 152s test_reference: 152s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 152s .. ok 152s 152s bgzip -c -b 65272 -s 5 /tmp/lUGP3voa4_/bgzip.dat.gz 152s .. ok 152s 152s bgzip -c -b 979200 -s 6 /tmp/lUGP3voa4_/bgzip.dat.gz 152s .. ok 152s 152s bgzip -c -b 652804 -s 6 /tmp/lUGP3voa4_/bgzip.dat.gz 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools faidx /tmp/lUGP3voa4_/faidx.fa 3:11-13 | grep -v '^>' 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools faidx /tmp/lUGP3voa4_/faidx.fa.gz 3:11-13 | grep -v '^>' 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools faidx /tmp/lUGP3voa4_/faidx.fa 2:998-1003 | grep -v '^>' 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools faidx /tmp/lUGP3voa4_/faidx.fa.gz 2:998-1003 | grep -v '^>' 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools faidx /tmp/lUGP3voa4_/faidx.fa 1:100-104 | grep -v '^>' 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools faidx /tmp/lUGP3voa4_/faidx.fa.gz 1:100-104 | grep -v '^>' 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools faidx /tmp/lUGP3voa4_/faidx.fa 1:99998-100007 | grep -v '^>' 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools faidx /tmp/lUGP3voa4_/faidx.fa.gz 1:99998-100007 | grep -v '^>' 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fqidx /tmp/lUGP3voa4_/fqidx.fq 3:11-13 153s .. ok 153s 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fqidx /tmp/lUGP3voa4_/fqidx.fq.gz 3:11-13 153s .. ok 153s 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fqidx /tmp/lUGP3voa4_/fqidx.fq 2:998-1003 153s .. ok 153s 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fqidx /tmp/lUGP3voa4_/fqidx.fq.gz 2:998-1003 153s .. ok 153s 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fqidx /tmp/lUGP3voa4_/fqidx.fq 1:100-104 153s .. ok 153s 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fqidx /tmp/lUGP3voa4_/fqidx.fq.gz 1:100-104 153s .. ok 153s 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fqidx /tmp/lUGP3voa4_/fqidx.fq 1:99998-100007 153s .. ok 153s 153s .. ok 153s 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fqidx /tmp/lUGP3voa4_/fqidx.fq.gz 1:99998-100007 153s .. ok 153s 153s .. ok 153s 153s test_dict: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/dict.fa 153s .. ok 153s 153s test_dict: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/lUGP3voa4_/dict.fa.gz 153s .. ok 153s 153s test_dict: 153s cat /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/dict.fa | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz 153s .. ok 153s 153s test_dict: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools dict -AH < /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/dict.alias.fa 153s .. ok 153s 153s test_dict: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools dict -H -l /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/dict.alt < /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/dict.alias.fa 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view /tmp/lUGP3voa4_/large_chrom.bam ref2 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view /tmp/lUGP3voa4_/large_chrom.bam ref2:1-541556283 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/lUGP3voa4_/test_input_1_b.bam.bai ref2 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/lUGP3voa4_/test_input_1_b.bam.bai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -O sam - -X -cp -R ref2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/lUGP3voa4_/test_input_1_b.bam.bai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/lUGP3voa4_/test_input_1_b_opt.bam.bai ref2 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/lUGP3voa4_/auto_indexed.csi && cat /tmp/lUGP3voa4_/auto_indexed.csi 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/lUGP3voa4_/auto_indexed.crai && cat /tmp/lUGP3voa4_/auto_indexed.crai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/lUGP3voa4_/auto_indexed.csi && cat /tmp/lUGP3voa4_/auto_indexed.csi 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -@ 2 /tmp/lUGP3voa4_/large_chrom.bam ref2 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -@ 2 /tmp/lUGP3voa4_/large_chrom.bam ref2:1-541556283 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/lUGP3voa4_/test_input_1_b.bam.bai ref2 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/lUGP3voa4_/test_input_1_b.bam.bai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -O sam - -X -cp -R ref2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/lUGP3voa4_/test_input_1_b.bam.bai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/lUGP3voa4_/test_input_1_b_opt.bam.bai ref2 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -@ 2 -M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/lUGP3voa4_/auto_indexed.csi && cat /tmp/lUGP3voa4_/auto_indexed.csi 153s .. ok 153s 153s test_index: 153s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/lUGP3voa4_/auto_indexed.crai && cat /tmp/lUGP3voa4_/auto_indexed.crai 153s .. ok 153s 154s test_index: 154s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/lUGP3voa4_/auto_indexed.csi && cat /tmp/lUGP3voa4_/auto_indexed.csi 154s .. ok 154s 154s test_mpileup: 154s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools mpileup -b /tmp/lUGP3voa4_/mpileup.bam.list -f /tmp/lUGP3voa4_/mpileup.ref.fa.gz -r17:100-150 154s .. ok 154s 154s test_mpileup: 154s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools mpileup -b /tmp/lUGP3voa4_/mpileup.cram.list -f /tmp/lUGP3voa4_/mpileup.ref.fa.gz -r17:100-150 154s .. ok 154s 154s test_mpileup: 154s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools mpileup -b /tmp/lUGP3voa4_/mpileup.bam.urllist -f /tmp/lUGP3voa4_/mpileup.ref.fa.gz -r17:100-150 154s .. ok 154s 154s test_mpileup: 154s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools mpileup -b /tmp/lUGP3voa4_/mpileup.cram.urllist -f /tmp/lUGP3voa4_/mpileup.ref.fa.gz -r17:100-150 154s .. ok 154s 154s test_mpileup: 154s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/lUGP3voa4_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lUGP3voa4_/mpileup.1.bam | grep -v mpileup 154s .. ok 154s 154s test_mpileup: 154s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/lUGP3voa4_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lUGP3voa4_/mpileup.1.cram | grep -v mpileup 154s .. ok 154s 154s test_mpileup: 154s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools mpileup /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/mpileup/overlap.bam | grep 128814202 154s .. ok 154s 154s test_usage: 154s samtools 154s test_view: 154s Generating test data file ./test/test.pl: no IO::Pty module or can't open pty; skipping usage tests 155s .................. done 155s 1: SAM -> BAM -> SAM .. ok 155s 155s 2: SAM -> uncompressed BAM .. ok 155s 155s 3: uncompressed BAM -> SAM and compare .. ok 155s 155s 4: SAM -> fast compressed BAM .. ok 155s 155s 5: fast compressed BAM -> SAM and compare .. ok 155s 155s 6: SAM -> CRAM -> SAM (UR header tags) .. ok 155s 155s 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 155s 156s 8: BAM -> CRAM with UR -> SAM .. ok 156s 156s 9: SAM -> BAM (M5 header tags) .. ok 156s 156s 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 156s 156s 11: CRAM -> BAM with UR .. ok 156s 156s 12: CRAM -> BAM with M5 .. ok 156s 156s 13: SAM -> SAM via stdout .. ok 156s 156s 14: SAM -> BAM via stdout .. ok 156s 157s 15: SAM -> CRAM via stdout .. ok 157s 157s 16: SAM from stdin -> SAM .. ok 157s 157s 17: BAM from stdin -> SAM .. ok 157s 157s 18: CRAM from stdin -> SAM .. ok 157s 157s 19: samtools view -H (SAM input) .. ok 157s 157s 20: samtools view -H (BAM input) .. ok 157s 157s 21: samtools view -H (CRAM input) .. ok 157s 157s 22: No headers (SAM input) .. ok 157s 157s 23: No headers (BAM input) .. ok 157s 158s 24: No headers (CRAM input) .. ok 158s 158s 25: Filter -f 128 (SAM input) .. ok 158s 158s 26: Count -f 128 (SAM input) .. ok 158s 158s 27: Filter -f 128 (BAM input) .. ok 158s 158s 28: Count -f 128 (BAM input) .. ok 158s 158s 29: Filter -f 128 (CRAM input) .. ok 158s 158s 30: Count -f 128 (CRAM input) .. ok 158s 158s 31: Filter -F 128 (SAM input) .. ok 158s 158s 32: Count -F 128 (SAM input) .. ok 