0s autopkgtest [19:14:57]: starting date and time: 2024-03-25 19:14:57+0000 0s autopkgtest [19:14:57]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:14:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ws7ueh5x/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade samtools --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-16.secgroup --name adt-noble-s390x-samtools-20240325-191457-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 115s autopkgtest [19:16:52]: testbed dpkg architecture: s390x 115s autopkgtest [19:16:52]: testbed apt version: 2.7.12 115s autopkgtest [19:16:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 117s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 117s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 117s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4045 kB] 118s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 118s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 118s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [693 kB] 118s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 118s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 118s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 118s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4173 kB] 119s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 119s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 119s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 121s Fetched 9648 kB in 4s (2601 kB/s) 122s Reading package lists... 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s Calculating upgrade... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 242 not upgraded. 128s Unknown architecture, assuming PC-style ttyS0 128s sh: Attempting to set up Debian/Ubuntu apt sources automatically 128s sh: Distribution appears to be Ubuntu 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s eatmydata is already the newest version (131-1). 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s dbus is already the newest version (1.14.10-4ubuntu1). 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s rng-tools-debian is already the newest version (2.4). 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s The following packages will be REMOVED: 133s cloud-init* python3-configobj* python3-debconf* 134s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 134s After this operation, 3256 kB disk space will be freed. 134s (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 ... 52170 files and directories currently installed.) 134s Removing cloud-init (24.1.2-0ubuntu1) ... 135s Removing python3-configobj (5.0.8-3) ... 135s Removing python3-debconf (1.5.86) ... 135s Processing triggers for man-db (2.12.0-3) ... 136s (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 ... 51781 files and directories currently installed.) 136s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 136s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 136s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 137s invoke-rc.d: policy-rc.d denied execution of try-restart. 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s linux-generic is already the newest version (6.8.0-11.11+1). 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 138s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 138s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 141s Reading package lists... 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Calculating upgrade... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s autopkgtest [19:17:19]: rebooting testbed after setup commands that affected boot 168s autopkgtest [19:17:45]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 176s autopkgtest [19:17:53]: @@@@@@@@@@@@@@@@@@@@ apt-source samtools 182s Get:1 http://ftpmaster.internal/ubuntu noble/universe samtools 1.19.2-1 (dsc) [2295 B] 182s Get:2 http://ftpmaster.internal/ubuntu noble/universe samtools 1.19.2-1 (tar) [5666 kB] 182s Get:3 http://ftpmaster.internal/ubuntu noble/universe samtools 1.19.2-1 (diff) [21.8 kB] 182s gpgv: Signature made Sat Feb 17 17:32:01 2024 UTC 182s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 182s gpgv: issuer "emollier@debian.org" 182s gpgv: Can't check signature: No public key 182s dpkg-source: warning: cannot verify inline signature for ./samtools_1.19.2-1.dsc: no acceptable signature found 182s autopkgtest [19:17:59]: testing package samtools version 1.19.2-1 183s autopkgtest [19:18:00]: build not needed 202s autopkgtest [19:18:19]: test run-unit-test: preparing testbed 207s Reading package lists... 207s Building dependency tree... 207s Reading state information... 208s Starting pkgProblemResolver with broken count: 0 208s Starting 2 pkgProblemResolver with broken count: 0 208s Done 208s The following additional packages will be installed: 208s libdeflate0 libhts3 libhtscodecs2 samtools samtools-test tabix 208s Suggested packages: 208s cwltool 208s Recommended packages: 208s libio-pty-perl 208s The following NEW packages will be installed: 208s autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 samtools samtools-test 208s tabix 208s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 4137 kB/4138 kB of archives. 208s After this operation, 23.0 MB of additional disk space will be used. 208s Get:1 /tmp/autopkgtest.bWnhw0/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 208s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 209s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 209s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 209s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x samtools s390x 1.19.2-1 [613 kB] 209s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x samtools-test all 1.19.2-1 [2401 kB] 210s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x tabix s390x 1.18+ds-1 [527 kB] 210s Fetched 4137 kB in 2s (2733 kB/s) 210s Selecting previously unselected package libdeflate0:s390x. 210s (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 ... 51726 files and directories currently installed.) 210s Preparing to unpack .../0-libdeflate0_1.19-1_s390x.deb ... 210s Unpacking libdeflate0:s390x (1.19-1) ... 210s Selecting previously unselected package libhtscodecs2:s390x. 210s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_s390x.deb ... 210s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 210s Selecting previously unselected package libhts3:s390x. 210s Preparing to unpack .../2-libhts3_1.18+ds-1_s390x.deb ... 210s Unpacking libhts3:s390x (1.18+ds-1) ... 210s Selecting previously unselected package samtools. 210s Preparing to unpack .../3-samtools_1.19.2-1_s390x.deb ... 210s Unpacking samtools (1.19.2-1) ... 210s Selecting previously unselected package samtools-test. 210s Preparing to unpack .../4-samtools-test_1.19.2-1_all.deb ... 210s Unpacking samtools-test (1.19.2-1) ... 211s Selecting previously unselected package tabix. 211s Preparing to unpack .../5-tabix_1.18+ds-1_s390x.deb ... 211s Unpacking tabix (1.18+ds-1) ... 211s Selecting previously unselected package autopkgtest-satdep. 211s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 211s Unpacking autopkgtest-satdep (0) ... 211s Setting up libhtscodecs2:s390x (1.6.0-1) ... 211s Setting up libdeflate0:s390x (1.19-1) ... 211s Setting up samtools-test (1.19.2-1) ... 211s Setting up tabix (1.18+ds-1) ... 211s Setting up libhts3:s390x (1.18+ds-1) ... 211s Setting up samtools (1.19.2-1) ... 211s Setting up autopkgtest-satdep (0) ... 211s Processing triggers for man-db (2.12.0-3) ... 211s Processing triggers for libc-bin (2.39-0ubuntu6) ... 216s (Reading database ... 52566 files and directories currently installed.) 216s Removing autopkgtest-satdep (0) ... 