0s autopkgtest [16:36:19]: starting date and time: 2025-03-15 16:36:19+0000 0s autopkgtest [16:36:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:36:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zuqc4pty/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-34.secgroup --name adt-plucky-arm64-samtools-20250315-163618-juju-7f2275-prod-proposed-migration-environment-15-86617ce0-90a0-49e8-9a7c-69392440a12c --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -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/ 155s autopkgtest [16:38:54]: testbed dpkg architecture: arm64 155s autopkgtest [16:38:54]: testbed apt version: 2.9.33 155s autopkgtest [16:38:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s autopkgtest [16:38:54]: testbed release detected to be: None 156s autopkgtest [16:38:55]: updating testbed package index (apt update) 157s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 157s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 157s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 157s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 157s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 158s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 158s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 158s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 158s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 158s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 158s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 159s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 159s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 159s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 159s Fetched 1078 kB in 2s (643 kB/s) 160s Reading package lists... 160s + lsb_release --codename --short 160s + RELEASE=plucky 160s + cat 160s + [ plucky != trusty ] 160s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 160s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Calculating upgrade... 161s Calculating upgrade... 162s The following packages will be upgraded: 162s pinentry-curses python3-jinja2 strace 162s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 647 kB of archives. 162s After this operation, 11.3 kB of additional disk space will be used. 162s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 163s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 163s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 163s Fetched 647 kB in 1s (571 kB/s) 164s (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 ... 117701 files and directories currently installed.) 164s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 164s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 164s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 164s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 164s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 164s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 164s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 164s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 164s Setting up strace (6.13+ds-1ubuntu1) ... 164s Processing triggers for man-db (2.13.0-1) ... 165s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 165s + /usr/lib/apt/apt-helper analyze-pattern ?true 165s + uname -r 165s + sed s/\./\\./g 165s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 165s + apt list ?obsolete 165s + tail -n+2 165s + cut -d/ -f1 165s + grep -v ^linux-.*6\.14\.0-10-generic.* 166s + obsolete_pkgs=linux-headers-6.11.0-8-generic 166s linux-headers-6.11.0-8 166s linux-image-6.11.0-8-generic 166s linux-modules-6.11.0-8-generic 166s linux-tools-6.11.0-8-generic 166s linux-tools-6.11.0-8 166s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 166s Reading package lists... 167s Building dependency tree... 167s Reading state information... 168s Solving dependencies... 169s The following packages will be REMOVED: 169s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 169s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 169s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 169s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 169s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 169s After this operation, 267 MB disk space will be freed. 169s (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 ... 117701 files and directories currently installed.) 169s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 169s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 169s Removing libpython3.12t64:arm64 (3.12.9-1) ... 169s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 170s Removing libnsl2:arm64 (1.3.0-3build3) ... 170s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 170s Removing libunwind8:arm64 (1.6.2-3.1) ... 170s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 170s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 172s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 172s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 172s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 172s /etc/kernel/postrm.d/initramfs-tools: 172s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 173s /etc/kernel/postrm.d/zz-flash-kernel: 173s flash-kernel: Kernel 6.11.0-8-generic has been removed. 173s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 173s /etc/kernel/postrm.d/zz-update-grub: 173s Sourcing file `/etc/default/grub' 173s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 173s Generating grub configuration file ... 173s Found linux image: /boot/vmlinuz-6.14.0-10-generic 173s Found initrd image: /boot/initrd.img-6.14.0-10-generic 174s Warning: os-prober will not be executed to detect other bootable partitions. 174s Systems on them will not be added to the GRUB boot configuration. 174s Check GRUB_DISABLE_OS_PROBER documentation entry. 174s Adding boot menu entry for UEFI Firmware Settings ... 174s done 174s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 174s Processing triggers for libc-bin (2.41-1ubuntu1) ... 174s (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 ... 81650 files and directories currently installed.) 174s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 174s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 174s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 175s + grep -q trusty /etc/lsb-release 175s + [ ! -d /usr/share/doc/unattended-upgrades ] 175s + [ ! -d /usr/share/doc/lxd ] 175s + [ ! -d /usr/share/doc/lxd-client ] 175s + [ ! -d /usr/share/doc/snapd ] 175s + type iptables 175s + cat 175s + chmod 755 /etc/rc.local 175s + . /etc/rc.local 175s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 175s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 175s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 175s + uname -m 175s + [ aarch64 = ppc64le ] 175s + [ -d /run/systemd/system ] 175s + systemd-detect-virt --quiet --vm 175s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 175s + cat 175s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 175s + echo COMPRESS=lz4 175s autopkgtest [16:39:14]: upgrading testbed (apt dist-upgrade and autopurge) 175s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 177s Starting 2 pkgProblemResolver with broken count: 0 177s Done 178s Entering ResolveByKeep 178s 178s Calculating upgrade... 179s The following packages will be upgraded: 179s libc-bin libc-dev-bin libc6 libc6-dev locales 179s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 9530 kB of archives. 179s After this operation, 0 B of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 181s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 181s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 185s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 186s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 190s Preconfiguring packages ... 191s Fetched 9530 kB in 11s (848 kB/s) 191s (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 ... 81647 files and directories currently installed.) 191s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 191s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 191s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 191s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 191s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 191s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 191s Setting up libc6:arm64 (2.41-1ubuntu2) ... 191s (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 ... 81647 files and directories currently installed.) 191s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 191s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 192s Setting up libc-bin (2.41-1ubuntu2) ... 192s (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 ... 81647 files and directories currently installed.) 192s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 192s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 192s Setting up locales (2.41-1ubuntu2) ... 193s Generating locales (this might take a while)... 196s en_US.UTF-8... done 196s Generation complete. 196s Setting up libc-dev-bin (2.41-1ubuntu2) ... 196s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 196s Processing triggers for man-db (2.13.0-1) ... 197s Processing triggers for systemd (257.3-1ubuntu3) ... 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 198s Starting pkgProblemResolver with broken count: 0 199s Starting 2 pkgProblemResolver with broken count: 0 199s Done 199s Solving dependencies... 