158s 158s 33: Filter -F 128 (BAM input) .. ok 158s 158s 34: Count -F 128 (BAM input) .. ok 158s 158s 35: Filter -F 128 (CRAM input) .. ok 158s 158s 36: Count -F 128 (CRAM input) .. ok 158s 158s 37: Filter -F 128 -f 2 (SAM input) .. ok 158s 158s 38: Count -F 128 -f 2 (SAM input) .. ok 158s 158s 39: Filter -F 128 -f 2 (BAM input) .. ok 158s 158s 40: Count -F 128 -f 2 (BAM input) .. ok 158s 159s 41: Filter -F 128 -f 2 (CRAM input) .. ok 159s 159s 42: Count -F 128 -f 2 (CRAM input) .. ok 159s 159s 43: Filter -r grp2 (SAM input) .. ok 159s 159s 44: Count -r grp2 (SAM input) .. ok 159s 159s 45: Filter -r grp2 (BAM input) .. ok 159s 159s 46: Count -r grp2 (BAM input) .. ok 159s 159s 47: Filter -r grp2 (CRAM input) .. ok 159s 159s 48: Count -r grp2 (CRAM input) .. ok 159s 159s 49: Filter -R /tmp/lUGP3voa4_/view.001.fogn (SAM input) .. ok 159s 159s 50: Count -R /tmp/lUGP3voa4_/view.001.fogn (SAM input) .. ok 159s 159s 51: Filter -R /tmp/lUGP3voa4_/view.001.fogn (BAM input) .. ok 159s 159s 52: Count -R /tmp/lUGP3voa4_/view.001.fogn (BAM input) .. ok 159s 159s 53: Filter -R /tmp/lUGP3voa4_/view.001.fogn (CRAM input) .. ok 159s 159s 54: Count -R /tmp/lUGP3voa4_/view.001.fogn (CRAM input) .. ok 159s 159s 55: Filter -R /tmp/lUGP3voa4_/view.001.fogn -r grp2 (SAM input).. ok 159s 159s 56: Count -R /tmp/lUGP3voa4_/view.001.fogn -r grp2 (SAM input).. ok 159s 159s 57: Filter -R /tmp/lUGP3voa4_/view.001.fogn -r grp2 (BAM input).. ok 159s 159s 58: Count -R /tmp/lUGP3voa4_/view.001.fogn -r grp2 (BAM input).. ok 159s 160s 59: Filter -R /tmp/lUGP3voa4_/view.001.fogn -r grp2 (CRAM input).. ok 160s 160s 60: Count -R /tmp/lUGP3voa4_/view.001.fogn -r grp2 (CRAM input).. ok 160s 160s 61: Filter -r grp2 -R /tmp/lUGP3voa4_/view.001.fogn (SAM input).. ok 160s 160s 62: Count -r grp2 -R /tmp/lUGP3voa4_/view.001.fogn (SAM input).. ok 160s 160s 63: Filter -r grp2 -R /tmp/lUGP3voa4_/view.001.fogn (BAM input).. ok 160s 160s 64: Count -r grp2 -R /tmp/lUGP3voa4_/view.001.fogn (BAM input).. ok 160s 160s 65: Filter -r grp2 -R /tmp/lUGP3voa4_/view.001.fogn (CRAM input).. ok 160s 160s 66: Count -r grp2 -R /tmp/lUGP3voa4_/view.001.fogn (CRAM input).. ok 160s 160s 67: Filter -N /tmp/lUGP3voa4_/view.001.forn (SAM input) .. ok 160s 160s 68: Count -N /tmp/lUGP3voa4_/view.001.forn (SAM input) .. ok 160s 160s 69: Filter -N /tmp/lUGP3voa4_/view.001.forn (BAM input) .. ok 160s 160s 70: Count -N /tmp/lUGP3voa4_/view.001.forn (BAM input) .. ok 160s 160s 71: Filter -N /tmp/lUGP3voa4_/view.001.forn (CRAM input) .. ok 160s 160s 72: Count -N /tmp/lUGP3voa4_/view.001.forn (CRAM input) .. ok 160s 160s 73: Filter -d BC (SAM input) .. ok 160s 160s 74: Count -d BC (SAM input) .. ok 160s 160s 75: Filter -d BC (BAM input) .. ok 160s 160s 76: Count -d BC (BAM input) .. ok 160s 161s 77: Filter -d BC (CRAM input) .. ok 161s 161s 78: Count -d BC (CRAM input) .. ok 161s 161s 79: Filter -d BC:TGCA (SAM input) .. ok 161s 161s 80: Count -d BC:TGCA (SAM input) .. ok 161s 161s 81: Filter -d BC:TGCA (BAM input) .. ok 161s 161s 82: Count -d BC:TGCA (BAM input) .. ok 161s 161s 83: Filter -d BC:TGCA (CRAM input) .. ok 161s 161s 84: Count -d BC:TGCA (CRAM input) .. ok 161s 161s 85: Filter -D BC:/tmp/lUGP3voa4_/view.001.fobc (SAM input) .. ok 161s 161s 86: Count -D BC:/tmp/lUGP3voa4_/view.001.fobc (SAM input) .. ok 161s 161s 87: Filter -D BC:/tmp/lUGP3voa4_/view.001.fobc (BAM input) .. ok 161s 161s 88: Count -D BC:/tmp/lUGP3voa4_/view.001.fobc (BAM input) .. ok 161s 161s 89: Filter -D BC:/tmp/lUGP3voa4_/view.001.fobc (CRAM input) .. ok 161s 161s 90: Count -D BC:/tmp/lUGP3voa4_/view.001.fobc (CRAM input) .. ok 161s 161s 91: Filter -D BC:/tmp/lUGP3voa4_/view.001.fobc -d BC:TGCA (SAM input).. ok 161s 161s 92: Count -D BC:/tmp/lUGP3voa4_/view.001.fobc -d BC:TGCA (SAM input).. ok 161s 161s 93: Filter -D BC:/tmp/lUGP3voa4_/view.001.fobc -d BC:TGCA (BAM input).. ok 161s 161s 94: Count -D BC:/tmp/lUGP3voa4_/view.001.fobc -d BC:TGCA (BAM input).. ok 161s 161s 95: Filter -D BC:/tmp/lUGP3voa4_/view.001.fobc -d BC:TGCA (CRAM input).. ok 161s 161s 96: Count -D BC:/tmp/lUGP3voa4_/view.001.fobc -d BC:TGCA (CRAM input).. ok 161s 161s 97: Filter -d BC:TGCA -D BC:/tmp/lUGP3voa4_/view.001.fobc (SAM input).. ok 161s 161s 98: Count -d BC:TGCA -D BC:/tmp/lUGP3voa4_/view.001.fobc (SAM input).. ok 161s 161s 99: Filter -d BC:TGCA -D BC:/tmp/lUGP3voa4_/view.001.fobc (BAM input).. ok 161s 161s 100: Count -d BC:TGCA -D BC:/tmp/lUGP3voa4_/view.001.fobc (BAM input).. ok 161s 162s 101: Filter -d BC:TGCA -D BC:/tmp/lUGP3voa4_/view.001.fobc (CRAM input).. ok 162s 162s 102: Count -d BC:TGCA -D BC:/tmp/lUGP3voa4_/view.001.fobc (CRAM input).. ok 162s 162s 103: Filter -D RG:/tmp/lUGP3voa4_/view.001.fogn (SAM input) .. ok 162s 162s 104: Count -D RG:/tmp/lUGP3voa4_/view.001.fogn (SAM input) .. ok 162s 162s 105: Filter -D RG:/tmp/lUGP3voa4_/view.001.fogn (BAM input) .. ok 162s 162s 106: Count -D RG:/tmp/lUGP3voa4_/view.001.fogn (BAM input) .. ok 162s 162s 107: Filter -D RG:/tmp/lUGP3voa4_/view.001.fogn (CRAM input).. ok 162s 162s 108: Count -D RG:/tmp/lUGP3voa4_/view.001.fogn (CRAM input) .. ok 162s 162s 109: Filter -d NE:TGCA (SAM input) .. ok 162s 162s 110: Count -d NE:TGCA (SAM input) .. ok 162s 162s 111: Filter -d NE:TGCA (BAM input) .. ok 162s 162s 112: Count -d NE:TGCA (BAM input) .. ok 162s 162s 113: Filter -d NE:TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" 162s samtools view: Invalid "tag:value" option: "TGCA" 162s .. ok 162s 162s 114: Count -d NE:TGCA (CRAM input) .. ok 162s 162s 115: Filter -d TGCA (SAM input) Failed command: 162s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test115.sam -h -d TGCA /tmp/lUGP3voa4_/view.001.sam --no-PG 162s 162s 162s .. expected failure 162s 162s 116: Count -d TGCA (SAM input) Failed command: 162s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -d TGCA /tmp/lUGP3voa4_/view.001.sam --no-PG 162s 162s 162s .. expected failure 162s 162s 117: Filter -d TGCA (BAM input) Failed command: 162s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test117.sam -h -d TGCA /tmp/lUGP3voa4_/view.test001.bam --no-PG 162s 162s 162s .. expected failure 162s 162s 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 162s samtools view: Invalid "tag:value" option: "TGCA" 163s samtools view: Invalid "tag:value" option: "TGCA" 163s samtools view: Invalid "tag:value" option: "TGCA" 163s samtools view: Invalid "tag:file" option: "BClong:/tmp/lUGP3voa4_/view.001.fobc" 163s samtools view: Invalid "tag:file" option: "BClong:/tmp/lUGP3voa4_/view.001.fobc" 163s samtools view: Invalid "tag:file" option: "BClong:/tmp/lUGP3voa4_/view.001.fobc" 163s samtools view: Invalid "tag:file" option: "BClong:/tmp/lUGP3voa4_/view.001.fobc" 163s samtools view: Invalid "tag:file" option: "BClong:/tmp/lUGP3voa4_/view.001.fobc" 163s samtools view: Invalid "tag:file" option: "BClong:/tmp/lUGP3voa4_/view.001.fobc" 163s samtools view: Different tag "BC" was specified before: "RG:grp2" 163s samtools view: Different tag "BC" was specified before: "RG:grp2" 163s samtools view: Different tag "BC" was specified before: "RG:grp2" 163s samtools view: Different tag "BC" was specified before: "RG:grp2" 163s samtools view: Different tag "BC" was specified before: "RG:grp2" 163s samtools view: Different tag "BC" was specified before: "RG:grp2" 163s Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -d TGCA /tmp/lUGP3voa4_/view.test001.bam --no-PG 163s 163s 163s .. expected failure 163s 163s 119: Filter -d TGCA (CRAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test119.sam -h -d TGCA /tmp/lUGP3voa4_/view.test006.cram --no-PG 163s 163s 163s .. expected failure 163s 163s 120: Count -d TGCA (CRAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -d TGCA /tmp/lUGP3voa4_/view.test006.cram --no-PG 163s 163s 163s .. expected failure 163s 163s 121: Filter -D BClong:/tmp/lUGP3voa4_/view.001.fobc (SAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test121.sam -h -D BClong:/tmp/lUGP3voa4_/view.001.fobc /tmp/lUGP3voa4_/view.001.sam --no-PG 163s 163s 163s .. expected failure 163s 163s 122: Count -D BClong:/tmp/lUGP3voa4_/view.001.fobc (SAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -D BClong:/tmp/lUGP3voa4_/view.001.fobc /tmp/lUGP3voa4_/view.001.sam --no-PG 163s 163s 163s .. expected failure 163s 163s 123: Filter -D BClong:/tmp/lUGP3voa4_/view.001.fobc (BAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test123.sam -h -D BClong:/tmp/lUGP3voa4_/view.001.fobc /tmp/lUGP3voa4_/view.test001.bam --no-PG 163s 163s 163s .. expected failure 163s 163s 124: Count -D BClong:/tmp/lUGP3voa4_/view.001.fobc (BAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -D BClong:/tmp/lUGP3voa4_/view.001.fobc /tmp/lUGP3voa4_/view.test001.bam --no-PG 163s 163s 163s .. expected failure 163s 163s 125: Filter -D BClong:/tmp/lUGP3voa4_/view.001.fobc (CRAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test125.sam -h -D BClong:/tmp/lUGP3voa4_/view.001.fobc /tmp/lUGP3voa4_/view.test006.cram --no-PG 163s 163s 163s .. expected failure 163s 163s 126: Count -D BClong:/tmp/lUGP3voa4_/view.001.fobc (CRAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -D BClong:/tmp/lUGP3voa4_/view.001.fobc /tmp/lUGP3voa4_/view.test006.cram --no-PG 163s 163s 163s .. expected failure 163s 163s 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/lUGP3voa4_/view.001.sam --no-PG 163s 163s 163s .. expected failure 163s 163s 128: Count -d BC:ACGT -d RG:grp2 (SAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lUGP3voa4_/view.001.sam --no-PG 163s 163s 163s .. expected failure 163s 163s 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/lUGP3voa4_/view.test001.bam --no-PG 163s 163s 163s .. expected failure 163s 163s 130: Count -d BC:ACGT -d RG:grp2 (BAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lUGP3voa4_/view.test001.bam --no-PG 163s 163s 163s .. expected failure 163s 163s 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -o /tmp/lUGP3voa4_/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/lUGP3voa4_/view.test006.cram --no-PG 163s 163s 163s .. expected failure 163s 163s 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) Failed command: 163s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lUGP3voa4_/view.test006.cram --no-PG 163s 163s 163s .. expected failure 163s 163s 133: Filter -d NM:13 (SAM input) .. ok 163s 163s 134: Count -d NM:13 (SAM input) .. ok 163s 163s 135: Filter -d NM:13 (BAM input) .. ok 163s 163s 136: Count -d NM:13 (BAM input) .. ok 163s 163s 137: Filter -d NM:13 (CRAM input) .. ok 163s 163s 138: Count -d NM:13 (CRAM input) .. ok 163s 163s 139: Filter -d ab:z (SAM input) .. ok 163s 163s 140: Count -d ab:z (SAM input) .. ok 163s 163s 141: Filter -d ab:z (BAM input) .. ok 163s 163s 142: Count -d ab:z (BAM input) .. ok 163s 163s 143: Filter -d ab:z (CRAM input) .. ok 163s 163s 144: Count -d ab:z (CRAM input) .. ok 163s 163s 145: Filter -l Library 2 (SAM input) .. ok 163s 163s 146: Count -l Library 2 (SAM input) .. ok 163s 163s 147: Filter -l Library 2 (BAM input) .. ok 163s 163s 148: Count -l Library 2 (BAM input) .. ok 163s 164s 149: Filter -l Library 2 (CRAM input) .. ok 164s 164s 150: Count -l Library 2 (CRAM input) .. ok 164s 164s 151: Filter -l Library 3 (SAM input) .. ok 164s 164s 152: Count -l Library 3 (SAM input) .. ok 164s 164s 153: Filter -l Library 3 (BAM input) .. ok 164s 164s 154: Count -l Library 3 (BAM input) .. ok 164s 164s 155: Filter -l Library 3 (CRAM input) .. ok 164s 164s 156: Count -l Library 3 (CRAM input) .. ok 164s 164s 157: Filter -q 50 (SAM input) .. ok 164s 164s 158: Count -q 50 (SAM input) .. ok 164s 164s 159: Filter -q 50 (BAM input) .. ok 164s 164s 160: Count -q 50 (BAM input) .. ok 164s 164s 161: Filter -q 50 (CRAM input) .. ok 164s 164s 162: Count -q 50 (CRAM input) .. ok 164s 164s 163: Filter -q 99 (SAM input) .. ok 164s 164s 164: Count -q 99 (SAM input) .. ok 164s 164s 165: Filter -q 99 (BAM input) .. ok 164s 164s 166: Count -q 99 (BAM input) .. ok 164s 165s 167: Filter -q 99 (CRAM input) .. ok 165s 165s 168: Count -q 99 (CRAM input) .. ok 165s 165s 169: Filter -q 100 (SAM input) .. ok 165s 165s 170: Count -q 100 (SAM input) .. ok 165s 165s 171: Filter -q 100 (BAM input) .. ok 165s 165s 172: Count -q 100 (BAM input) .. ok 165s 165s 173: Filter -q 100 (CRAM input) .. ok 165s 165s 174: Count -q 100 (CRAM input) .. ok 165s 165s 175: Filter -x fa (SAM input) .. ok 165s 165s 176: Count -x fa (SAM input) .. ok 165s 165s 177: Filter -x fa (BAM input) .. ok 165s 165s 178: Count -x fa (BAM input) .. ok 165s 165s 179: Filter -x fa (CRAM input) .. ok 165s 165s 180: Count -x fa (CRAM input) .. ok 165s 165s 181: Filter -x fa -x ha (SAM input) .. ok 165s 165s 182: Count -x fa -x ha (SAM input) .. ok 165s 165s 183: Filter -x fa -x ha (BAM input) .. ok 165s 165s 184: Count -x fa -x ha (BAM input) .. ok 165s 166s 185: Filter -x fa -x ha (CRAM input) .. ok 166s 166s 186: Count -x fa -x ha (CRAM input) .. ok 166s 166s 187: Filter -x fa,ha (SAM input) .. ok 166s 166s 188: Count -x fa,ha (SAM input) .. ok 166s 166s 189: Filter -x fa,ha (BAM input) .. ok 166s 166s 190: Count -x fa,ha (BAM input) .. ok 166s 166s 191: Filter -x fa,ha (CRAM input) .. ok 166s 166s 192: Count -x fa,ha (CRAM input) .. ok 166s 166s 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 166s 166s 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 166s 166s 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 166s 166s 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 166s 166s 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 166s 166s 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 166s 166s 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 166s 166s 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 166s 166s 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 166s 166s 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 166s 167s 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 167s 167s 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 167s 167s 205: Filter -x fa -r grp2 (SAM input) .. ok 167s 167s 206: Count -x fa -r grp2 (SAM input) .. ok 167s 167s 207: Filter -x fa -r grp2 (BAM input) .. ok 167s 167s 208: Count -x fa -r grp2 (BAM input) .. ok 167s 167s 209: Filter -x fa -r grp2 (CRAM input) .. ok 167s 167s 210: Count -x fa -r grp2 (CRAM input) .. ok 167s 167s 211: Filter -x RG -r grp2 (SAM input) .. ok 167s 167s 212: Count -x RG -r grp2 (SAM input) .. ok 167s 167s 213: Filter -x RG -r grp2 (BAM input) .. ok 167s 167s 214: Count -x RG -r grp2 (BAM input) .. ok 167s 167s 215: Filter -x RG -r grp2 (CRAM input) .. ok 167s 167s 216: Count -x RG -r grp2 (CRAM input) .. ok 167s 167s 217: Filter -m 10 (SAM input) .. ok 167s 167s 218: Count -m 10 (SAM input) .. ok 167s 167s 219: Filter -m 10 (BAM input) .. ok 167s 167s 220: Count -m 10 (BAM input) .. ok 167s 168s 221: Filter -m 10 (CRAM input) .. ok 168s 168s 222: Count -m 10 (CRAM input) .. ok 168s 168s 223: Filter -m 11 (SAM input) .. ok 168s 168s 224: Count -m 11 (SAM input) .. ok 168s 168s 225: Filter -m 11 (BAM input) .. ok 168s 168s 226: Count -m 11 (BAM input) .. ok 168s 168s 227: Filter -m 11 (CRAM input) .. ok 168s 169s 228: Count -m 11 (CRAM input) .. ok 169s 169s 229: Filter -m 15 (SAM input) .. ok 169s 169s 230: Count -m 15 (SAM input) .. ok 169s 169s 231: Filter -m 15 (BAM input) .. ok 169s 169s 232: Count -m 15 (BAM input) .. ok 169s 169s 233: Filter -m 15 (CRAM input) .. ok 169s 169s 234: Count -m 15 (CRAM input) .. ok 169s 169s 235: Filter -m 16 (SAM input) .. ok 169s 169s 236: Count -m 16 (SAM input) .. ok 169s 169s 237: Filter -m 16 (BAM input) .. ok 169s 169s 238: Count -m 16 (BAM input) .. ok 169s 170s 239: Filter -m 16 (CRAM input) .. ok 170s 170s 240: Count -m 16 (CRAM input) .. ok 170s 170s 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 170s 170s 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 170s 170s 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 170s 170s 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 170s 170s 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 170s 171s 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 171s 171s 247: Filter -e [BC] (SAM input) .. ok 171s 171s 248: Count -e [BC] (SAM input) .. ok 171s 171s 249: Filter -e [BC] (BAM input) .. ok 171s 171s 250: Count -e [BC] (BAM