216s autopkgtest [19:18:33]: test run-unit-test: [----------------------- 217s test_reference: 217s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reference test/reference/mpileup.1.tmp.cram 217s .. ok 217s 217s test_reference: 217s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reference -e test/reference/mpileup.1.tmp.cram 217s .. ok 217s 217s test_reference: 217s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 217s .. ok 217s 217s test_reference: 217s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 217s .. ok 217s 217s test_reference: 217s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram 217s .. ok 217s 217s test_reference: 217s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram 217s .. ok 217s 217s test_reference: 217s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 217s .. ok 217s 217s test_reference: 217s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 217s .. ok 217s 217s bgzip -c -b 65272 -s 5 /tmp/eDmTdhfBJS/bgzip.dat.gz 217s .. ok 217s 217s bgzip -c -b 979200 -s 6 /tmp/eDmTdhfBJS/bgzip.dat.gz 217s .. ok 217s 217s bgzip -c -b 652804 -s 6 /tmp/eDmTdhfBJS/bgzip.dat.gz 218s .. ok 218s 218s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools faidx /tmp/eDmTdhfBJS/faidx.fa 3:11-13 | grep -v '^>' 218s .. ok 218s 218s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools faidx /tmp/eDmTdhfBJS/faidx.fa.gz 3:11-13 | grep -v '^>' 218s .. ok 218s 218s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools faidx /tmp/eDmTdhfBJS/faidx.fa 2:998-1003 | grep -v '^>' 218s .. ok 218s 218s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools faidx /tmp/eDmTdhfBJS/faidx.fa.gz 2:998-1003 | grep -v '^>' 218s .. ok 218s 218s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools faidx /tmp/eDmTdhfBJS/faidx.fa 1:100-104 | grep -v '^>' 218s .. ok 218s 218s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools faidx /tmp/eDmTdhfBJS/faidx.fa.gz 1:100-104 | grep -v '^>' 218s .. ok 218s 218s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools faidx /tmp/eDmTdhfBJS/faidx.fa 1:99998-100007 | grep -v '^>' 218s .. ok 218s 218s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools faidx /tmp/eDmTdhfBJS/faidx.fa.gz 1:99998-100007 | grep -v '^>' 218s .. ok 218s 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fqidx /tmp/eDmTdhfBJS/fqidx.fq 3:11-13 219s .. ok 219s 219s .. ok 219s 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fqidx /tmp/eDmTdhfBJS/fqidx.fq.gz 3:11-13 219s .. ok 219s 219s .. ok 219s 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fqidx /tmp/eDmTdhfBJS/fqidx.fq 2:998-1003 219s .. ok 219s 219s .. ok 219s 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fqidx /tmp/eDmTdhfBJS/fqidx.fq.gz 2:998-1003 219s .. ok 219s 219s .. ok 219s 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fqidx /tmp/eDmTdhfBJS/fqidx.fq 1:100-104 219s .. ok 219s 219s .. ok 219s 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fqidx /tmp/eDmTdhfBJS/fqidx.fq.gz 1:100-104 219s .. ok 219s 219s .. ok 219s 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fqidx /tmp/eDmTdhfBJS/fqidx.fq 1:99998-100007 219s .. ok 219s 219s .. ok 219s 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fqidx /tmp/eDmTdhfBJS/fqidx.fq.gz 1:99998-100007 219s .. ok 219s 219s .. ok 219s 219s test_dict: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/dict.fa 219s .. ok 219s 219s test_dict: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/eDmTdhfBJS/dict.fa.gz 219s .. ok 219s 219s test_dict: 219s cat /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/dict.fa | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz 219s .. ok 219s 219s test_dict: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools dict -AH < /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/dict.alias.fa 219s .. ok 219s 219s test_dict: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools dict -H -l /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/dict.alt < /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/dict.alias.fa 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view /tmp/eDmTdhfBJS/large_chrom.bam ref2 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view /tmp/eDmTdhfBJS/large_chrom.bam ref2:1-541556283 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eDmTdhfBJS/test_input_1_b.bam.bai ref2 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eDmTdhfBJS/test_input_1_b.bam.bai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -O sam - -X -cp -R ref2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/eDmTdhfBJS/test_input_1_b.bam.bai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eDmTdhfBJS/test_input_1_b_opt.bam.bai ref2 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/eDmTdhfBJS/auto_indexed.csi && cat /tmp/eDmTdhfBJS/auto_indexed.csi 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/eDmTdhfBJS/auto_indexed.crai && cat /tmp/eDmTdhfBJS/auto_indexed.crai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/eDmTdhfBJS/auto_indexed.csi && cat /tmp/eDmTdhfBJS/auto_indexed.csi 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -@ 2 /tmp/eDmTdhfBJS/large_chrom.bam ref2 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -@ 2 /tmp/eDmTdhfBJS/large_chrom.bam ref2:1-541556283 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eDmTdhfBJS/test_input_1_b.bam.bai ref2 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eDmTdhfBJS/test_input_1_b.bam.bai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -O sam - -X -cp -R ref2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/eDmTdhfBJS/test_input_1_b.bam.bai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/eDmTdhfBJS/test_input_1_b_opt.bam.bai ref2 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -@ 2 -M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/eDmTdhfBJS/auto_indexed.csi && cat /tmp/eDmTdhfBJS/auto_indexed.csi 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/eDmTdhfBJS/auto_indexed.crai && cat /tmp/eDmTdhfBJS/auto_indexed.crai 219s .. ok 219s 219s test_index: 219s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/eDmTdhfBJS/auto_indexed.csi && cat /tmp/eDmTdhfBJS/auto_indexed.csi 219s .. ok 219s 220s test_mpileup: 220s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools mpileup -b /tmp/eDmTdhfBJS/mpileup.bam.list -f /tmp/eDmTdhfBJS/mpileup.ref.fa.gz -r17:100-150 220s .. ok 220s 220s test_mpileup: 220s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools mpileup -b /tmp/eDmTdhfBJS/mpileup.cram.list -f /tmp/eDmTdhfBJS/mpileup.ref.fa.gz -r17:100-150 220s .. ok 220s 220s test_mpileup: 220s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools mpileup -b /tmp/eDmTdhfBJS/mpileup.bam.urllist -f /tmp/eDmTdhfBJS/mpileup.ref.fa.gz -r17:100-150 220s .. ok 220s 220s test_mpileup: 220s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools mpileup -b /tmp/eDmTdhfBJS/mpileup.cram.urllist -f /tmp/eDmTdhfBJS/mpileup.ref.fa.gz -r17:100-150 220s .. ok 220s 220s test_mpileup: 220s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/eDmTdhfBJS/mpileup.ref.fa.gz -r17:1050-1060 /tmp/eDmTdhfBJS/mpileup.1.bam | grep -v mpileup 220s .. ok 220s 220s test_mpileup: 220s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/eDmTdhfBJS/mpileup.ref.fa.gz -r17:1050-1060 /tmp/eDmTdhfBJS/mpileup.1.cram | grep -v mpileup 220s .. ok 220s 220s test_mpileup: 220s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools mpileup /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/mpileup/overlap.bam | grep 128814202 220s ./test/test.pl: no IO::Pty module or can't open pty; skipping usage tests 220s .. ok 220s 220s test_usage: 220s samtools 220s test_view: 221s Generating test data file .................. done 221s 1: SAM -> BAM -> SAM .. ok 221s 221s 2: SAM -> uncompressed BAM .. ok 221s 221s 3: uncompressed BAM -> SAM and compare .. ok 221s 221s 4: SAM -> fast compressed BAM .. ok 221s 221s 5: fast compressed BAM -> SAM and compare .. ok 221s 222s 6: SAM -> CRAM -> SAM (UR header tags) .. ok 222s 222s 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 222s 223s 8: BAM -> CRAM with UR -> SAM .. ok 223s 223s 9: SAM -> BAM (M5 header tags) .. ok 223s 223s 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 223s 224s 11: CRAM -> BAM with UR .. ok 224s 224s 12: CRAM -> BAM with M5 .. ok 224s 224s 13: SAM -> SAM via stdout .. ok 224s 224s 14: SAM -> BAM via stdout .. ok 224s 225s 15: SAM -> CRAM via stdout .. ok 225s 225s 16: SAM from stdin -> SAM .. ok 225s 225s 17: BAM from stdin -> SAM .. ok 225s 226s 18: CRAM from stdin -> SAM .. ok 226s 226s 19: samtools view -H (SAM input) .. ok 226s 226s 20: samtools view -H (BAM input) .. ok 226s 226s 21: samtools view -H (CRAM input) .. ok 226s 226s 22: No headers (SAM input) .. ok 226s 226s 23: No headers (BAM input) .. ok 226s 226s 24: No headers (CRAM input) .. ok 226s 226s 25: Filter -f 128 (SAM input) .. ok 226s 226s 26: Count -f 128 (SAM input) .. ok 226s 226s 27: Filter -f 128 (BAM input) .. ok 226s 226s 28: Count -f 128 (BAM input) .. ok 226s 227s 29: Filter -f 128 (CRAM input) .. ok 227s 227s 30: Count -f 128 (CRAM input) .. ok 227s 227s 31: Filter -F 128 (SAM input) .. ok 227s 227s 32: Count -F 128 (SAM input) .. ok 227s 227s 33: Filter -F 128 (BAM input) .. ok 227s 227s 34: Count -F 128 (BAM input) .. ok 227s 227s 35: Filter -F 128 (CRAM input) .. ok 227s 227s 36: Count -F 128 (CRAM input) .. ok 227s 227s 37: Filter -F 128 -f 2 (SAM input) .. ok 227s 227s 38: Count -F 128 -f 2 (SAM input) .. ok 227s 227s 39: Filter -F 128 -f 2 (BAM input) .. ok 227s 227s 40: Count -F 128 -f 2 (BAM input) .. ok 227s 228s 41: Filter -F 128 -f 2 (CRAM input) .. ok 228s 228s 42: Count -F 128 -f 2 (CRAM input) .. ok 228s 228s 43: Filter -r grp2 (SAM input) .. ok 228s 228s 44: Count -r grp2 (SAM input) .. ok 228s 228s 45: Filter -r grp2 (BAM input) .. ok 228s 228s 46: Count -r grp2 (BAM input) .. ok 228s 228s 47: Filter -r grp2 (CRAM input) .. ok 228s 228s 48: Count -r grp2 (CRAM input) .. ok 228s 228s 49: Filter -R /tmp/eDmTdhfBJS/view.001.fogn (SAM input) .. ok 228s 228s 50: Count -R /tmp/eDmTdhfBJS/view.001.fogn (SAM input) .. ok 228s 228s 51: Filter -R /tmp/eDmTdhfBJS/view.001.fogn (BAM input) .. ok 228s 228s 52: Count -R /tmp/eDmTdhfBJS/view.001.fogn (BAM input) .. ok 228s 229s 53: Filter -R /tmp/eDmTdhfBJS/view.001.fogn (CRAM input) .. ok 229s 229s 54: Count -R /tmp/eDmTdhfBJS/view.001.fogn (CRAM input) .. ok 229s 229s 55: Filter -R /tmp/eDmTdhfBJS/view.001.fogn -r grp2 (SAM input).. ok 229s 229s 56: Count -R /tmp/eDmTdhfBJS/view.001.fogn -r grp2 (SAM input).. ok 229s 229s 57: Filter -R /tmp/eDmTdhfBJS/view.001.fogn -r grp2 (BAM input).. ok 229s 229s 58: Count -R /tmp/eDmTdhfBJS/view.001.fogn -r grp2 (BAM input).. ok 229s 229s 59: Filter -R /tmp/eDmTdhfBJS/view.001.fogn -r grp2 (CRAM input).. ok 229s 229s 60: Count -R /tmp/eDmTdhfBJS/view.001.fogn -r grp2 (CRAM input).. ok 229s 229s 61: Filter -r grp2 -R /tmp/eDmTdhfBJS/view.001.fogn (SAM input).. ok 229s 229s 62: Count -r grp2 -R /tmp/eDmTdhfBJS/view.001.fogn (SAM input).. ok 229s 229s 63: Filter -r grp2 -R /tmp/eDmTdhfBJS/view.001.fogn (BAM input).. ok 229s 229s 64: Count -r grp2 -R /tmp/eDmTdhfBJS/view.001.fogn (BAM input).. ok 229s 230s 65: Filter -r grp2 -R /tmp/eDmTdhfBJS/view.001.fogn (CRAM input).. ok 230s 230s 66: Count -r grp2 -R /tmp/eDmTdhfBJS/view.001.fogn (CRAM input).. ok 230s 230s 67: Filter -N /tmp/eDmTdhfBJS/view.001.forn (SAM input) .. ok 230s 230s 68: Count -N /tmp/eDmTdhfBJS/view.001.forn (SAM input) .. ok 230s 230s 69: Filter -N /tmp/eDmTdhfBJS/view.001.forn (BAM input) .. ok 230s 230s 70: Count -N /tmp/eDmTdhfBJS/view.001.forn (BAM input) .. ok 230s 230s 71: Filter -N /tmp/eDmTdhfBJS/view.001.forn (CRAM input) .. ok 230s 230s 72: Count -N /tmp/eDmTdhfBJS/view.001.forn (CRAM input) .. ok 230s 230s 73: Filter -d BC (SAM input) .. ok 230s 230s 74: Count -d BC (SAM input) .. ok 230s 230s 75: Filter -d BC (BAM input) .. ok 230s 230s 76: Count -d BC (BAM input) .. ok 230s 231s 77: Filter -d BC (CRAM input) .. ok 231s 231s 78: Count -d BC (CRAM input) .. ok 231s 231s 79: Filter -d BC:TGCA (SAM input) .. ok 231s 231s 80: Count -d BC:TGCA (SAM input) .. ok 231s 231s 81: Filter -d BC:TGCA (BAM input) .. ok 231s 231s 82: Count -d BC:TGCA (BAM input) .. ok 231s 232s 83: Filter -d BC:TGCA (CRAM input) .. ok 232s 232s 84: Count -d BC:TGCA (CRAM input) .. ok 232s 232s 85: Filter -D BC:/tmp/eDmTdhfBJS/view.001.fobc (SAM input) .. ok 232s 232s 86: Count -D BC:/tmp/eDmTdhfBJS/view.001.fobc (SAM input) .. ok 232s 232s 87: Filter -D BC:/tmp/eDmTdhfBJS/view.001.fobc (BAM input) .. ok 232s 232s 88: Count -D BC:/tmp/eDmTdhfBJS/view.001.fobc (BAM input) .. ok 232s 232s 89: Filter -D BC:/tmp/eDmTdhfBJS/view.001.fobc (CRAM input) .. ok 232s 232s 90: Count -D BC:/tmp/eDmTdhfBJS/view.001.fobc (CRAM input) .. ok 232s 232s 91: Filter -D BC:/tmp/eDmTdhfBJS/view.001.fobc -d BC:TGCA (SAM input).. ok 232s 232s 92: Count -D BC:/tmp/eDmTdhfBJS/view.001.fobc -d BC:TGCA (SAM input).. ok 232s 232s 93: Filter -D BC:/tmp/eDmTdhfBJS/view.001.fobc -d BC:TGCA (BAM input).. ok 232s 232s 94: Count -D BC:/tmp/eDmTdhfBJS/view.001.fobc -d BC:TGCA (BAM input).. ok 232s 233s 95: Filter -D BC:/tmp/eDmTdhfBJS/view.001.fobc -d BC:TGCA (CRAM input).. ok 233s 233s 96: Count -D BC:/tmp/eDmTdhfBJS/view.001.fobc -d BC:TGCA (CRAM input).. ok 233s 233s 97: Filter -d BC:TGCA -D BC:/tmp/eDmTdhfBJS/view.001.fobc (SAM input).. ok 233s 233s 98: Count -d BC:TGCA -D BC:/tmp/eDmTdhfBJS/view.001.fobc (SAM input).. ok 233s 233s 99: Filter -d BC:TGCA -D BC:/tmp/eDmTdhfBJS/view.001.fobc (BAM input).. ok 233s 233s 100: Count -d BC:TGCA -D BC:/tmp/eDmTdhfBJS/view.001.fobc (BAM input).. ok 233s 233s 101: Filter -d BC:TGCA -D BC:/tmp/eDmTdhfBJS/view.001.fobc (CRAM input).. ok 233s 233s 102: Count -d BC:TGCA -D BC:/tmp/eDmTdhfBJS/view.001.fobc (CRAM input).. ok 233s 233s 103: Filter -D RG:/tmp/eDmTdhfBJS/view.001.fogn (SAM input) .. ok 233s 233s 104: Count -D RG:/tmp/eDmTdhfBJS/view.001.fogn (SAM input) .. ok 233s 233s 105: Filter -D RG:/tmp/eDmTdhfBJS/view.001.fogn (BAM input) .. ok 233s 233s 106: Count -D RG:/tmp/eDmTdhfBJS/view.001.fogn (BAM input) .. ok 233s 234s 107: Filter -D RG:/tmp/eDmTdhfBJS/view.001.fogn (CRAM input).. ok 234s 234s 108: Count -D RG:/tmp/eDmTdhfBJS/view.001.fogn (CRAM input) .. ok 234s 234s 109: Filter -d NE:TGCA (SAM input) .. ok 234s 234s 110: Count -d NE:TGCA (SAM input) .. ok 234s 234s 111: Filter -d NE:TGCA (BAM input) .. ok 234s 234s 112: Count -d NE:TGCA (BAM input) .. ok 234s 234s 113: Filter -d NE:TGCA (CRAM input) .. ok 234s 234s 114: Count -d NE:TGCA (CRAM input) .. ok 234s 234s 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" 234s Failed command: 234s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test115.sam -h -d TGCA /tmp/eDmTdhfBJS/view.001.sam --no-PG 234s 234s 234s .. expected failure 234s 234s 116: Count -d TGCA (SAM input) Failed command: 234s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -d TGCA /tmp/eDmTdhfBJS/view.001.sam --no-PG 234s 234s 234s .. expected failure 234s 234s 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 234s samtools view: Invalid "tag:value" option: "TGCA" 234s Failed command: 234s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test117.sam -h -d TGCA /tmp/eDmTdhfBJS/view.test001.bam --no-PG 234s 234s 234s .. expected failure 234s 234s 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 234s Failed command: 234s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -d TGCA /tmp/eDmTdhfBJS/view.test001.bam --no-PG 234s 234s 234s .. expected failure 234s 234s 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" 235s Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test119.sam -h -d TGCA /tmp/eDmTdhfBJS/view.test006.cram --no-PG 235s 235s 235s .. expected failure 235s 235s 120: Count -d TGCA (CRAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -d TGCA /tmp/eDmTdhfBJS/view.test006.cram --no-PG 235s 235s 235s .. expected failure 235s 235s 121: Filter -D BClong:/tmp/eDmTdhfBJS/view.001.fobc (SAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test121.sam -h -D BClong:/tmp/eDmTdhfBJS/view.001.fobc /tmp/eDmTdhfBJS/view.001.sam --no-PG 235s 235s 235s .. expected failure 235s 235s 122: Count -D BClong:/tmp/eDmTdhfBJS/view.001.fobc (SAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -D BClong:/tmp/eDmTdhfBJS/view.001.fobc /tmp/eDmTdhfBJS/view.001.sam --no-PG 235s 235s 235s .. expected failure 235s 235s 123: Filter -D BClong:/tmp/eDmTdhfBJS/view.001.fobc (BAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test123.sam -h -D BClong:/tmp/eDmTdhfBJS/view.001.fobc /tmp/eDmTdhfBJS/view.test001.bam --no-PG 235s 235s 235s .. expected failure 235s 235s 124: Count -D BClong:/tmp/eDmTdhfBJS/view.001.fobc (BAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -D BClong:/tmp/eDmTdhfBJS/view.001.fobc /tmp/eDmTdhfBJS/view.test001.bam --no-PG 235s 235s 235s .. expected failure 235s 235s 125: Filter -D BClong:/tmp/eDmTdhfBJS/view.001.fobc (CRAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test125.sam -h -D BClong:/tmp/eDmTdhfBJS/view.001.fobc /tmp/eDmTdhfBJS/view.test006.cram --no-PG 235s 235s 235s .. expected failure 235s 235s 126: Count -D BClong:/tmp/eDmTdhfBJS/view.001.fobc (CRAM input)samtools view: Invalid "tag:value" option: "TGCA" 235s samtools view: Invalid "tag:file" option: "BClong:/tmp/eDmTdhfBJS/view.001.fobc" 235s samtools view: Invalid "tag:file" option: "BClong:/tmp/eDmTdhfBJS/view.001.fobc" 235s samtools view: Invalid "tag:file" option: "BClong:/tmp/eDmTdhfBJS/view.001.fobc" 235s samtools view: Invalid "tag:file" option: "BClong:/tmp/eDmTdhfBJS/view.001.fobc" 235s samtools view: Invalid "tag:file" option: "BClong:/tmp/eDmTdhfBJS/view.001.fobc" 235s samtools view: Invalid "tag:file" option: "BClong:/tmp/eDmTdhfBJS/view.001.fobc" 235s samtools view: Different tag "BC" was specified before: "RG:grp2" 235s samtools view: Different tag "BC" was specified before: "RG:grp2" 235s samtools view: Different tag "BC" was specified before: "RG:grp2" 235s samtools view: Different tag "BC" was specified before: "RG:grp2" 235s samtools view: Different tag "BC" was specified before: "RG:grp2" 235s samtools view: Different tag "BC" was specified before: "RG:grp2" 235s Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -D BClong:/tmp/eDmTdhfBJS/view.001.fobc /tmp/eDmTdhfBJS/view.test006.cram --no-PG 235s 235s 235s .. expected failure 235s 235s 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/eDmTdhfBJS/view.001.sam --no-PG 235s 235s 235s .. expected failure 235s 