199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 200s autopkgtest [16:39:39]: rebooting testbed after setup commands that affected boot 227s autopkgtest [16:40:06]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 231s autopkgtest [16:40:10]: @@@@@@@@@@@@@@@@@@@@ apt-source samtools 242s Get:1 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (dsc) [2281 B] 242s Get:2 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (tar) [5683 kB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (diff) [22.1 kB] 242s gpgv: Signature made Thu Feb 6 21:19:50 2025 UTC 242s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 242s gpgv: issuer "emollier@debian.org" 242s gpgv: Can't check signature: No public key 242s dpkg-source: warning: cannot verify inline signature for ./samtools_1.21-1.dsc: no acceptable signature found 242s autopkgtest [16:40:21]: testing package samtools version 1.21-1 243s autopkgtest [16:40:22]: build not needed 245s autopkgtest [16:40:24]: test run-unit-test: preparing testbed 245s Reading package lists... 246s Building dependency tree... 246s Reading state information... 246s Starting pkgProblemResolver with broken count: 0 246s Starting 2 pkgProblemResolver with broken count: 0 246s Done 247s The following NEW packages will be installed: 247s libdeflate0 libhts3t64 libhtscodecs2 samtools samtools-test tabix 247s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 247s Need to get 4119 kB of archives. 247s After this operation, 23.5 MB of additional disk space will be used. 247s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 247s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 247s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 248s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.21-1 [609 kB] 248s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools-test all 1.21-1 [2413 kB] 251s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 tabix arm64 1.21+ds-1 [527 kB] 252s Fetched 4119 kB in 4s (925 kB/s) 252s Selecting previously unselected package libdeflate0:arm64. 252s (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 ... 81647 files and directories currently installed.) 252s Preparing to unpack .../0-libdeflate0_1.23-1_arm64.deb ... 252s Unpacking libdeflate0:arm64 (1.23-1) ... 252s Selecting previously unselected package libhtscodecs2:arm64. 252s Preparing to unpack .../1-libhtscodecs2_1.6.1-2_arm64.deb ... 252s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 252s Selecting previously unselected package libhts3t64:arm64. 252s Preparing to unpack .../2-libhts3t64_1.21+ds-1_arm64.deb ... 252s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 252s Selecting previously unselected package samtools. 252s Preparing to unpack .../3-samtools_1.21-1_arm64.deb ... 252s Unpacking samtools (1.21-1) ... 252s Selecting previously unselected package samtools-test. 252s Preparing to unpack .../4-samtools-test_1.21-1_all.deb ... 252s Unpacking samtools-test (1.21-1) ... 252s Selecting previously unselected package tabix. 252s Preparing to unpack .../5-tabix_1.21+ds-1_arm64.deb ... 252s Unpacking tabix (1.21+ds-1) ... 253s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 253s Setting up libdeflate0:arm64 (1.23-1) ... 253s Setting up libhts3t64:arm64 (1.21+ds-1) ... 253s Setting up samtools-test (1.21-1) ... 253s Setting up tabix (1.21+ds-1) ... 253s Setting up samtools (1.21-1) ... 253s Processing triggers for man-db (2.13.0-1) ... 254s Processing triggers for libc-bin (2.41-1ubuntu2) ... 255s autopkgtest [16:40:34]: test run-unit-test: [----------------------- 256s test_reference: 256s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reference test/reference/mpileup.1.tmp.cram 256s .. ok 256s 256s test_reference: 256s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reference -e test/reference/mpileup.1.tmp.cram 256s .. ok 256s 256s test_reference: 256s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 256s .. ok 256s 256s test_reference: 256s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 256s .. ok 256s 256s test_reference: 256s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram 256s .. ok 256s 256s test_reference: 256s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram 256s .. ok 256s 256s test_reference: 256s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 256s .. ok 256s 256s test_reference: 256s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 256s .. ok 256s 256s bgzip -c -b 65272 -s 5 /tmp/eStjVEae7_/bgzip.dat.gz 256s .. ok 256s 256s bgzip -c -b 979200 -s 6 /tmp/eStjVEae7_/bgzip.dat.gz 256s .. ok 256s 256s bgzip -c -b 652804 -s 6 /tmp/eStjVEae7_/bgzip.dat.gz 256s .. ok 256s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools faidx /tmp/eStjVEae7_/faidx.fa 3:11-13 | grep -v '^>' 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools faidx /tmp/eStjVEae7_/faidx.fa.gz 3:11-13 | grep -v '^>' 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools faidx /tmp/eStjVEae7_/faidx.fa 2:998-1003 | grep -v '^>' 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools faidx /tmp/eStjVEae7_/faidx.fa.gz 2:998-1003 | grep -v '^>' 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools faidx /tmp/eStjVEae7_/faidx.fa 1:100-104 | grep -v '^>' 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools faidx /tmp/eStjVEae7_/faidx.fa.gz 1:100-104 | grep -v '^>' 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools faidx /tmp/eStjVEae7_/faidx.fa 1:99998-100007 | grep -v '^>' 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools faidx /tmp/eStjVEae7_/faidx.fa.gz 1:99998-100007 | grep -v '^>' 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fqidx /tmp/eStjVEae7_/fqidx.fq 3:11-13 257s .. ok 257s 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fqidx /tmp/eStjVEae7_/fqidx.fq.gz 3:11-13 257s .. ok 257s 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fqidx /tmp/eStjVEae7_/fqidx.fq 2:998-1003 257s .. ok 257s 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fqidx /tmp/eStjVEae7_/fqidx.fq.gz 2:998-1003 257s .. ok 257s 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fqidx /tmp/eStjVEae7_/fqidx.fq 1:100-104 257s .. ok 257s 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fqidx /tmp/eStjVEae7_/fqidx.fq.gz 1:100-104 257s .. ok 257s 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fqidx /tmp/eStjVEae7_/fqidx.fq 1:99998-100007 257s .. ok 257s 257s .. ok 257s 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fqidx /tmp/eStjVEae7_/fqidx.fq.gz 1:99998-100007 257s .. ok 257s 257s .. ok 257s 257s test_dict: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/dict.fa 257s .. ok 257s 257s test_dict: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/eStjVEae7_/dict.fa.gz 257s .. ok 257s 257s test_dict: 257s cat /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/dict.fa | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz 257s .. ok 257s 257s test_dict: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools dict -AH < /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/dict.alias.fa 257s .. ok 257s 257s test_dict: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools dict -H -l /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/dict.alt < /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/dict.alias.fa 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view /tmp/eStjVEae7_/large_chrom.bam ref2 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view /tmp/eStjVEae7_/large_chrom.bam ref2:1-541556283 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eStjVEae7_/test_input_1_b.bam.bai ref2 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eStjVEae7_/test_input_1_b.bam.bai 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -O sam - -X -cp -R ref2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/eStjVEae7_/test_input_1_b.bam.bai 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eStjVEae7_/test_input_1_b_opt.bam.bai ref2 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 257s .. ok 257s 257s test_index: 257s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 257s .. ok 257s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/eStjVEae7_/auto_indexed.csi && cat /tmp/eStjVEae7_/auto_indexed.csi 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/eStjVEae7_/auto_indexed.crai && cat /tmp/eStjVEae7_/auto_indexed.crai 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/eStjVEae7_/auto_indexed.csi && cat /tmp/eStjVEae7_/auto_indexed.csi 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -@ 2 /tmp/eStjVEae7_/large_chrom.bam ref2 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -@ 2 /tmp/eStjVEae7_/large_chrom.bam ref2:1-541556283 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eStjVEae7_/test_input_1_b.bam.bai ref2 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eStjVEae7_/test_input_1_b.bam.bai 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -O sam - -X -cp -R ref2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/eStjVEae7_/test_input_1_b.bam.bai 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eStjVEae7_/test_input_1_b_opt.bam.bai ref2 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -@ 2 -M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/eStjVEae7_/auto_indexed.csi && cat /tmp/eStjVEae7_/auto_indexed.csi 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/eStjVEae7_/auto_indexed.crai && cat /tmp/eStjVEae7_/auto_indexed.crai 258s .. ok 258s 258s test_index: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/eStjVEae7_/auto_indexed.csi && cat /tmp/eStjVEae7_/auto_indexed.csi 258s .. ok 258s 258s test_mpileup: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools mpileup -b /tmp/eStjVEae7_/mpileup.bam.list -f /tmp/eStjVEae7_/mpileup.ref.fa.gz -r17:100-150 258s .. ok 258s 258s test_mpileup: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools mpileup -b /tmp/eStjVEae7_/mpileup.cram.list -f /tmp/eStjVEae7_/mpileup.ref.fa.gz -r17:100-150 258s .. ok 258s 258s test_mpileup: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools mpileup -b /tmp/eStjVEae7_/mpileup.bam.urllist -f /tmp/eStjVEae7_/mpileup.ref.fa.gz -r17:100-150 258s .. ok 258s 258s test_mpileup: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools mpileup -b /tmp/eStjVEae7_/mpileup.cram.urllist -f /tmp/eStjVEae7_/mpileup.ref.fa.gz -r17:100-150 258s .. ok 258s 258s test_mpileup: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/eStjVEae7_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/eStjVEae7_/mpileup.1.bam | grep -v mpileup 258s .. ok 258s 258s test_mpileup: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/eStjVEae7_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/eStjVEae7_/mpileup.1.cram | grep -v mpileup 258s .. ok 258s 258s test_mpileup: 258s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools mpileup /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/mpileup/overlap.bam | grep 128814202 258s ./test/test.pl: no IO::Pty module or can't open pty; skipping usage tests 258s .. ok 258s 258s test_usage: 258s samtools 258s test_view: 259s Generating test data file .................. done 259s 1: SAM -> BAM -> SAM .. ok 259s 259s 2: SAM -> uncompressed BAM .. ok 259s 259s 3: uncompressed BAM -> SAM and compare .. ok 259s 259s 4: SAM -> fast compressed BAM .. ok 259s 259s 5: fast compressed BAM -> SAM and compare .. ok 259s 260s 6: SAM -> CRAM -> SAM (UR header tags) .. ok 260s 260s 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 260s 261s 8: BAM -> CRAM with UR -> SAM .. ok 261s 261s 9: SAM -> BAM (M5 header tags) .. ok 261s 261s 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 261s 261s 11: CRAM -> BAM with UR .. ok 261s 261s 12: CRAM -> BAM with M5 .. ok 261s 261s 13: SAM -> SAM via stdout .. ok 261s 261s 14: SAM -> BAM via stdout .. ok 261s 262s 15: SAM -> CRAM via stdout .. ok 262s 262s 16: SAM from stdin -> SAM .. ok 262s 262s 17: BAM from stdin -> SAM .. ok 262s 262s 18: CRAM from stdin -> SAM .. ok 262s 262s 19: samtools view -H (SAM input) .. ok 262s 262s 20: samtools view -H (BAM input) .. ok 262s 262s 21: samtools view -H (CRAM input) .. ok 262s 262s 22: No headers (SAM input) .. ok 262s 263s 23: No headers (BAM input) .. ok 263s 263s 24: No headers (CRAM input) .. ok 263s 263s 25: Filter -f 128 (SAM input) .. ok 263s 263s 26: Count -f 128 (SAM input) .. ok 263s 263s 27: Filter -f 128 (BAM input) .. ok 263s 263s 28: Count -f 128 (BAM input) .. ok 263s 263s 29: Filter -f 128 (CRAM input) .. ok 263s 263s 30: Count -f 128 (CRAM input) .. ok 263s 263s 31: Filter -F 128 (SAM input) .. ok 263s 263s 32: Count -F 128 (SAM input) .. ok 263s 263s 33: Filter -F 128 (BAM input) .. ok 263s 263s 34: Count -F 128 (BAM input) .. ok 263s 264s 35: Filter -F 128 (CRAM input) .. ok 264s 264s 36: Count -F 128 (CRAM input) .. ok 264s 264s 37: Filter -F 128 -f 2 (SAM input) .. ok 264s 264s 38: Count -F 128 -f 2 (SAM input) .. ok 264s 264s 39: Filter -F 128 -f 2 (BAM input) .. ok 264s 264s 40: Count -F 128 -f 2 (BAM input) .. ok 264s 264s 41: Filter -F 128 -f 2 (CRAM input) .. ok 264s 264s 42: Count -F 128 -f 2 (CRAM input) .. ok 264s 264s 43: Filter -r grp2 (SAM input) .. ok 264s 264s 44: Count -r grp2 (SAM input) .. ok 264s 264s 45: Filter -r grp2 (BAM input) .. ok 264s 264s 46: Count -r grp2 (BAM input) .. ok 264s 264s 47: Filter -r grp2 (CRAM input) .. ok 264s 264s 48: Count -r grp2 (CRAM input) .. ok 264s 264s 49: Filter -R /tmp/eStjVEae7_/view.001.fogn (SAM input) .. ok 264s 264s 50: Count -R /tmp/eStjVEae7_/view.001.fogn (SAM input) .. ok 264s 264s 51: Filter -R /tmp/eStjVEae7_/view.001.fogn (BAM input) .. ok 264s 264s 52: Count -R /tmp/eStjVEae7_/view.001.fogn (BAM input) .. ok 264s 265s 53: Filter -R /tmp/eStjVEae7_/view.001.fogn (CRAM input) .. ok 265s 265s 54: Count -R /tmp/eStjVEae7_/view.001.fogn (CRAM input) .. ok 265s 265s 55: Filter -R /tmp/eStjVEae7_/view.001.fogn -r grp2 (SAM input).. ok 265s 265s 56: Count -R /tmp/eStjVEae7_/view.001.fogn -r grp2 (SAM input).. ok 265s 265s 57: Filter -R /tmp/eStjVEae7_/view.001.fogn -r grp2 (BAM input).. ok 265s 265s 58: Count -R /tmp/eStjVEae7_/view.001.fogn -r grp2 (BAM input).. ok 265s 265s 59: Filter -R /tmp/eStjVEae7_/view.001.fogn -r grp2 (CRAM input).. ok 265s 265s 60: Count -R /tmp/eStjVEae7_/view.001.fogn -r grp2 (CRAM input).. ok 265s 265s 61: Filter -r grp2 -R /tmp/eStjVEae7_/view.001.fogn (SAM input).. ok 265s 265s 62: Count -r grp2 -R /tmp/eStjVEae7_/view.001.fogn (SAM input).. ok 265s 265s 63: Filter -r grp2 -R /tmp/eStjVEae7_/view.001.fogn (BAM input).. ok 265s 265s 64: Count -r grp2 -R /tmp/eStjVEae7_/view.001.fogn (BAM input).. ok 265s 266s 65: Filter -r grp2 -R /tmp/eStjVEae7_/view.001.fogn (CRAM input).. ok 266s 266s 66: Count -r grp2 -R /tmp/eStjVEae7_/view.001.fogn (CRAM input).. ok 266s 266s 67: Filter -N /tmp/eStjVEae7_/view.001.forn (SAM input) .. ok 266s 266s 68: Count -N /tmp/eStjVEae7_/view.001.forn (SAM input) .. ok 266s 266s 69: Filter -N /tmp/eStjVEae7_/view.001.forn (BAM input) .. ok 266s 266s 70: Count -N /tmp/eStjVEae7_/view.001.forn (BAM input) .. ok 266s 266s 71: Filter -N /tmp/eStjVEae7_/view.001.forn (CRAM input) .. ok 266s 266s 72: Count -N /tmp/eStjVEae7_/view.001.forn (CRAM input) .. ok 266s 266s 73: Filter -d BC (SAM input) .. ok 266s 266s 74: Count -d BC (SAM input) .. ok 266s 266s 75: Filter -d BC (BAM input) .. ok 266s 266s 76: Count -d BC (BAM input) .. ok 266s 266s 77: Filter -d BC (CRAM input) .. ok 266s 266s 78: Count -d BC (CRAM input) .. ok 266s 266s 79: Filter -d BC:TGCA (SAM input) .. ok 266s 266s 80: Count -d BC:TGCA (SAM input) .. ok 266s 266s 81: Filter -d BC:TGCA (BAM input) .. ok 266s 266s 82: Count -d BC:TGCA (BAM input) .. ok 266s 267s 83: Filter -d BC:TGCA (CRAM input) .. ok 267s 267s 84: Count -d BC:TGCA (CRAM input) .. ok 267s 267s 85: Filter -D BC:/tmp/eStjVEae7_/view.001.fobc (SAM input) .. ok 267s 267s 86: Count -D BC:/tmp/eStjVEae7_/view.001.fobc (SAM input) .. ok 267s 267s 87: Filter -D BC:/tmp/eStjVEae7_/view.001.fobc (BAM input) .. ok 267s 267s 88: Count -D BC:/tmp/eStjVEae7_/view.001.fobc (BAM input) .. ok 267s 267s 89: Filter -D BC:/tmp/eStjVEae7_/view.001.fobc (CRAM input) .. ok 267s 267s 90: Count -D BC:/tmp/eStjVEae7_/view.001.fobc (CRAM input) .. ok 267s 267s 91: Filter -D BC:/tmp/eStjVEae7_/view.001.fobc -d BC:TGCA (SAM input).. ok 267s 267s 92: Count -D BC:/tmp/eStjVEae7_/view.001.fobc -d BC:TGCA (SAM input).. ok 267s 267s 93: Filter -D BC:/tmp/eStjVEae7_/view.001.fobc -d BC:TGCA (BAM input).. ok 267s 267s 94: Count -D BC:/tmp/eStjVEae7_/view.001.fobc -d BC:TGCA (BAM input).. ok 267s 267s 95: Filter -D BC:/tmp/eStjVEae7_/view.001.fobc -d BC:TGCA (CRAM input).. ok 267s 267s 96: Count -D BC:/tmp/eStjVEae7_/view.001.fobc -d BC:TGCA (CRAM input).. ok 267s 267s 97: Filter -d BC:TGCA -D BC:/tmp/eStjVEae7_/view.001.fobc (SAM input).. ok 267s 267s 98: Count -d BC:TGCA -D BC:/tmp/eStjVEae7_/view.001.fobc (SAM input).. ok 267s 267s 99: Filter -d BC:TGCA -D BC:/tmp/eStjVEae7_/view.001.fobc (BAM input).. ok 267s 267s 100: Count -d BC:TGCA -D BC:/tmp/eStjVEae7_/view.001.fobc (BAM input).. ok 267s 268s 101: Filter -d BC:TGCA -D BC:/tmp/eStjVEae7_/view.001.fobc (CRAM input).. ok 268s 268s 102: Count -d BC:TGCA -D BC:/tmp/eStjVEae7_/view.001.fobc (CRAM input).. ok 268s 268s 103: Filter -D RG:/tmp/eStjVEae7_/view.001.fogn (SAM input) .. ok 268s 268s 104: Count -D RG:/tmp/eStjVEae7_/view.001.fogn (SAM input) .. ok 268s 268s 105: Filter -D RG:/tmp/eStjVEae7_/view.001.fogn (BAM input) .. ok 268s 268s 106: Count -D RG:/tmp/eStjVEae7_/view.001.fogn (BAM input) .. ok 268s 268s 107: Filter -D RG:/tmp/eStjVEae7_/view.001.fogn (CRAM input).. ok 268s 268s 108: Count -D RG:/tmp/eStjVEae7_/view.001.fogn (CRAM input) .. ok 268s 268s 109: Filter -d NE:TGCA (SAM input) .. ok 268s 268s 110: Count -d NE:TGCA (SAM input) .. ok 268s 268s 111: Filter -d NE:TGCA (BAM input) .. ok 268s 268s 112: Count -d NE:TGCA (BAM input) .. ok 268s 268s 113: Filter -d NE:TGCA (CRAM input) .. ok 268s 268s 114: Count -d NE:TGCA (CRAM input) .. ok 268s 268s 115: Filter -d TGCA (SAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test115.sam -h -d TGCA /tmp/eStjVEae7_/view.001.sam --no-PG 268s 268s 268s .. expected failure 268s 268s 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" 268s samtools view: Invalid "tag:value" option: "TGCA" 268s Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -d TGCA /tmp/eStjVEae7_/view.001.sam --no-PG 268s 268s 268s .. expected failure 268s 268s 117: Filter -d TGCA (BAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test117.sam -h -d TGCA /tmp/eStjVEae7_/view.test001.bam --no-PG 268s 268s 268s .. expected failure 268s 268s 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 268s Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -d TGCA /tmp/eStjVEae7_/view.test001.bam --no-PG 268s 268s 268s .. expected failure 268s 268s 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" 268s Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test119.sam -h -d TGCA /tmp/eStjVEae7_/view.test006.cram --no-PG 268s 268s 268s .. expected failure 268s 268s 120: Count -d TGCA (CRAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -d TGCA /tmp/eStjVEae7_/view.test006.cram --no-PG 268s 268s 268s .. expected failure 268s 268s 121: Filter -D BClong:/tmp/eStjVEae7_/view.001.fobc (SAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test121.sam -h -D BClong:/tmp/eStjVEae7_/view.001.fobc /tmp/eStjVEae7_/view.001.sam --no-PG 268s 268s 268s .. expected failure 268s 268s 122: Count -D BClong:/tmp/eStjVEae7_/view.001.fobc (SAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -D BClong:/tmp/eStjVEae7_/view.001.fobc /tmp/eStjVEae7_/view.001.sam --no-PG 268s 268s 268s .. expected failure 268s 268s 123: Filter -D BClong:/tmp/eStjVEae7_/view.001.fobc (BAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test123.sam -h -D BClong:/tmp/eStjVEae7_/view.001.fobc /tmp/eStjVEae7_/view.test001.bam --no-PG 268s 268s 268s .. expected failure 268s 268s 124: Count -D BClong:/tmp/eStjVEae7_/view.001.fobc (BAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -D BClong:/tmp/eStjVEae7_/view.001.fobc /tmp/eStjVEae7_/view.test001.bam --no-PG 268s 268s 