input) .. ok 171s 171s 251: Filter -e [BC] (CRAM input) .. ok 171s 171s 252: Count -e [BC] (CRAM input) .. ok 171s 171s 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 171s 171s 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 171s 171s 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 171s 171s 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 171s 172s 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 172s 172s 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 172s 172s 259: Filter -e mapq >= 50 (SAM input) .. ok 172s 172s 260: Count -e mapq >= 50 (SAM input) .. ok 172s 172s 261: Filter -e mapq >= 50 (BAM input) .. ok 172s 172s 262: Count -e mapq >= 50 (BAM input) .. ok 172s 172s 263: Filter -e mapq >= 50 (CRAM input) .. ok 172s 173s 264: Count -e mapq >= 50 (CRAM input) .. ok 173s 173s 265: Filter -e mapq >= 99 (SAM input) .. ok 173s 173s 266: Count -e mapq >= 99 (SAM input) .. ok 173s 173s 267: Filter -e mapq >= 99 (BAM input) .. ok 173s 173s 268: Count -e mapq >= 99 (BAM input) .. ok 173s 173s 269: Filter -e mapq >= 99 (CRAM input) .. ok 173s 173s 270: Count -e mapq >= 99 (CRAM input) .. ok 173s 173s 271: Filter -e mapq >= 100 (SAM input) .. ok 173s 173s 272: Count -e mapq >= 100 (SAM input) .. ok 173s 173s 273: Filter -e mapq >= 100 (BAM input) .. ok 173s 173s 274: Count -e mapq >= 100 (BAM input) .. ok 173s 174s 275: Filter -e mapq >= 100 (CRAM input) .. ok 174s 174s 276: Count -e mapq >= 100 (CRAM input) .. ok 174s 174s 277: 1bp reads file SAM -> BAM -> SAM .. ok 174s 175s 278: 1bp reads file SAM -> CRAM -> SAM .. ok 175s 175s 278: Region Z (BAM input) .. ok 175s 175s 279: Count Z (BAM input) .. ok 175s 175s 280: Region Z (CRAM input) .. ok 175s 175s 281: Count Z (CRAM input) .. ok 175s 175s 282: Region Z:30 (BAM input) .. ok 175s 175s 283: Count Z:30 (BAM input) .. ok 175s 175s 284: Region Z:30 (CRAM input) .. ok 175s 175s 285: Count Z:30 (CRAM input) .. ok 175s 175s 286: Region Z:20-40 (BAM input) .. ok 175s 175s 287: Count Z:20-40 (BAM input) .. ok 175s 176s 288: Region Z:20-40 (CRAM input) .. ok 176s 176s 289: Count Z:20-40 (CRAM input) .. ok 176s 176s 290: Region ref1 (BAM input) .. ok 176s 176s 291: Count ref1 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 176s [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 176s .. ok 176s 176s 292: Region ref1 (CRAM input) .. ok 176s 176s 293: Count ref1 (CRAM input) .. ok 176s 176s 294: Region ref1:15 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 176s .. ok 176s 176s 295: Count ref1:15 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 176s .. ok 176s 176s 296: Region ref1:15 (CRAM input) .. ok 176s 176s 297: Count ref1:15 (CRAM input) .. ok 176s 176s 298: Region ref1:15-45 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 176s .. ok 176s 176s 299: Count ref1:15-45 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 176s .. ok 176s 177s 300: Region ref1:15-45 (CRAM input) .. ok 177s 177s 301: Count ref1:15-45 (CRAM input) .. ok 177s 177s 302: Region ref1:15-45 ref2 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 177s .. ok 177s 177s 303: Count ref1:15-45 ref2 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 177s .. ok 177s 177s 304: Region ref1:15-45 ref2 (CRAM input) .. ok 177s 177s 305: Count ref1:15-45 ref2 (CRAM input) .. ok 177s 177s 306: Region ref1:15-45 ref2:16 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 177s .. ok 177s 177s 307: Count ref1:15-45 ref2:16 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 177s .. ok 177s 177s 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 177s 177s 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 177s 177s 310: Region ref1:15-45 ref2:16-31 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 177s .. ok 177s 177s 311: Count ref1:15-45 ref2:16-31 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 177s .. ok 177s 178s 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 178s 178s 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 178s 178s 314: Region ref1:15-15 ref1:45-45 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 178s .. ok 178s 178s 315: Count ref1:15-15 ref1:45-45 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 178s .. ok 178s 178s 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 178s 178s 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 178s 178s 318: Region -f 128 ref1 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 178s [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 178s .. ok 178s 178s 319: Count -f 128 ref1 (BAM input) .. ok 178s 178s 320: Region -f 128 ref1 (CRAM input) .. ok 178s 178s 321: Count -f 128 ref1 (CRAM input) .. ok 178s 178s 322: Region -q 50 ref1:15-45 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 178s .. ok 178s 178s 323: Count -q 50 ref1:15-45 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 178s .. ok 178s 179s 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 179s 179s 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 179s 179s 326: Region -r grp2 ref1:15-45 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 179s .. ok 179s 179s 327: Count -r grp2 ref1:15-45 (BAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 179s .. ok 179s 181s 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 181s 181s 329: Count -r grp2 ref1:15-45 (CRAM input) [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 181s .. ok 181s 181s 330: Region * (BAM input) .. ok 181s 181s 331: Count * (BAM input) .. ok 181s 181s 332: Region * (CRAM input) .. ok 181s 181s 333: Count * (CRAM input) .. ok 181s 181s 334: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 181s 181s 335: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 181s 181s 336: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 181s 181s 337: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 181s 181s 338: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 181s 181s 339: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 181s 181s 340: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 181s 181s 341: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 181s 181s 342: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 181s 181s 343: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 181s 181s 344: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 181s 181s 345: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 181s 181s 346: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 181s 181s 347: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 181s 181s 348: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 181s 181s 349: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 181s 181s 350: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 181s 181s 351: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 181s 181s 352: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 181s 181s 353: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 181s 181s 354: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 181s 181s 355: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 181s 181s 356: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 181s .. ok 181s 181s 357: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 181s 181s 358: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 181s 181s 359: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 181s 181s 360: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 181s 181s 361: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 181s 181s 362: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 181s 181s 363: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 181s 182s 364: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 182s 182s 365: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 182s 182s 366: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 182s 182s 367: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 182s 182s 368: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 182s 182s 369: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 182s 182s 370: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 182s [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 