235s 128: Count -d BC:ACGT -d RG:grp2 (SAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/eDmTdhfBJS/view.001.sam --no-PG 235s 235s 235s .. expected failure 235s 235s 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/eDmTdhfBJS/view.test001.bam --no-PG 235s 235s 235s .. expected failure 235s 235s 130: Count -d BC:ACGT -d RG:grp2 (BAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/eDmTdhfBJS/view.test001.bam --no-PG 235s 235s 235s .. expected failure 235s 235s 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -o /tmp/eDmTdhfBJS/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/eDmTdhfBJS/view.test006.cram --no-PG 235s 235s 235s .. expected failure 235s 235s 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) Failed command: 235s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/eDmTdhfBJS/view.test006.cram --no-PG 235s 235s 235s .. expected failure 235s 235s 133: Filter -d NM:13 (SAM input) .. ok 235s 235s 134: Count -d NM:13 (SAM input) .. ok 235s 235s 135: Filter -d NM:13 (BAM input) .. ok 235s 235s 136: Count -d NM:13 (BAM input) .. ok 235s 235s 137: Filter -d NM:13 (CRAM input) .. ok 235s 236s 138: Count -d NM:13 (CRAM input) .. ok 236s 236s 139: Filter -d ab:z (SAM input) .. ok 236s 236s 140: Count -d ab:z (SAM input) .. ok 236s 236s 141: Filter -d ab:z (BAM input) .. ok 236s 236s 142: Count -d ab:z (BAM input) .. ok 236s 236s 143: Filter -d ab:z (CRAM input) .. ok 236s 236s 144: Count -d ab:z (CRAM input) .. ok 236s 236s 145: Filter -l Library 2 (SAM input) .. ok 236s 236s 146: Count -l Library 2 (SAM input) .. ok 236s 236s 147: Filter -l Library 2 (BAM input) .. ok 236s 236s 148: Count -l Library 2 (BAM input) .. ok 236s 237s 149: Filter -l Library 2 (CRAM input) .. ok 237s 237s 150: Count -l Library 2 (CRAM input) .. ok 237s 237s 151: Filter -l Library 3 (SAM input) .. ok 237s 237s 152: Count -l Library 3 (SAM input) .. ok 237s 237s 153: Filter -l Library 3 (BAM input) .. ok 237s 237s 154: Count -l Library 3 (BAM input) .. ok 237s 237s 155: Filter -l Library 3 (CRAM input) .. ok 237s 237s 156: Count -l Library 3 (CRAM input) .. ok 237s 237s 157: Filter -q 50 (SAM input) .. ok 237s 237s 158: Count -q 50 (SAM input) .. ok 237s 237s 159: Filter -q 50 (BAM input) .. ok 237s 237s 160: Count -q 50 (BAM input) .. ok 237s 238s 161: Filter -q 50 (CRAM input) .. ok 238s 238s 162: Count -q 50 (CRAM input) .. ok 238s 238s 163: Filter -q 99 (SAM input) .. ok 238s 238s 164: Count -q 99 (SAM input) .. ok 238s 238s 165: Filter -q 99 (BAM input) .. ok 238s 238s 166: Count -q 99 (BAM input) .. ok 238s 239s 167: Filter -q 99 (CRAM input) .. ok 239s 239s 168: Count -q 99 (CRAM input) .. ok 239s 239s 169: Filter -q 100 (SAM input) .. ok 239s 239s 170: Count -q 100 (SAM input) .. ok 239s 239s 171: Filter -q 100 (BAM input) .. ok 239s 239s 172: Count -q 100 (BAM input) .. ok 239s 239s 173: Filter -q 100 (CRAM input) .. ok 239s 239s 174: Count -q 100 (CRAM input) .. ok 239s 239s 175: Filter -x fa (SAM input) .. ok 239s 239s 176: Count -x fa (SAM input) .. ok 239s 239s 177: Filter -x fa (BAM input) .. ok 239s 239s 178: Count -x fa (BAM input) .. ok 239s 242s 179: Filter -x fa (CRAM input) .. ok 242s 242s 180: Count -x fa (CRAM input) .. ok 242s 242s 181: Filter -x fa -x ha (SAM input) .. ok 242s 242s 182: Count -x fa -x ha (SAM input) .. ok 242s 242s 183: Filter -x fa -x ha (BAM input) .. ok 242s 242s 184: Count -x fa -x ha (BAM input) .. ok 242s 242s 185: Filter -x fa -x ha (CRAM input) .. ok 242s 242s 186: Count -x fa -x ha (CRAM input) .. ok 242s 242s 187: Filter -x fa,ha (SAM input) .. ok 242s 242s 188: Count -x fa,ha (SAM input) .. ok 242s 242s 189: Filter -x fa,ha (BAM input) .. ok 242s 242s 190: Count -x fa,ha (BAM input) .. ok 242s 242s 191: Filter -x fa,ha (CRAM input) .. ok 242s 242s 192: Count -x fa,ha (CRAM input) .. ok 242s 242s 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 242s 242s 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 242s 242s 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 242s 242s 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 242s 242s 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 242s 242s 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 242s 242s 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 242s 242s 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 242s 242s 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 242s 242s 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 242s 242s 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 242s 242s 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 242s 242s 205: Filter -x fa -r grp2 (SAM input) .. ok 242s 242s 206: Count -x fa -r grp2 (SAM input) .. ok 242s 242s 207: Filter -x fa -r grp2 (BAM input) .. ok 242s 242s 208: Count -x fa -r grp2 (BAM input) .. ok 242s 242s 209: Filter -x fa -r grp2 (CRAM input) .. ok 242s 242s 210: Count -x fa -r grp2 (CRAM input) .. ok 242s 242s 211: Filter -x RG -r grp2 (SAM input) .. ok 242s 242s 212: Count -x RG -r grp2 (SAM input) .. ok 242s 242s 213: Filter -x RG -r grp2 (BAM input) .. ok 242s 242s 214: Count -x RG -r grp2 (BAM input) .. ok 242s 243s 215: Filter -x RG -r grp2 (CRAM input) .. ok 243s 243s 216: Count -x RG -r grp2 (CRAM input) .. ok 243s 243s 217: Filter -m 10 (SAM input) .. ok 243s 243s 218: Count -m 10 (SAM input) .. ok 243s 243s 219: Filter -m 10 (BAM input) .. ok 243s 243s 220: Count -m 10 (BAM input) .. ok 243s 243s 221: Filter -m 10 (CRAM input) .. ok 243s 244s 222: Count -m 10 (CRAM input) .. ok 244s 244s 223: Filter -m 11 (SAM input) .. ok 244s 244s 224: Count -m 11 (SAM input) .. ok 244s 244s 225: Filter -m 11 (BAM input) .. ok 244s 244s 226: Count -m 11 (BAM input) .. ok 244s 244s 227: Filter -m 11 (CRAM input) .. ok 244s 245s 228: Count -m 11 (CRAM input) .. ok 245s 245s 229: Filter -m 15 (SAM input) .. ok 245s 245s 230: Count -m 15 (SAM input) .. ok 245s 245s 231: Filter -m 15 (BAM input) .. ok 245s 245s 232: Count -m 15 (BAM input) .. ok 245s 245s 233: Filter -m 15 (CRAM input) .. ok 245s 246s 234: Count -m 15 (CRAM input) .. ok 246s 246s 235: Filter -m 16 (SAM input) .. ok 246s 246s 236: Count -m 16 (SAM input) .. ok 246s 246s 237: Filter -m 16 (BAM input) .. ok 246s 246s 238: Count -m 16 (BAM input) .. ok 246s 246s 239: Filter -m 16 (CRAM input) .. ok 246s 247s 240: Count -m 16 (CRAM input) .. ok 247s 247s 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 247s 247s 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 247s 247s 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 247s 247s 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 247s 247s 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247s 248s 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 248s 248s 247: Filter -e [BC] (SAM input) .. ok 248s 248s 248: Count -e [BC] (SAM input) .. ok 248s 248s 249: Filter -e [BC] (BAM input) .. ok 248s 248s 250: Count -e [BC] (BAM input) .. ok 248s 248s 251: Filter -e [BC] (CRAM input) .. ok 248s 249s 252: Count -e [BC] (CRAM input) .. ok 249s 249s 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 249s 249s 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 249s 249s 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 249s 249s 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 249s 249s 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 249s 250s 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 250s 250s 259: Filter -e mapq >= 50 (SAM input) .. ok 250s 250s 260: Count -e mapq >= 50 (SAM input) .. ok 250s 250s 261: Filter -e mapq >= 50 (BAM input) .. ok 250s 250s 262: Count -e mapq >= 50 (BAM input) .. ok 250s 251s 263: Filter -e mapq >= 50 (CRAM input) .. ok 251s 251s 264: Count -e mapq >= 50 (CRAM input) .. ok 251s 251s 265: Filter -e mapq >= 99 (SAM input) .. ok 251s 251s 266: Count -e mapq >= 99 (SAM input) .. ok 251s 251s 267: Filter -e mapq >= 99 (BAM input) .. ok 251s 251s 268: Count -e mapq >= 99 (BAM input) .. ok 251s 252s 269: Filter -e mapq >= 99 (CRAM input) .. ok 252s 252s 270: Count -e mapq >= 99 (CRAM input) .. ok 252s 252s 271: Filter -e mapq >= 100 (SAM input) .. ok 252s 252s 272: Count -e mapq >= 100 (SAM input) .. ok 252s 252s 273: Filter -e mapq >= 100 (BAM input) .. ok 252s 252s 274: Count -e mapq >= 100 (BAM input) .. ok 252s 253s 275: Filter -e mapq >= 100 (CRAM input) .. ok 253s 253s 276: Count -e mapq >= 100 (CRAM input) .. ok 253s 253s 277: 1bp reads file SAM -> BAM -> SAM .. ok 253s 254s 278: 1bp reads file SAM -> CRAM -> SAM .. ok 254s 254s 278: Region Z (BAM input) .. ok 254s 254s 279: Count Z (BAM input) .. ok 254s 255s 280: Region Z (CRAM input) .. ok 255s 255s 281: Count Z (CRAM input) .. ok 255s 255s 282: Region Z:30 (BAM input) .. ok 255s 255s 283: Count Z:30 (BAM