268s .. expected failure 268s 268s 125: Filter -D BClong:/tmp/eStjVEae7_/view.001.fobc (CRAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test125.sam -h -D BClong:/tmp/eStjVEae7_/view.001.fobc /tmp/eStjVEae7_/view.test006.cram --no-PG 268s 268s 268s .. expected failure 268s 268s 126: Count -D BClong:/tmp/eStjVEae7_/view.001.fobc (CRAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -D BClong:/tmp/eStjVEae7_/view.001.fobc /tmp/eStjVEae7_/view.test006.cram --no-PG 268s 268s 268s .. expected failure 268s 268s 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/eStjVEae7_/view.001.sam --no-PG 268s 268s 268s .. expected failure 268s 268s 128: Count -d BC:ACGT -d RG:grp2 (SAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/eStjVEae7_/view.001.sam --no-PG 268s 268s 268s .. expected failure 268s 268s 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 268s samtools view: Invalid "tag:value" option: "TGCA" 268s samtools view: Invalid "tag:file" option: "BClong:/tmp/eStjVEae7_/view.001.fobc" 268s samtools view: Invalid "tag:file" option: "BClong:/tmp/eStjVEae7_/view.001.fobc" 268s samtools view: Invalid "tag:file" option: "BClong:/tmp/eStjVEae7_/view.001.fobc" 268s samtools view: Invalid "tag:file" option: "BClong:/tmp/eStjVEae7_/view.001.fobc" 268s samtools view: Invalid "tag:file" option: "BClong:/tmp/eStjVEae7_/view.001.fobc" 268s samtools view: Invalid "tag:file" option: "BClong:/tmp/eStjVEae7_/view.001.fobc" 268s samtools view: Different tag "BC" was specified before: "RG:grp2" 268s samtools view: Different tag "BC" was specified before: "RG:grp2" 268s samtools view: Different tag "BC" was specified before: "RG:grp2" 268s samtools view: Different tag "BC" was specified before: "RG:grp2" 268s samtools view: Different tag "BC" was specified before: "RG:grp2" 268s Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/eStjVEae7_/view.test001.bam --no-PG 268s 268s 268s .. expected failure 268s 268s 130: Count -d BC:ACGT -d RG:grp2 (BAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/eStjVEae7_/view.test001.bam --no-PG 268s 268s 268s .. expected failure 268s 268s 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -o /tmp/eStjVEae7_/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/eStjVEae7_/view.test006.cram --no-PG 268s 268s 268s .. expected failure 268s 268s 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) Failed command: 268s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/eStjVEae7_/view.test006.cram --no-PG 268s 268s 268s .. expected failure 268s 268s 133: Filter -d NM:13 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" 268s .. ok 268s 268s 134: Count -d NM:13 (SAM input) .. ok 268s 268s 135: Filter -d NM:13 (BAM input) .. ok 268s 268s 136: Count -d NM:13 (BAM input) .. ok 268s 269s 137: Filter -d NM:13 (CRAM input) .. ok 269s 269s 138: Count -d NM:13 (CRAM input) .. ok 269s 269s 139: Filter -d ab:z (SAM input) .. ok 269s 269s 140: Count -d ab:z (SAM input) .. ok 269s 269s 141: Filter -d ab:z (BAM input) .. ok 269s 269s 142: Count -d ab:z (BAM input) .. ok 269s 269s 143: Filter -d ab:z (CRAM input) .. ok 269s 269s 144: Count -d ab:z (CRAM input) .. ok 269s 269s 145: Filter -l Library 2 (SAM input) .. ok 269s 269s 146: Count -l Library 2 (SAM input) .. ok 269s 270s 147: Filter -l Library 2 (BAM input) .. ok 270s 270s 148: Count -l Library 2 (BAM input) .. ok 270s 270s 149: Filter -l Library 2 (CRAM input) .. ok 270s 270s 150: Count -l Library 2 (CRAM input) .. ok 270s 270s 151: Filter -l Library 3 (SAM input) .. ok 270s 270s 152: Count -l Library 3 (SAM input) .. ok 270s 270s 153: Filter -l Library 3 (BAM input) .. ok 270s 270s 154: Count -l Library 3 (BAM input) .. ok 270s 270s 155: Filter -l Library 3 (CRAM input) .. ok 270s 270s 156: Count -l Library 3 (CRAM input) .. ok 270s 270s 157: Filter -q 50 (SAM input) .. ok 270s 270s 158: Count -q 50 (SAM input) .. ok 270s 270s 159: Filter -q 50 (BAM input) .. ok 270s 270s 160: Count -q 50 (BAM input) .. ok 270s 271s 161: Filter -q 50 (CRAM input) .. ok 271s 271s 162: Count -q 50 (CRAM input) .. ok 271s 271s 163: Filter -q 99 (SAM input) .. ok 271s 271s 164: Count -q 99 (SAM input) .. ok 271s 271s 165: Filter -q 99 (BAM input) .. ok 271s 271s 166: Count -q 99 (BAM input) .. ok 271s 271s 167: Filter -q 99 (CRAM input) .. ok 271s 271s 168: Count -q 99 (CRAM input) .. ok 271s 271s 169: Filter -q 100 (SAM input) .. ok 271s 271s 170: Count -q 100 (SAM input) .. ok 271s 271s 171: Filter -q 100 (BAM input) .. ok 271s 271s 172: Count -q 100 (BAM input) .. ok 271s 271s 173: Filter -q 100 (CRAM input) .. ok 271s 271s 174: Count -q 100 (CRAM input) .. ok 271s 271s 175: Filter -x fa (SAM input) .. ok 271s 271s 176: Count -x fa (SAM input) .. ok 271s 271s 177: Filter -x fa (BAM input) .. ok 271s 271s 178: Count -x fa (BAM input) .. ok 271s 272s 179: Filter -x fa (CRAM input) .. ok 272s 272s 180: Count -x fa (CRAM input) .. ok 272s 272s 181: Filter -x fa -x ha (SAM input) .. ok 272s 272s 182: Count -x fa -x ha (SAM input) .. ok 272s 272s 183: Filter -x fa -x ha (BAM input) .. ok 272s 272s 184: Count -x fa -x ha (BAM input) .. ok 272s 272s 185: Filter -x fa -x ha (CRAM input) .. ok 272s 272s 186: Count -x fa -x ha (CRAM input) .. ok 272s 272s 187: Filter -x fa,ha (SAM input) .. ok 272s 272s 188: Count -x fa,ha (SAM input) .. ok 272s 272s 189: Filter -x fa,ha (BAM input) .. ok 272s 272s 190: Count -x fa,ha (BAM input) .. ok 272s 276s 191: Filter -x fa,ha (CRAM input) .. ok 276s 276s 192: Count -x fa,ha (CRAM input) .. ok 276s 276s 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 276s 276s 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 276s 276s 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 276s 276s 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 276s 276s 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 276s 276s 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 276s 276s 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 276s 276s 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 276s 276s 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 276s 276s 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 276s 276s 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 276s 276s 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 276s 276s 205: Filter -x fa -r grp2 (SAM input) .. ok 276s 276s 206: Count -x fa -r grp2 (SAM input) .. ok 276s 276s 207: Filter -x fa -r grp2 (BAM input) .. ok 276s 276s 208: Count -x fa -r grp2 (BAM input) .. ok 276s 276s 209: Filter -x fa -r grp2 (CRAM input) .. ok 276s 276s 210: Count -x fa -r grp2 (CRAM input) .. ok 276s 276s 211: Filter -x RG -r grp2 (SAM input) .. ok 276s 276s 212: Count -x RG -r grp2 (SAM input) .. ok 276s 276s 213: Filter -x RG -r grp2 (BAM input) .. ok 276s 276s 214: Count -x RG -r grp2 (BAM input) .. ok 276s 276s 215: Filter -x RG -r grp2 (CRAM input) .. ok 276s 276s 216: Count -x RG -r grp2 (CRAM input) .. ok 276s 276s 217: Filter -m 10 (SAM input) .. ok 276s 276s 218: Count -m 10 (SAM input) .. ok 276s 276s 219: Filter -m 10 (BAM input) .. ok 276s 276s 220: Count -m 10 (BAM input) .. ok 276s 276s 221: Filter -m 10 (CRAM input) .. ok 276s 276s 222: Count -m 10 (CRAM input) .. ok 276s 276s 223: Filter -m 11 (SAM input) .. ok 276s 276s 224: Count -m 11 (SAM input) .. ok 276s 276s 225: Filter -m 11 (BAM input) .. ok 276s 276s 226: Count -m 11 (BAM input) .. ok 276s 276s 227: Filter -m 11 (CRAM input) .. ok 276s 276s 228: Count -m 11 (CRAM input) .. ok 276s 276s 229: Filter -m 15 (SAM input) .. ok 276s 276s 230: Count -m 15 (SAM input) .. ok 276s 276s 231: Filter -m 15 (BAM input) .. ok 276s 276s 232: Count -m 15 (BAM input) .. ok 276s 276s 233: Filter -m 15 (CRAM input) .. ok 276s 276s 234: Count -m 15 (CRAM input) .. ok 276s 276s 235: Filter -m 16 (SAM input) .. ok 276s 276s 236: Count -m 16 (SAM input) .. ok 276s 276s 237: Filter -m 16 (BAM input) .. ok 276s 276s 238: Count -m 16 (BAM input) .. ok 276s 276s 239: Filter -m 16 (CRAM input) .. ok 276s 277s 240: Count -m 16 (CRAM input) .. ok 277s 277s 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 277s 277s 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 277s 277s 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 277s 277s 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 277s 277s 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 277s 277s 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 277s 277s 247: Filter -e [BC] (SAM input) .. ok 277s 277s 248: Count -e [BC] (SAM input) .. ok 277s 277s 249: Filter -e [BC] (BAM input) .. ok 277s 277s 250: Count -e [BC] (BAM input) .. ok 277s 278s 251: Filter -e [BC] (CRAM input) .. ok 278s 278s 252: Count -e [BC] (CRAM input) .. ok 278s 278s 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 278s 278s 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 278s 278s 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 278s 278s 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 278s 278s 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 278s 279s 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 279s 279s 259: Filter -e mapq >= 50 (SAM input) .. ok 279s 279s 260: Count -e mapq >= 50 (SAM input) .. ok 279s 279s 261: Filter -e mapq >= 50 (BAM input) .. ok 279s 279s 262: Count -e mapq >= 50 (BAM input) .. ok 279s 279s 263: Filter -e mapq >= 50 (CRAM input) .. ok 279s 279s 264: Count -e mapq >= 50 (CRAM input) .. ok 279s 279s 265: Filter -e mapq >= 99 (SAM input) .. ok 279s 279s 266: Count -e mapq >= 99 (SAM input) .. ok 279s 279s 267: Filter -e mapq >= 99 (BAM input) .. ok 279s 279s 268: Count -e mapq >= 99 (BAM input) .. ok 279s 280s 269: Filter -e mapq >= 99 (CRAM input) .. ok 280s 280s 270: Count -e mapq >= 99 (CRAM input) .. ok 280s 280s 271: Filter -e mapq >= 100 (SAM input) .. ok 280s 280s 272: Count -e mapq >= 100 (SAM input) .. ok 280s 280s 273: Filter -e mapq >= 100 (BAM input) .. ok 280s 280s 274: Count -e mapq >= 100 (BAM input) .. ok 280s 280s 275: Filter -e mapq >= 100 (CRAM input) .. ok 280s 281s 276: Count -e mapq >= 100 (CRAM input) .. ok 281s 281s 277: 1bp reads file SAM -> BAM -> SAM .. ok 281s 282s 278: 1bp reads file SAM -> CRAM -> SAM .. ok 282s 282s 278: Region Z (BAM input) .. ok 282s 282s 279: Count Z (BAM input) .. ok 282s 282s 280: Region Z (CRAM input) .. ok 282s 282s 281: Count Z (CRAM input) .. ok 282s 282s 282: Region Z:30 (BAM input) .. ok 282s 282s 283: Count Z:30 (BAM input) .. ok 282s 282s 284: Region Z:30 (CRAM input) .. ok 282s 282s 285: Count Z:30 (CRAM input) .. ok 282s 282s 286: Region Z:20-40 (BAM input) .. ok 282s 282s 287: Count Z:20-40 (BAM input) .. ok 282s 283s 288: Region Z:20-40 (CRAM input) .. ok 283s 283s 289: Count Z:20-40 (CRAM input) .. ok 283s 283s 290: Region ref1 (BAM input) .. ok 283s 283s 291: Count ref1 (BAM input) .. ok 283s 283s 292: Region ref1 (CRAM input) .. ok 283s 283s 293: Count ref1 (CRAM input) .. ok 283s 283s 294: Region ref1:15 (BAM input) .. ok 283s 283s 295: Count ref1:15 (BAM input) .. ok 283s 283s 296: Region ref1:15 (CRAM input) .. ok 283s 283s 297: Count ref1:15 (CRAM input) .. ok 283s 283s 298: Region ref1:15-45 (BAM input) .. ok 283s 283s 299: Count ref1:15-45 (BAM input) .. ok 283s 284s 300: Region ref1:15-45 (CRAM input) .. ok 284s 284s 301: Count ref1:15-45 (CRAM input) .. ok 284s 284s 302: Region ref1:15-45 ref2 (BAM input) .. ok 284s 284s 303: Count ref1:15-45 ref2 (BAM input) .. ok 284s 284s 304: Region ref1:15-45 ref2 (CRAM input) .. ok 284s 284s 305: Count ref1:15-45 ref2 (CRAM input) .. ok 284s 284s 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 284s 284s 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 284s 284s 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 284s 284s 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 284s 284s 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 284s 284s 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 284s 285s 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 285s 285s 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 285s 285s 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 285s 285s 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 285s 285s 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 285s 285s 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 285s 285s 318: Region -f 128 ref1 (BAM input) .. ok 285s 285s 319: Count -f 128 ref1 (BAM input) .. ok 285s 286s 320: Region -f 128 ref1 (CRAM input) .. ok 286s 286s 321: Count -f 128 ref1 (CRAM input) .. ok 286s 286s 322: Region -q 50 ref1:15-45 (BAM input) .. ok 286s 286s 323: Count -q 50 ref1:15-45 (BAM input) .. ok 286s 286s 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 286s 286s 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 286s 286s 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 286s 286s 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 286s 286s 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 286s 286s 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 286s 286s 330: Region * (BAM input) .. ok 286s 286s 331: Count * (BAM input) .. ok 286s 286s 332: Region * (CRAM input) .. ok 286s 286s 333: Count * (CRAM input) .. ok 286s 286s 334: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 286s 286s 335: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 286s 287s 336: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 287s 287s 337: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 287s 287s 338: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 287s 287s 339: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 287s 287s 340: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 287s 287s 341: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 287s 287s 342: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 287s 287s 343: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 287s 287s 344: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 287s 287s 345: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 287s 287s 346: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 287s 287s 347: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 287s 288s 348: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 288s 288s 349: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 288s 288s 350: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 288s 288s 351: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 288s 288s 352: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 288s 288s 353: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 288s 288s 354: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 288s 288s 355: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 288s 288s 356: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 288s 288s 357: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 288s 288s 358: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 288s 288s 359: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 288s 289s 360: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 289s 289s 361: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 289s 289s 362: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 289s 289s 363: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 289s 289s 364: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 289s 289s 365: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 289s 289s 366: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 289s 289s 367: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 289s 290s 368: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 290s 290s 369: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 290s 290s 370: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 290s 290s 371: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 290s 296s 372: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 296s 296s 373: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 296s 296s 374: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 296s 296s 375: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 296s 296s 376: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 296s 296s 377: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 296s 296s 378: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 296s 296s 379: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 296s 296s 380: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 296s 296s 381: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 296s 296s 382: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 296s 296s 383: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 296s 296s 384: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 296s 296s 385: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 296s 296s 386: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 296s 296s 387: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 296s 296s 388: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 296s 296s 389: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 296s 296s 390: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 296s 296s 391: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 296s 296s 392: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 296s 296s 393: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 296s 296s 394: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 296s 296s 395: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 296s 296s 396: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 296s 296s 397: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 296s 296s 398: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 296s 296s 399: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 296s 296s 400: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 296s 296s 401: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 296s 296s 402: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 296s 296s 403: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 296s 296s 404: Region -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 296s 296s 405: Count -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 296s 296s 406: -L with nested regions .. ok 296s 296s 407: Make BAM with no M5/UR tags .. ok 296s 296s 408: Add @SQ with -t (SAM -> SAM) .. ok 296s 296s 409: Add @SQ with -T (SAM -> SAM) .. ok 296s 296s 410: Add @SQ with -t (BAM -> SAM) .. ok 296s 296s 411: Add @SQ with -T (BAM -> SAM) .. ok 296s 296s 412: Add @SQ with -t (SAM -> BAM) .. ok 296s 296s 413: Add @SQ with -T (SAM -> BAM) .. ok 296s 296s 414: Add @SQ with -t (BAM -> BAM) .. ok 296s 296s 415: Add @SQ with -T (BAM -> BAM) .. ok 296s 296s 416: Add @SQ with -t (SAM -> CRAM) .. ok 296s 296s 417: Add @SQ with -T (SAM -> CRAM) .. ok 296s 296s 418: Add @SQ with -t (BAM -> CRAM) .. ok 296s 296s 419: Add @SQ with -T (BAM -> CRAM) .. ok 296s 296s 420: Make CRAM with no UR field .. ok 296s 296s 421: Decoding CRAM with no UR field via -T .. ok 296s 296s 422: CIGAR B-operator removal .. ok 296s 296s 423: Big SAM -> BAM .. ok 296s 296s 424: Big SAM -> BAM (2 threads) .. ok 296s 296s 425: Big SAM -> BAM (4 threads) .. ok 296s 297s 426: Big SAM -> CRAM .. ok 297s 298s 427: Big SAM -> CRAM (2 threads) .. ok 298s 299s 428: Big SAM -> CRAM (4 threads) .. ok 299s 300s 429: Subsample 0.2 (SAM input) ............ ok 300s 301s 430: Subsample 0.5 (SAM input) ............ ok 301s 303s 431: Subsample 0.8 (SAM input) ............ ok 303s 303s 432: Subsample 0.2 (BAM input) ............ ok 303s 304s 433: Subsample 0.5 (BAM input) ............ ok 304s 305s 434: Subsample 0.8 (BAM input) ............ ok 305s 309s 435: Subsample 0.2 (CRAM input) ............ ok 309s 314s 436: Subsample 0.5 (CRAM input) ............ ok 314s 319s 437: Subsample 0.8 (CRAM input) ............ ok 319s 319s 438: SAM add PG .. ok 319s 319s 439: Unset dup flag, remove dt and do tags .. ok 319s 319s 440: Unmap dup flagged reads. .. ok 319s 319s 441: Unmap dup flagged reads. .. ok 319s 320s 442: fetch pairs .. ok 320s 320s 443: fetch pairs .. ok 320s 320s 444: fetch pairs .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -h 0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -h 1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -h 5 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -h 29 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -h 30 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -n 0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -n 1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -n 5 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_head: 320s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools head -h 5 -n 5 < /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.sam 320s .. ok 320s 320s test_cat: 320s Generating test data file .................. done 320s Generate BAM file #1 .. ok 320s 320s Generate BAM region file #1 .. ok 320s 320s Generate CRAM file #1 .. ok 320s 320s Generating test data file .................. done 320s Generate BAM file #2 .. ok 320s 320s Generate BAM region file #2 .. ok 320s 321s Generate CRAM file #2 .. ok 321s 321s Generating test data file .................. done 321s Generate BAM file #3 .. ok 321s 321s Generate BAM region file #3 .. ok 321s 321s Generate CRAM file #3 .. ok 321s 321s Generating test data file .................. done 321s Generate BAM file #4 .. ok 321s 321s Generate BAM region file #4 .. ok 321s 321s Generate CRAM file #4 .. ok 321s 322s 1: cat BAM files .. ok 322s 322s 2: cat recompressed BAM files .. ok 322s 322s 3: cat CRAM files .. ok 322s 324s 4: cat CRAM subregion files .. ok 324s 324s 5: cat BAM files to stdout .. ok 324s 324s 6: cat recompressed BAM files to stdout .. ok 324s 324s 7: cat CRAM files to stdout .. ok 324s 326s 8: cat CRAM subregion files to stdout .. ok 326s 326s 9: cat CRAM part 1/2 .. ok 326s 326s 9: cat CRAM part 2/2 .. ok 326s 327s 9: cat CRAM parts 1/2 + 2/2 .. ok 327s 327s 10: cat BAM files with new header .. ok 327s 327s 11: cat recompressed BAM files with new header .. ok 327s 327s 12: cat CRAM files with new header .. ok 327s 327s test_import: 327s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/0.fq 327s .. ok 327s 327s test_import: 327s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/0.fq 327s .. ok 327s 327s test_import: 327s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq 327s .. ok 327s 327s test_import: 327s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq 327s .. ok 327s 327s test_import: 327s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq 327s .. ok 327s 327s test_import: 327s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq 327s .. ok 327s 327s test_import: 327s /tmp/autopkgtest.JB23VD/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.JB23VD/autopkgtest_tmp/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq 327s .. ok 327s 327s test_import: 327s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT,MD,ia -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/import/2.interleaved.fq -T "" 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/import/3.interleaved.fq -i 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T "*" 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T "" 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/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 328s .. ok 328s 328s test_import: 328s /tmp/autopkgtest.JB23VD/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 328s .. ok 328s 328s test_bam2fq: 328s Generate BAM file .. ok 328s 328s Generate CRAM file .. ok 328s 328s 1: fastq (SAM input) .. ok 328s 328s 2: fastq -n (SAM input) .. ok 328s 328s 3: fastq (BAM input) .. ok 328s 328s 4: fastq -n (BAM input) .. ok 328s 328s 5: fastq (CRAM input) .. ok 328s 328s 6: fastq -n (CRAM input) .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.002.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.003.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.004.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.004.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.010.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -t -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -t -T MD,ia -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.004.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.703.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fasta -N -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -s /tmp/eStjVEae7_/bam2fq.discard.s.fq -0 /tmp/eStjVEae7_/bam2fq.discard.0.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.013.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq --index-format 'i8n1i8' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.014.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/au[M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s [M::bam2fq_mainloop] discarded 0 singletons 328s [M::bam2fq_mainloop] processed 36 reads 328s topkgtest_tmp/samtools fastq -N -T '' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -t -T '*' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -T '*' -d MD:10 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -T '*' -d NM:0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -N -T '*' -d ia /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -d NM:13 -d NM:14 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -D NM:test/dat/bam2fq.NM-D /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -D MD:test/dat/bam2fq.MD-D /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s Generate BAM file (2 threads) .. ok 328s 328s Generate CRAM file (2 threads) .. ok 328s 328s 1: fastq (SAM input) (2 threads) .. ok 328s 328s 2: fastq -n (SAM input) (2 threads) .. ok 328s 328s 3: fastq (BAM input) (2 threads) .. ok 328s 328s 4: fastq -n (BAM input) (2 threads) .. ok 328s 328s 5: fastq (CRAM input) (2 threads) .. ok 328s 328s 6: fastq -n (CRAM input) (2 threads) .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.002.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.003.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.004.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.004.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.010.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -t -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T MD,ia -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.004.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -i --index-format 'i*i*' -s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.005.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.703.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fasta -@ 2 -N -1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -s /tmp/eStjVEae7_/bam2fq.discard.s.fq -0 /tmp/eStjVEae7_/bam2fq.discard.0.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.013.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.014.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -T '' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T '*' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d MD:10 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d NM:0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d ia /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 328s .. ok 328s 328s test_bam2fq: 328s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -d NM:13 -d NM:14 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 329s .. ok 329s 329s test_bam2fq: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 329s .. ok 329s 329s test_bam2fq: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/bam2fq.001.sam 329s .. ok 329s 329s test_depad: 329s Generate BAM file .. ok 329s 329s depad (SAM input) .. ok 329s 329s depad -s (SAM input) .. ok 329s 329s depad -u (SAM input) .. ok 329s 329s depad -1 (SAM input) .. ok 329s 329s depad (BAM input) .. ok 329s 329s depad -s (BAM input) .. ok 329s 329s depad -u (BAM input) .. ok 329s 329s depad -1 (BAM input) .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/1_map_cigar_large.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/4_X_cigar_full_seq.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/5_insert_cigar_large.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa -i 0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/7_supp.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/7_supp_large.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/8_secondary.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/8_secondary_large.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/10_map_cigar.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -t /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -g 4 -t /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -g 4 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/13_barcodes_ok.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 329s 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 329s .. expected failure 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 329s 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 329s .. expected failure 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 329s 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 329s .. expected failure 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -I s1 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -I grp2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -I grp3 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -I Sample /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 329s .. ok 329s 329s test_stats: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/mpileup/ce.fa /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/stat/15.big_del.sam | tail -n+4 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_c.