182s .. ok 182s 182s 371: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 182s 182s 372: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 182s 182s 373: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 182s .. ok 182s 182s 374: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 182s 182s 375: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 182s .. ok 182s 183s 376: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 183s 183s 377: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 183s 183s 378: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 183s .. ok 183s 183s 379: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 183s .. ok 183s 183s 380: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 183s 183s 381: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 183s 183s 382: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 183s 183s 383: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 183s 183s 384: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 183s 183s 385: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 183s 183s 386: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 183s 183s 387: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 183s 184s 388: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 184s 184s 389: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 184s 184s 390: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 184s 184s 391: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 184s 184s 392: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 184s 184s 393: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 184s [W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 184s .. ok 184s 184s 394: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 184s 184s 395: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 184s 184s 396: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 184s 184s 397: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 184s 184s 398: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 184s .. ok 184s 184s 399: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 184s .. ok 184s 185s 400: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 185s 185s 401: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 185s 185s 402: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 185s .. ok 185s 185s 403: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 185s 185s 404: Region -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input)[W::hts_idx_load3] The index file is older than the data file: /tmp/lUGP3voa4_/view.test001.bam.bai 185s .. ok 185s 185s 405: Count -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 185s 185s 406: -L with nested regions .. ok 185s 185s 407: Make BAM with no M5/UR tags .. ok 185s 185s 408: Add @SQ with -t (SAM -> SAM) .. ok 185s 185s 409: Add @SQ with -T (SAM -> SAM) .. ok 185s 185s 410: Add @SQ with -t (BAM -> SAM) .. ok 185s 185s 411: Add @SQ with -T (BAM -> SAM) .. ok 185s 185s 412: Add @SQ with -t (SAM -> BAM) .. ok 185s 185s 413: Add @SQ with -T (SAM -> BAM) .. ok 185s 185s 414: Add @SQ with -t (BAM -> BAM) .. ok 185s 185s 415: Add @SQ with -T (BAM -> BAM) .. ok 185s 185s 416: Add @SQ with -t (SAM -> CRAM) .. ok 185s 186s 417: Add @SQ with -T (SAM -> CRAM) .. ok 186s 186s 418: Add @SQ with -t (BAM -> CRAM) .. ok 186s 186s 419: Add @SQ with -T (BAM -> CRAM) .. ok 186s 186s 420: Make CRAM with no UR field .. ok 186s 186s 421: Decoding CRAM with no UR field via -T .. ok 186s 186s 422: CIGAR B-operator removal .. ok 186s 187s 423: Big SAM -> BAM .. ok 187s 187s 424: Big SAM -> BAM (2 threads) .. ok 187s 187s 425: Big SAM -> BAM (4 threads) .. ok 187s 188s 426: Big SAM -> CRAM .. ok 188s 189s 427: Big SAM -> CRAM (2 threads) .. ok 189s 191s 428: Big SAM -> CRAM (4 threads) .. ok 191s 192s 429: Subsample 0.2 (SAM input) ............ ok 192s 193s 430: Subsample 0.5 (SAM input) ............ ok 193s 194s 431: Subsample 0.8 (SAM input) ............ ok 194s 195s 432: Subsample 0.2 (BAM input) ............ ok 195s 196s 433: Subsample 0.5 (BAM input) ............ ok 196s 197s 434: Subsample 0.8 (BAM input) ............ ok 197s 201s 435: Subsample 0.2 (CRAM input) ............ ok 201s 205s 436: Subsample 0.5 (CRAM input) ............ ok 205s 209s 437: Subsample 0.8 (CRAM input) ............ ok 209s 209s 438: SAM add PG .. ok 209s 209s 439: Unset dup flag, remove dt and do tags .. ok 209s 209s 440: Unmap dup flagged reads. .. ok 209s 209s 441: Unmap dup flagged reads. .. ok 209s 209s 442: fetch pairs .. ok 209s 209s 443: fetch pairs .. ok 209s 209s 444: fetch pairs .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -h 0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -h 1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -h 5 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -h 29 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -h 30 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -n 0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -n 1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -n 5 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_head: 209s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools head -h 5 -n 5 < /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.sam 209s .. ok 209s 209s test_cat: 209s Generating test data file .................. done 209s Generate BAM file #1 .. ok 209s 209s Generate BAM region file #1 .. ok 209s 210s Generate CRAM file #1 .. ok 210s 210s Generating test data file .................. done 210s Generate BAM file #2 .. ok 210s 210s Generate BAM region file #2 .. ok 210s 210s Generate CRAM file #2 .. ok 210s 210s Generating test data file .................. done 210s Generate BAM file #3 .. ok 210s 210s Generate BAM region file #3 .. ok 210s 210s Generate CRAM file #3 .. ok 210s 210s Generating test data file .................. done 210s Generate BAM file #4 .. ok 210s 210s Generate BAM region file #4 .. ok 210s 211s Generate CRAM file #4 .. ok 211s 211s 1: cat BAM files .. ok 211s 211s 2: cat recompressed BAM files .. ok 211s 211s 3: cat CRAM files .. ok 211s 213s 4: cat CRAM subregion files .. ok 213s 213s 5: cat BAM files to stdout .. ok 213s 213s 6: cat recompressed BAM files to stdout .. ok 213s 213s 7: cat CRAM files to stdout .. ok 213s 215s 8: cat CRAM subregion files to stdout .. ok 215s 215s 9: cat CRAM part 1/2 .. ok 215s 215s 9: cat CRAM part 2/2 .. ok 215s 216s 9: cat CRAM parts 1/2 + 2/2 .. ok 216s 216s 10: cat BAM files with new header .. ok 216s 216s 11: cat recompressed BAM files with new header .. ok 216s 216s 12: cat CRAM files with new header .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/0.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/0.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT,MD,ia -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/import/2.interleaved.fq -T "" 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/import/3.interleaved.fq -i 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T "*" 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T "" 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq 216s .. ok 216s 216s test_import: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ 216s .. ok 216s 216s test_bam2fq: 216s Generate BAM file .. ok 216s 216s Generate CRAM file [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s .. ok 216s 216s 1: fastq (SAM input) .. ok 216s 216s 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s [M::bam2fq_mainloop] discarded 0 singletons 216s .. ok 216s 216s 3: fastq (BAM input) .. ok 216s 216s 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads 216s [M::bam2fq_mainloop] discarded 0 singletons 216s .. ok 216s 216s 5: fastq (CRAM input) .. ok 216s 216s 6: fastq -n (CRAM input) .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s [M::bam2fq_mainloop] processed 36 reads 216s [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.002.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.003.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.004.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.004.