input) .. ok 255s 255s 284: Region Z:30 (CRAM input) .. ok 255s 255s 285: Count Z:30 (CRAM input) .. ok 255s 255s 286: Region Z:20-40 (BAM input) .. ok 255s 255s 287: Count Z:20-40 (BAM input) .. ok 255s 256s 288: Region Z:20-40 (CRAM input) .. ok 256s 256s 289: Count Z:20-40 (CRAM input) .. ok 256s 256s 290: Region ref1 (BAM input) .. ok 256s 256s 291: Count ref1 (BAM input) .. ok 256s 256s 292: Region ref1 (CRAM input) .. ok 256s 256s 293: Count ref1 (CRAM input) .. ok 256s 256s 294: Region ref1:15 (BAM input) .. ok 256s 256s 295: Count ref1:15 (BAM input) .. ok 256s 257s 296: Region ref1:15 (CRAM input) .. ok 257s 257s 297: Count ref1:15 (CRAM input) .. ok 257s 257s 298: Region ref1:15-45 (BAM input) .. ok 257s 257s 299: Count ref1:15-45 (BAM input) .. ok 257s 258s 300: Region ref1:15-45 (CRAM input) .. ok 258s 258s 301: Count ref1:15-45 (CRAM input) .. ok 258s 258s 302: Region ref1:15-45 ref2 (BAM input) .. ok 258s 258s 303: Count ref1:15-45 ref2 (BAM input) .. ok 258s 258s 304: Region ref1:15-45 ref2 (CRAM input) .. ok 258s 258s 305: Count ref1:15-45 ref2 (CRAM input) .. ok 258s 258s 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 258s 258s 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 258s 259s 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 259s 259s 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 259s 259s 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 259s 259s 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 259s 259s 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 259s 259s 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 259s 259s 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 259s 259s 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 259s 260s 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 260s 260s 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 260s 260s 318: Region -f 128 ref1 (BAM input) .. ok 260s 260s 319: Count -f 128 ref1 (BAM input) .. ok 260s 260s 320: Region -f 128 ref1 (CRAM input) .. ok 260s 260s 321: Count -f 128 ref1 (CRAM input) .. ok 260s 260s 322: Region -q 50 ref1:15-45 (BAM input) .. ok 260s 260s 323: Count -q 50 ref1:15-45 (BAM input) .. ok 260s 261s 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 261s 261s 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 261s 261s 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 261s 261s 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 261s 261s 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 261s 261s 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 261s 261s 330: Region * (BAM input) .. ok 261s 261s 331: Count * (BAM input) .. ok 261s 261s 332: Region * (CRAM input) .. ok 261s 261s 333: Count * (CRAM input) .. ok 261s 261s 334: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 261s 261s 335: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 261s 262s 336: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 262s 262s 337: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 262s 262s 338: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 262s 262s 339: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 262s 262s 340: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 262s 262s 341: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 262s 262s 342: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 262s 262s 343: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 262s 263s 344: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 263s 263s 345: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 263s 263s 346: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 263s 263s 347: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 263s 263s 348: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 263s 263s 349: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 263s 263s 350: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 263s 263s 351: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 263s 264s 352: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 264s 264s 353: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 264s 264s 354: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 264s 264s 355: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 264s 265s 356: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 265s 265s 357: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 265s 265s 358: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 265s 265s 359: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 265s 265s 360: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 265s 265s 361: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 265s 265s 362: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 265s 265s 363: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 265s 266s 364: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 266s 266s 365: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 266s 266s 366: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 266s 266s 367: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 266s 266s 368: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 266s 266s 369: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 266s 266s 370: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 266s 266s 371: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 266s 267s 372: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 267s 267s 373: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 267s 267s 374: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 267s 267s 375: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 267s 267s 376: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 267s 268s 377: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 268s 268s 378: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 268s 268s 379: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 268s 268s 380: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 268s 268s 381: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 268s 268s 382: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 268s 268s 383: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 268s 269s 384: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 269s 269s 385: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 269s 269s 386: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 269s 269s 387: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 269s 269s 388: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 269s 269s 389: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 269s 269s 390: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 269s 269s 391: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 269s 270s 392: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 270s 270s 393: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 270s 270s 394: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 270s 270s 395: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 270s 270s 396: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 270s 270s 397: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 270s 270s 398: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 270s 270s 399: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 270s 271s 400: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 271s 271s 401: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 271s 271s 402: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 271s 271s 403: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 271s 272s 404: Region -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 272s 272s 405: Count -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 272s 272s 406: Make BAM with no M5/UR tags .. ok 272s 272s 407: Add @SQ with -t (SAM -> SAM) .. ok 272s 272s 408: Add @SQ with -T (SAM -> SAM) .. ok 272s 272s 409: Add @SQ with -t (BAM -> SAM) .. ok 272s 272s 410: Add @SQ with -T (BAM -> SAM) .. ok 272s 272s 411: Add @SQ with -t (SAM -> BAM) .. ok 272s 272s 412: Add @SQ with -T (SAM -> BAM) .. ok 272s 272s 413: Add @SQ with -t (BAM -> BAM) .. ok 272s 272s 414: Add @SQ with -T (BAM -> BAM) .. ok 272s 272s 415: Add @SQ with -t (SAM -> CRAM) .. ok 272s 273s 416: Add @SQ with -T (SAM -> CRAM) .. ok 273s 274s 417: Add @SQ with -t (BAM -> CRAM) .. ok 274s 274s 418: Add @SQ with -T (BAM -> CRAM) .. ok 274s 274s 419: Make CRAM with no UR field .. ok 274s 274s 420: Decoding CRAM with no UR field via -T .. ok 274s 274s 421: CIGAR B-operator removal .. ok 274s 275s 422: Big SAM -> BAM .. ok 275s 276s 423: Big SAM -> BAM (2 threads) .. ok 276s 276s 424: Big SAM -> BAM (4 threads) .. ok 276s 278s 425: Big SAM -> CRAM .. ok 278s 280s 426: Big SAM -> CRAM (2 threads) .. ok 280s 282s 427: Big SAM -> CRAM (4 threads) .. ok 282s 284s 428: Subsample 0.2 (SAM input) ............ ok 284s 287s 429: Subsample 0.5 (SAM input) ............ ok 287s 289s 430: Subsample 0.8 (SAM input) ............ ok 289s 290s 431: Subsample 0.2 (BAM input) ............ ok 290s 292s 432: Subsample 0.5 (BAM input) ............ ok 292s 294s 433: Subsample 0.8 (BAM input) ............ ok 294s 301s 434: Subsample 0.2 (CRAM input) ............ ok 301s 309s 435: Subsample 0.5 (CRAM input) ............ ok 309s 317s 436: Subsample 0.8 (CRAM input) ............ ok 317s 317s 437: SAM add PG .. ok 317s 317s 438: Unset dup flag, remove dt and do tags .. ok 317s 317s 439: Unmap dup flagged reads. .. ok 317s 317s 440: Unmap dup flagged reads. .. ok 317s 317s 441: fetch pairs .. ok 317s 318s 442: fetch pairs .. ok 318s 318s 443: fetch pairs .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -h 0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -h 1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -h 5 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -h 29 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -h 30 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -n 0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -n 1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -n 5 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_head: 318s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools head -h 5 -n 5 < /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.sam 318s .. ok 318s 318s test_cat: 318s Generating test data file .................. done 318s Generate BAM file #1 .. ok 318s 318s Generate CRAM file #1 .. ok 318s 319s Generating test data file .................. done 319s Generate BAM file #2 .. ok 319s 319s Generate CRAM file #2 .. ok 319s 319s Generating test data file .................. done 319s Generate BAM file #3 .. ok 319s 320s Generate CRAM file #3 .. ok 320s 320s Generating test data file .................. done 320s Generate BAM file #4 .. ok 320s 320s Generate CRAM file #4 .. ok 320s 321s 1: cat BAM files .. ok 321s 321s 2: cat recompressed BAM files .. ok 321s 321s 3: cat CRAM files .. ok 321s 321s 4: cat BAM files to stdout .. ok 321s 321s 5: cat recompressed BAM files to stdout .. ok 321s 322s 6: cat CRAM files to stdout .. ok 322s 322s 7: cat BAM files with new header .. ok 322s 322s 8: cat recompressed BAM files with new header .. ok 322s 323s 9: cat CRAM files with new header .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import -0 test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/0.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import -s test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/0.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import -s test/bam2fq/5.s.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT,MD,ia -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/import/2.interleaved.fq -T "" 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/import/3.interleaved.fq -i 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/import/4.aux.fq -T "*" 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/import/4.aux.fq -T "" 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import test/import/4.aux.fq -T XZ,XA,AA 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq 323s .. ok 323s 323s test_import: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ 323s .. ok 323s 323s test_bam2fq: 323s Generate BAM file .. ok 323s 323s Generate CRAM file .. ok 323s 323s 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.002.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.003.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.004.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.004.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.010.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -t -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -t -T MD,ia -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.004.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.703.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fasta -N -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -s /tmp/eDmTdhfBJS/bam2fq.discard.s.fq -0 /tmp/eDmTdhfBJS/bam2fq.discard.0.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.013.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq --index-format 'i8n1i8' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.014.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -T '' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -t -T '*' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -T '*' -d MD:10 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -T '*' -d NM:0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -N -T '*' -d ia /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s Generate BAM file (2 threads) .. ok 323s 323s Generate CRAM file (2 threads) .. ok 323s 323s 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 323s [M::bam2fq_mainloop] processed 36 reads 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.002.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.003.sam 323s .. ok 323s 323s test_bam2fq: 323s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.004.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.004.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.010.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -t -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T MD,ia -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.004.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -i --index-format 'i*i*' -s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.005.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.703.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fasta -@ 2 -N -1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -s /tmp/eDmTdhfBJS/bam2fq.discard.s.fq -0 /tmp/eDmTdhfBJS/bam2fq.discard.0.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.013.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.014.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -T '' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T '*' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d MD:10 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d NM:0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_bam2fq: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d ia /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/bam2fq.001.sam 324s .. ok 324s 324s test_depad: 324s Generate BAM file .. ok 324s 324s depad (SAM input) .. ok 324s 324s depad -s (SAM input) .. ok 324s 324s depad -u (SAM input) .. ok 324s 324s depad -1 (SAM input) .. ok 324s 324s depad (BAM input) .. ok 324s 324s depad -s (BAM input) .. ok 324s 324s depad -u (BAM input) .. ok 324s 324s depad -1 (BAM input) .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/1_map_cigar_large.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/4_X_cigar_full_seq.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/5_insert_cigar_large.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa -i 0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/7_supp.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/7_supp_large.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/8_secondary.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/8_secondary_large.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/10_map_cigar.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -t /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -g 4 -t /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -g 4 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 324s .. ok 324s 324s test_stats: 324s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 325s .. ok 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/13_barcodes_ok.sam | tail -n+4 325s .. ok 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 325s .. ok 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 325s 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 325s .. expected failure 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 325s 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 325s .. expected failure 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 325s 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 325s .. expected failure 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -I s1 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 325s .. ok 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -I grp2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 325s .. ok 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -I grp3 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 325s .. ok 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -I Sample /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 325s .. ok 325s 325s test_stats: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/mpileup/ce.fa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/stat/15.big_del.sam | tail -n+4 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_c.