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_c.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -s 1 -O sam -b /tmp/qLpgcJpF1V - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -r -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_c.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -cp -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -o - -s 1 -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_c.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/eStjVEae7_/merge.tag.1.bam /tmp/eStjVEae7_/merge.tag.2.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/eStjVEae7_/merge.tag.3.bam /tmp/eStjVEae7_/merge.tag.4.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge --no-PG -O SAM - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge --no-PG -O SAM -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/merge.bed - /tmp/eStjVEae7_/merge.bed.1.bam /tmp/eStjVEae7_/merge.bed.2.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge --no-PG -r -O SAM - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge --no-PG -O SAM --template-coordinate - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/test_template_coordinate.1.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/test_template_coordinate.2.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_c.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_c.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam -b /tmp/rg9Br58mqU - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -r -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_c.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -cp -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 329s .. ok 329s 329s test_merge: 329s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -o - -s 1 -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_c.sam 329s .. ok 329s 330s test_merge: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/eStjVEae7_/merge.tag.1.bam /tmp/eStjVEae7_/merge.tag.2.bam 330s .. ok 330s 330s test_merge: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/eStjVEae7_/merge.tag.3.bam /tmp/eStjVEae7_/merge.tag.4.bam 330s .. ok 330s 330s test_merge: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 330s .. ok 330s 330s test_merge: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/merge.bed - /tmp/eStjVEae7_/merge.bed.1.bam /tmp/eStjVEae7_/merge.bed.2.bam 330s .. ok 330s 330s test_merge: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 --no-PG -r -O SAM - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 330s .. ok 330s 330s test_merge: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/test_template_coordinate.1.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/merge/test_template_coordinate.2.sam 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eStjVEae7_/sortout 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eStjVEae7_/sortout.bam 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eStjVEae7_/sorttmp 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -N -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/sort_name_input_1.sam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -t RG -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -n -t RG -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -t AS -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -t FI -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort --template-coordinate -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -M -K10 -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -M -K10 -I /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -MH -K10 -I /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eStjVEae7_/sortout 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eStjVEae7_/sortout.bam 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eStjVEae7_/sorttmp 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -N -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/sort_name_input_1.sam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -t RG -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -n -t RG -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -t AS -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -t FI -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 --template-coordinate -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -I /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 330s .. ok 330s 330s test_sort: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -@ 2 -MH -K10 -I /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 330s .. ok 330s 330s test_collate: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate --output-fmt=sam -O /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam 330s .. ok 330s 330s test_collate: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam 330s .. ok 330s 330s test_collate: 330s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/collate2.tmp 331s .. ok 331s 331s test_collate: 331s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate --output-fmt=sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/collate3.tmp 331s .. ok 331s 331s test_collate: 331s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate --output-fmt=sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/1_fast_collate.sam 331s .. ok 331s 331s test_collate: 331s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate --output-fmt=sam -f -r 4 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 331s .. ok 331s 331s test_collate: 331s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -O /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam 332s .. ok 332s 332s test_collate: 332s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam 333s .. ok 333s 333s test_collate: 333s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/collate2.tmp 334s .. ok 334s 334s test_collate: 334s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/collate3.tmp 335s .. ok 335s 335s test_collate: 335s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/1_fast_collate.sam 336s .. ok 336s 336s test_collate: 336s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f -r 4 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 337s 337s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 337s 337s .. expected failure 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/5_ct.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/sanitize.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_ok+.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_ok-.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_draft.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_not_updated.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_not_updated_noML.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_not_updated_noMN.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_bad_MN.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_MN_only.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_ML_only.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_ML_wrong_len.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_noseq.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_bounds.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 337s 337s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 337s 337s .. expected failure 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/5_ct.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/sanitize.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_ok+.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_ok-.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_draft.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_not_updated.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_not_updated_noML.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_not_updated_noMN.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_bad_MN.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_MN_only.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_ML_only.sam - 337s .. ok 337s 337s test_fixmate: 337s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_ML_wrong_len.sam - 338s .. ok 338s 338s test_fixmate: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_noseq.sam - 338s .. ok 338s 338s test_fixmate: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/fixmate/mod_bounds.sam - 338s .. ok 338s 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools calmd -uAr /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.ref.fa 338s .. ok 338s 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools calmd -@ 2 -uAr /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.ref.fa 338s .. ok 338s 338s test_idxstat: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam 338s .. ok 338s 338s test_idxstat: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.cram 338s .. ok 338s 338s test_idxstat: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.sam 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck -v /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 338s .. ok 338s 338s test_quickcheck: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools quickcheck -uv /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 338s .. ok 338s 338s test_reheader: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 338s .. ok 338s 338s test_reheader: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 338s .. ok 338s 338s test_reheader: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 338s .. ok 338s 338s test_reheader: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram && /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' 338s .. ok 338s 338s test_reheader: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram && /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' 338s .. ok 338s 338s test_reheader: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 338s .. ok 338s 338s test_reheader: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/1_fixup.