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.010.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -t -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -t -T MD,ia -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.004.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.703.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fasta -N -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -s /tmp/lUGP3voa4_/bam2fq.discard.s.fq -0 /tmp/lUGP3voa4_/bam2fq.discard.0.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.013.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq --index-format 'i8n1i8' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.014.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -T '' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -t -T '*' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -T '*' -d MD:10 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -T '*' -d NM:0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -N -T '*' -d ia /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -d NM:13 -d NM:14 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -D NM:test/dat/bam2fq.NM-D /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -D MD:test/dat/bam2fq.MD-D /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s Generate BAM file (2 threads) .. ok 216s 216s Generate CRAM file (2 threads) .. ok 216s 216s 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s .. ok 216s 216s 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s .. ok 216s 216s 3: fastq (BAM input) (2 threads) .. ok 216s 216s 4: fastq -n (BAM input) (2 threads) .. ok 216s 216s 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s .. ok 216s 216s 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 216s [M::bam2fq_mainloop] processed 36 reads 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.002.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.003.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.004.sam 216s .. ok 216s 216s test_bam2fq: 216s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.004.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.010.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -t -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T MD,ia -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.004.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -i --index-format 'i*i*' -s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.005.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.703.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fasta -@ 2 -N -1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -s /tmp/lUGP3voa4_/bam2fq.discard.s.fq -0 /tmp/lUGP3voa4_/bam2fq.discard.0.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.013.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.014.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -T '' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T '*' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d MD:10 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d NM:0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d ia /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -d NM:13 -d NM:14 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_bam2fq: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/bam2fq.001.sam 217s .. ok 217s 217s test_depad: 217s Generate BAM file .. ok 217s 217s depad (SAM input) .. ok 217s 217s depad -s (SAM input) .. ok 217s 217s depad -u (SAM input) .. ok 217s 217s depad -1 (SAM input) .. ok 217s 217s depad (BAM input) .. ok 217s 217s depad -s (BAM input) .. ok 217s 217s depad -u (BAM input) .. ok 217s 217s depad -1 (BAM input) .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/1_map_cigar_large.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/4_X_cigar_full_seq.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/5_insert_cigar_large.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa -i 0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/7_supp.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/7_supp_large.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/8_secondary.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/8_secondary_large.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/10_map_cigar.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -t /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -g 4 -t /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -g 4 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/13_barcodes_ok.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 217s 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 217s .. expected failure 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 217s 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 217s .. expected failure 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 217s 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 217s .. expected failure 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -I s1 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -I grp2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -I grp3 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -I Sample /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 217s .. ok 217s 217s test_stats: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/mpileup/ce.fa /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/stat/15.big_del.sam | tail -n+4 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_c.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_c.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -s 1 -O sam -b /tmp/NaGqu_PapL - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -r -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_c.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -cp -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -o - -s 1 -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_c.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/lUGP3voa4_/merge.tag.1.bam /tmp/lUGP3voa4_/merge.tag.2.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/lUGP3voa4_/merge.tag.3.bam /tmp/lUGP3voa4_/merge.tag.4.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge --no-PG -O SAM - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge --no-PG -O SAM -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/merge.bed - /tmp/lUGP3voa4_/merge.bed.1.bam /tmp/lUGP3voa4_/merge.bed.2.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge --no-PG -r -O SAM - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge --no-PG -O SAM --template-coordinate - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/test_template_coordinate.1.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/test_template_coordinate.2.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_c.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_c.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam -b /tmp/gslSwPc2YB - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -r -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_c.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -cp -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -o - -s 1 -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_c.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/lUGP3voa4_/merge.tag.1.bam /tmp/lUGP3voa4_/merge.tag.2.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/lUGP3voa4_/merge.tag.3.bam /tmp/lUGP3voa4_/merge.tag.4.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/merge.bed - /tmp/lUGP3voa4_/merge.bed.1.bam /tmp/lUGP3voa4_/merge.bed.2.bam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 --no-PG -r -O SAM - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 217s .. ok 217s 217s test_merge: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/test_template_coordinate.1.