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_c.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -s 1 -O sam -b /tmp/Kea3PkqSmE - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -r -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_c.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -cp -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -o - -s 1 -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_c.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/eDmTdhfBJS/merge.tag.1.bam /tmp/eDmTdhfBJS/merge.tag.2.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/eDmTdhfBJS/merge.tag.3.bam /tmp/eDmTdhfBJS/merge.tag.4.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge --no-PG -O SAM - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge --no-PG -O SAM -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/merge/merge.bed - /tmp/eDmTdhfBJS/merge.bed.1.bam /tmp/eDmTdhfBJS/merge.bed.2.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge --no-PG -r -O SAM - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_c.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_c.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam -b /tmp/lB6gtHU6VG - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -r -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_c.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -cp -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -o - -s 1 -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_c.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/eDmTdhfBJS/merge.tag.1.bam /tmp/eDmTdhfBJS/merge.tag.2.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/eDmTdhfBJS/merge.tag.3.bam /tmp/eDmTdhfBJS/merge.tag.4.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/merge/merge.bed - /tmp/eDmTdhfBJS/merge.bed.1.bam /tmp/eDmTdhfBJS/merge.bed.2.bam 325s .. ok 325s 325s test_merge: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -@ 2 --no-PG -r -O SAM - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eDmTdhfBJS/sortout 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eDmTdhfBJS/sortout.bam 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eDmTdhfBJS/sorttmp 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -N -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -t RG -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -n -t RG -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -t AS -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -t FI -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort --template-coordinate -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -M -K10 -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -M -K10 -I /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -MH -K10 -I /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eDmTdhfBJS/sortout 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eDmTdhfBJS/sortout.bam 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/eDmTdhfBJS/sorttmp 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -N -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -t RG -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -n -t RG -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 325s .. ok 325s 325s test_sort: 325s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -t AS -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 326s .. ok 326s 326s test_sort: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -t FI -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 326s .. ok 326s 326s test_sort: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 --template-coordinate -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 326s .. ok 326s 326s test_sort: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -O SAM -o - 326s .. ok 326s 326s test_sort: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -I /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 326s .. ok 326s 326s test_sort: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -@ 2 -MH -K10 -I /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 326s .. ok 326s 326s test_collate: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate --output-fmt=sam -O /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam 326s .. ok 326s 326s test_collate: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam 326s .. ok 326s 326s test_collate: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/collate2.tmp 326s .. ok 326s 326s test_collate: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate --output-fmt=sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/collate3.tmp 326s .. ok 326s 326s test_collate: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate --output-fmt=sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/1_fast_collate.sam 326s .. ok 326s 326s test_collate: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate --output-fmt=sam -f -r 4 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 326s .. ok 326s 326s test_collate: 326s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -O /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam 327s .. ok 327s 327s test_collate: 327s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam 328s .. ok 328s 328s test_collate: 328s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/collate2.tmp 329s .. ok 329s 329s test_collate: 329s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/collate3.tmp 330s .. ok 330s 330s test_collate: 330s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/1_fast_collate.sam 331s .. ok 331s 331s test_collate: 331s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f -r 4 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 332s 332s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 332s 332s .. expected failure 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/5_ct.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/sanitize.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 332s 332s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 332s 332s .. expected failure 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/5_ct.sam - 332s .. ok 332s 332s test_fixmate: 332s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 333s .. ok 333s 333s test_fixmate: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 333s .. ok 333s 333s test_fixmate: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 333s .. ok 333s 333s test_fixmate: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/fixmate/sanitize.sam - 333s .. ok 333s 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools calmd -uAr /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.ref.fa 333s .. ok 333s 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools calmd -@ 2 -uAr /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.ref.fa 333s .. ok 333s 333s test_idxstat: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam 333s .. ok 333s 333s test_idxstat: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.cram 333s .. ok 333s 333s test_idxstat: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.sam 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck -v /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 333s .. ok 333s 333s test_quickcheck: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools quickcheck -uv /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 333s .. ok 333s 333s test_reheader: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 333s .. ok 333s 333s test_reheader: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 333s .. ok 333s 333s test_reheader: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 333s .. ok 333s 333s test_reheader: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram && /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' 333s .. ok 333s 333s test_reheader: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram && /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' 333s .. ok 333s 333s test_reheader: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 333s .. ok 333s 333s test_reheader: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/1_fixup.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -O sam -m orphan_only /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -O sam -R '1#9' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/1_fixup.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/1_fixup.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/1_fixup.