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -O sam -m orphan_only /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -O sam -R '1#9' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/1_fixup.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/1_fixup.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/1_fixup.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/1_fixup.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m orphan_only /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -R '1#9' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/1_fixup.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/1_fixup.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 338s .. ok 338s 338s test_addrprg: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/addrprg/1_fixup.sam 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/1_name_sort.sam - 338s 338s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 338s 338s 338s .. expected failure 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/2_bad_order.sam - 338s 338s ERR: samtools markdup: error, not in coordinate sorted order. 338s 338s 338s .. expected failure 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 338s 338s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 338s 338s samtools markdup: error, unable to assign pair hash key. 338s 338s 338s .. expected failure 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 338s 338s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 338s 338s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 338s 338s 338s .. expected failure 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/5_markdup.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -O sam -r --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/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.JB23VD/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/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.JB23VD/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/17_read_group.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/1_name_sort.sam - 338s 338s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 338s 338s 338s .. expected failure 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/2_bad_order.sam - 338s 338s ERR: samtools markdup: error, not in coordinate sorted order. 338s 338s 338s .. expected failure 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 338s 338s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 338s 338s samtools markdup: error, unable to assign pair hash key. 338s 338s 338s .. expected failure 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 338s 338s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 338s 338s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 338s 338s 338s .. expected failure 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/5_markdup.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -O sam -r --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 338s .. ok 338s 338s test_markdup: 338s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 339s .. ok 339s 339s test_markdup: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 339s .. ok 339s 339s test_markdup: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 339s .. ok 339s 339s test_markdup: 339s /tmp/autopkgtest.JB23VD/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.JB23VD/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 339s .. ok 339s 339s test_markdup: 339s /tmp/autopkgtest.JB23VD/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.JB23VD/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 339s .. ok 339s 339s test_markdup: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/17_read_group.sam - 339s .. ok 339s 339s test_markdup: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 339s .. ok 339s 339s test_bedcov: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools bedcov /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bedcov/bedcov.bam 339s .. ok 339s 339s test_bedcov: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools bedcov -j /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bedcov/bedcov.bam 339s .. ok 339s 339s test_bedcov: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools bedcov -g512 -G2048 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bedcov/bedcov.bam 339s .. ok 339s 339s test_bedcov: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools bedcov -c /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/bedcov/bedcov.bam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -p 5 -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split --output-fmt sam -d RG -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split --output-fmt sam -d an -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split --output-fmt sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -d nn -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.d_nn.unk.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split_d_nn.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split --output-fmt sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.d_nn.0unk.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split_d_nn.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -p 5 -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d RG -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -d nn -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.d_nn.unk.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split_d_nn.sam 339s .. ok 339s 339s test_split: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -f /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split.tmp.d_nn.0unk.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/split/split_d_nn.sam 339s .. ok 339s 339s test_large_positions: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG /tmp/eStjVEae7_/longref.sam.gz 339s .. ok 339s 339s test_large_positions: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG /tmp/eStjVEae7_/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 339s .. ok 339s 339s test_large_positions: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view -h --no-PG -L /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/large_pos/test.bed /tmp/eStjVEae7_/longref.sam.gz 339s .. ok 339s 339s test_large_positions: 339s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/large_pos/longref_name.sam 340s .. ok 340s 340s test_large_positions: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools merge -O sam --no-PG - /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/large_pos/longref.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/large_pos/longref2.sam 340s .. ok 340s 340s test_large_positions: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools depth /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/large_pos/longref.sam 340s .. ok 340s 340s test_large_positions: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools depth -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/large_pos/test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/large_pos/longref.sam 340s .. ok 340s 340s test_large_positions: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/eStjVEae7_/longref.sam.gz 340s .. ok 340s 340s test_large_positions: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools fixmate -O sam --no-PG - - | 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --primer-counts /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/3_multi_ref_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/3_multi_ref_data.sam 340s .. ok 340s 340s test_ampliconclip: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 340s .. ok 340s 340s test_ampliconstats: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_hard_clipped.expected.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_soft_clipped.expected.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/1_soft_clipped_strand.expected.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' 340s .. ok 340s 340s test_ampliconstats: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 340s .. ok 340s 340s test_ampliconstats: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 340s .. ok 340s 340s test_reset: 340s cat /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag < /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools view 340s .. ok 340s 340s test_reset: 340s cat /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.bam 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/test_input_1_a.cram 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG sam_to_fixed_bam /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index --no-PG /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG" 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s test_reset: 340s /tmp/autopkgtest.JB23VD/autopkgtest_tmp/samtools reset /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.JB23VD/autopkgtest_tmp/test/reset/output 340s .. ok 340s 340s 340s Number of tests: 340s total .. 951 340s passed .. 920 340s failed .. 0 340s expected failure .. 31 340s unexpected pass .. 0 340s 341s autopkgtest [16:42:00]: test run-unit-test: -----------------------] 342s run-unit-test PASS 342s autopkgtest [16:42:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 342s autopkgtest [16:42:01]: @@@@@@@@@@@@@@@@@@@@ summary 342s run-unit-test PASS 351s nova [W] Using flock in prodstack6-arm64 351s Creating nova instance adt-plucky-arm64-samtools-20250315-163618-juju-7f2275-prod-proposed-migration-environment-15-86617ce0-90a0-49e8-9a7c-69392440a12c from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 351s nova [W] Timed out waiting for b1621fe0-1728-4e7a-be39-1a563b841d72 to get deleted.