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/merge/test_template_coordinate.2.sam 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/lUGP3voa4_/sortout 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/lUGP3voa4_/sortout.bam 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/lUGP3voa4_/sorttmp 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -N -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/sort_name_input_1.sam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -t RG -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -n -t RG -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -t AS -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -t FI -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort --template-coordinate -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -M -K10 -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -M -K10 -I /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -MH -K10 -I /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/lUGP3voa4_/sortout 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/lUGP3voa4_/sortout.bam 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/lUGP3voa4_/sorttmp 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -N -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/sort_name_input_1.sam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -t RG -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -n -t RG -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 217s .. ok 217s 217s test_sort: 217s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -t AS -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 218s .. ok 218s 218s test_sort: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -t FI -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 218s .. ok 218s 218s test_sort: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 --template-coordinate -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 218s .. ok 218s 218s test_sort: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -O SAM -o - 218s .. ok 218s 218s test_sort: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -I /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 218s .. ok 218s 218s test_sort: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -@ 2 -MH -K10 -I /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 218s .. ok 218s 218s test_collate: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate --output-fmt=sam -O /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam 218s .. ok 218s 218s test_collate: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam 218s .. ok 218s 218s test_collate: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/collate2.tmp 218s .. ok 218s 218s test_collate: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate --output-fmt=sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/collate3.tmp 218s .. ok 218s 218s test_collate: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate --output-fmt=sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/1_fast_collate.sam 218s .. ok 218s 218s test_collate: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate --output-fmt=sam -f -r 4 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 218s .. ok 218s 218s test_collate: 218s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -O /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam 219s .. ok 219s 219s test_collate: 219s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam 220s .. ok 220s 220s test_collate: 220s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/collate2.tmp 221s .. ok 221s 221s test_collate: 221s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/collate3.tmp 222s .. ok 222s 222s test_collate: 222s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/1_fast_collate.sam 223s .. ok 223s 223s test_collate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f -r 4 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 223s 223s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 223s 223s .. expected failure 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/5_ct.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/sanitize.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_ok+.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_ok-.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_draft.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_not_updated.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_not_updated_noML.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_not_updated_noMN.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_bad_MN.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_MN_only.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_ML_only.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_ML_wrong_len.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_noseq.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_bounds.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 223s 223s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 223s 223s .. expected failure 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 223s .. ok 223s 223s test_fixmate: 223s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/5_ct.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/sanitize.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_ok+.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_ok-.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_draft.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_not_updated.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_not_updated_noML.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_not_updated_noMN.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_bad_MN.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_MN_only.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_ML_only.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_ML_wrong_len.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_noseq.sam - 224s .. ok 224s 224s test_fixmate: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/fixmate/mod_bounds.sam - 224s .. ok 224s 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools calmd -uAr /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.ref.fa 224s .. ok 224s 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools calmd -@ 2 -uAr /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.ref.fa 224s .. ok 224s 224s test_idxstat: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam 224s .. ok 224s 224s test_idxstat: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.cram 224s .. ok 224s 224s test_idxstat: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.sam 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck -v /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 224s .. ok 224s 224s test_quickcheck: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools quickcheck -uv /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 224s .. ok 224s 224s test_reheader: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 224s .. ok 224s 224s test_reheader: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 224s .. ok 224s 224s test_reheader: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 224s .. ok 224s 224s test_reheader: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram && /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' 224s .. ok 224s 224s test_reheader: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram && /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' 224s .. ok 224s 224s test_reheader: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 224s .. ok 224s 224s test_reheader: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/1_fixup.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -O sam -m orphan_only /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -O sam -R '1#9' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/1_fixup.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/1_fixup.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/1_fixup.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/1_fixup.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m orphan_only /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -R '1#9' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/1_fixup.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/1_fixup.