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/1_fixup.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m orphan_only /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -R '1#9' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/1_fixup.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/1_fixup.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 333s .. ok 333s 333s test_addrprg: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/addrprg/1_fixup.sam 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/1_name_sort.sam - 333s 333s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 333s 333s 333s .. expected failure 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/2_bad_order.sam - 333s 333s ERR: samtools markdup: error, not in coordinate sorted order. 333s 333s 333s .. expected failure 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 333s 333s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 333s 333s samtools markdup: error, unable to assign pair hash key. 333s 333s 333s .. expected failure 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 333s 333s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 333s 333s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 333s 333s 333s .. expected failure 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/5_markdup.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -O sam -r --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/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.bWnhw0/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/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.bWnhw0/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/17_read_group.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/1_name_sort.sam - 333s 333s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 333s 333s 333s .. expected failure 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/2_bad_order.sam - 333s 333s ERR: samtools markdup: error, not in coordinate sorted order. 333s 333s 333s .. expected failure 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 333s 333s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 333s 333s samtools markdup: error, unable to assign pair hash key. 333s 333s 333s .. expected failure 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 333s 333s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 333s 333s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 333s 333s 333s .. expected failure 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/5_markdup.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -O sam -r --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 333s .. ok 333s 333s test_markdup: 333s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/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.bWnhw0/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/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.bWnhw0/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/17_read_group.sam - 334s .. ok 334s 334s test_markdup: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 334s .. ok 334s 334s test_bedcov: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools bedcov /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bedcov/bedcov.bam 334s .. ok 334s 334s test_bedcov: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools bedcov -j /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bedcov/bedcov.bam 334s .. ok 334s 334s test_bedcov: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools bedcov -g512 -G2048 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bedcov/bedcov.bam 334s .. ok 334s 334s test_bedcov: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools bedcov -c /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/bedcov/bedcov.bam 334s .. ok 334s 334s test_split: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.sam 334s .. ok 334s 334s test_split: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools split --output-fmt sam -d RG -u /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.sam 334s .. ok 334s 334s test_split: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools split --output-fmt sam -d an -u /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.sam 334s .. ok 334s 334s test_split: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools split --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.sam 334s .. ok 334s 334s test_split: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.sam 334s .. ok 334s 334s test_split: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d RG -u /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.sam 334s .. ok 334s 334s test_split: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -u /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.sam 334s .. ok 334s 334s test_split: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/split/split.sam 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG /tmp/eDmTdhfBJS/longref.sam.gz 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG /tmp/eDmTdhfBJS/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view -h --no-PG -L /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/large_pos/test.bed /tmp/eDmTdhfBJS/longref.sam.gz 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/large_pos/longref_name.sam 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools merge -O sam --no-PG - /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/large_pos/longref.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/large_pos/longref2.sam 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools depth /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/large_pos/longref.sam 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools depth -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/large_pos/test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/large_pos/longref.sam 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/eDmTdhfBJS/longref.sam.gz 334s .. ok 334s 334s test_large_positions: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools fixmate -O sam --no-PG - - | 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 334s .. ok 334s 334s test_ampliconclip: 334s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 335s .. ok 335s 335s test_ampliconclip: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 335s .. ok 335s 335s test_ampliconclip: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 335s .. ok 335s 335s test_ampliconclip: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 335s .. ok 335s 335s test_ampliconclip: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 335s .. ok 335s 335s test_ampliconclip: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 335s .. ok 335s 335s test_ampliconclip: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 335s .. ok 335s 335s test_ampliconstats: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_hard_clipped.expected.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_soft_clipped.expected.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/1_soft_clipped_strand.expected.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' 335s .. ok 335s 335s test_ampliconstats: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 335s .. ok 335s 335s test_ampliconstats: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 335s .. ok 335s 335s test_reset: 335s cat /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset < /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools view 335s .. ok 335s 335s test_reset: 335s cat /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.bam 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/test_input_1_a.cram 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa_index /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG sam_to_fixed_bam /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa_index --no-PG /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG" 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output 335s .. ok 335s 335s test_reset: 335s /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/samtools reset /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.bWnhw0/autopkgtest_tmp/test/reset/output 336s .. ok 336s 336s 336s Number of tests: 336s total .. 894 336s passed .. 863 336s failed .. 0 336s expected failure .. 31 336s unexpected pass .. 0 336s 336s autopkgtest [19:20:33]: test run-unit-test: -----------------------] 337s run-unit-test PASS 337s autopkgtest [19:20:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 337s autopkgtest [19:20:34]: @@@@@@@@@@@@@@@@@@@@ summary 337s run-unit-test PASS 367s Creating nova instance adt-noble-s390x-samtools-20240325-191457-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...