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 224s .. ok 224s 224s test_addrprg: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/addrprg/1_fixup.sam 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/1_name_sort.sam - 224s 224s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 224s 224s 224s .. expected failure 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/2_bad_order.sam - 224s 224s ERR: samtools markdup: error, not in coordinate sorted order. 224s 224s 224s .. expected failure 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 224s 224s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 224s 224s samtools markdup: error, unable to assign pair hash key. 224s 224s 224s .. expected failure 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 224s 224s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 224s 224s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 224s 224s 224s .. expected failure 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/5_markdup.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -O sam -r --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/17_read_group.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/1_name_sort.sam - 224s 224s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 224s 224s 224s .. expected failure 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/2_bad_order.sam - 224s 224s ERR: samtools markdup: error, not in coordinate sorted order. 224s 224s 224s .. expected failure 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 224s 224s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 224s 224s samtools markdup: error, unable to assign pair hash key. 224s 224s 224s .. expected failure 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 224s 224s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 224s 224s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 224s 224s 224s .. expected failure 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/5_markdup.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -O sam -r --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 224s .. ok 224s 224s test_markdup: 224s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/17_read_group.sam - 225s .. ok 225s 225s test_markdup: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 225s .. ok 225s 225s test_bedcov: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools bedcov /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bedcov/bedcov.bam 225s .. ok 225s 225s test_bedcov: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools bedcov -j /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bedcov/bedcov.bam 225s .. ok 225s 225s test_bedcov: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools bedcov -g512 -G2048 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bedcov/bedcov.bam 225s .. ok 225s 225s test_bedcov: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools bedcov -c /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/bedcov/bedcov.bam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -p 5 -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split --output-fmt sam -d RG -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split --output-fmt sam -d an -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split --output-fmt sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -d nn -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.d_nn.unk.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split_d_nn.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split --output-fmt sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.d_nn.0unk.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split_d_nn.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -p 5 -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d RG -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -d nn -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.d_nn.unk.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split_d_nn.sam 225s .. ok 225s 225s test_split: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -f /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split.tmp.d_nn.0unk.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/split/split_d_nn.sam 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG /tmp/lUGP3voa4_/longref.sam.gz 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG /tmp/lUGP3voa4_/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view -h --no-PG -L /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/large_pos/test.bed /tmp/lUGP3voa4_/longref.sam.gz 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/large_pos/longref_name.sam 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools merge -O sam --no-PG - /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/large_pos/longref.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/large_pos/longref2.sam 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools depth /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/large_pos/longref.sam 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools depth -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/large_pos/test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/large_pos/longref.sam 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/lUGP3voa4_/longref.sam.gz 225s .. ok 225s 225s test_large_positions: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools fixmate -O sam --no-PG - - | 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --primer-counts /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/3_multi_ref_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/3_multi_ref_data.sam 225s .. ok 225s 225s test_ampliconclip: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 225s .. ok 225s 225s test_ampliconstats: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_hard_clipped.expected.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_soft_clipped.expected.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/1_soft_clipped_strand.expected.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' 225s .. ok 225s 225s test_ampliconstats: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 225s .. ok 225s 225s test_ampliconstats: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 225s .. ok 225s 225s test_reset: 225s cat /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view 225s .. ok 225s 225s test_reset: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag < /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view 225s .. ok 225s 225s test_reset: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools view 225s .. ok 225s 225s test_reset: 225s cat /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam 225s .. ok 225s 225s test_reset: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.bam 225s .. ok 225s 225s test_reset: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/test_input_1_a.cram 225s .. ok 225s 225s test_reset: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' 225s .. ok 225s 225s test_reset: 225s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG sam_to_fixed_bam /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index --no-PG /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG" 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s test_reset: 226s /tmp/autopkgtest.ry02B7/autopkgtest_tmp/samtools reset /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.ry02B7/autopkgtest_tmp/test/reset/output 226s .. ok 226s 226s 226s Number of tests: 226s total .. 951 226s passed .. 920 226s failed .. 0 226s expected failure .. 31 226s unexpected pass .. 0 226s 226s autopkgtest [19:03:28]: test run-unit-test: -----------------------] 227s run-unit-test PASS 227s autopkgtest [19:03:29]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 227s autopkgtest [19:03:29]: @@@@@@@@@@@@@@@@@@@@ summary 227s run-unit-test PASS 232s nova [W] Using flock in prodstack6-s390x 232s Creating nova instance adt-plucky-s390x-samtools-20250315-185942-juju-7f2275-prod-proposed-migration-environment-15-3a1d6f84-e60a-4e2a-9742-5395949624cb from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 232s nova [W] Timed out waiting for 1f963e6c-849b-4248-9c5a-e3ebd98bd0bc to get deleted.