0s autopkgtest [18:11:36]: starting date and time: 2024-03-25 18:11:36+0000 0s autopkgtest [18:11:36]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:11:36]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xuvedi4v/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-ppc64el-9.secgroup --name adt-noble-ppc64el-samtools-20240325-181136-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 178s autopkgtest [18:14:34]: testbed dpkg architecture: ppc64el 179s autopkgtest [18:14:35]: testbed apt version: 2.7.12 179s autopkgtest [18:14:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 180s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 181s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3989 kB] 183s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 183s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 183s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 183s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [702 kB] 183s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 183s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 183s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 183s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4271 kB] 184s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 184s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 184s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 187s Fetched 9715 kB in 5s (2067 kB/s) 190s Reading package lists... 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Calculating upgrade... 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 191s 0 upgraded, 0 newly installed, 0 to remove and 246 not upgraded. 192s sh: Attempting to set up Debian/Ubuntu apt sources automatically 192s sh: Distribution appears to be Ubuntu 193s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s eatmydata is already the newest version (131-1). 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Reading package lists... 193s Building dependency tree... 193s Reading state information... 194s dbus is already the newest version (1.14.10-4ubuntu1). 194s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s rng-tools-debian is already the newest version (2.4). 194s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 194s Reading package lists... 196s Building dependency tree... 196s Reading state information... 196s The following packages will be REMOVED: 196s cloud-init* python3-configobj* python3-debconf* 196s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 196s After this operation, 3256 kB disk space will be freed. 196s (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 ... 70156 files and directories currently installed.) 196s Removing cloud-init (24.1.2-0ubuntu1) ... 196s Removing python3-configobj (5.0.8-3) ... 196s Removing python3-debconf (1.5.86) ... 196s Processing triggers for man-db (2.12.0-3) ... 196s (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 ... 69767 files and directories currently installed.) 196s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 197s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 197s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 197s invoke-rc.d: policy-rc.d denied execution of try-restart. 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s linux-generic is already the newest version (6.8.0-11.11+1). 197s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 198s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 198s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 203s Reading package lists...Reading package lists... 203s Building dependency tree... 203s Reading state information... 203s Calculating upgrade... 203s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s Reading package lists... 203s Building dependency tree... 203s Reading state information... 203s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s 203s autopkgtest [18:14:58]: rebooting testbed after setup commands that affected boot 367s autopkgtest [18:17:43]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 371s autopkgtest [18:17:47]: @@@@@@@@@@@@@@@@@@@@ apt-source samtools 378s Get:1 http://ftpmaster.internal/ubuntu noble/universe samtools 1.19.2-1 (dsc) [2295 B] 378s Get:2 http://ftpmaster.internal/ubuntu noble/universe samtools 1.19.2-1 (tar) [5666 kB] 378s Get:3 http://ftpmaster.internal/ubuntu noble/universe samtools 1.19.2-1 (diff) [21.8 kB] 378s gpgv: Signature made Sat Feb 17 17:32:01 2024 UTC 378s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 378s gpgv: issuer "emollier@debian.org" 378s gpgv: Can't check signature: No public key 378s dpkg-source: warning: cannot verify inline signature for ./samtools_1.19.2-1.dsc: no acceptable signature found 378s autopkgtest [18:17:52]: testing package samtools version 1.19.2-1 379s autopkgtest [18:17:55]: build not needed 398s autopkgtest [18:18:14]: test run-unit-test: preparing testbed 406s Reading package lists... 406s Building dependency tree... 406s Reading state information... 406s Starting pkgProblemResolver with broken count: 0 406s Starting 2 pkgProblemResolver with broken count: 0 406s Done 407s The following additional packages will be installed: 407s libdeflate0 libhts3 libhtscodecs2 samtools samtools-test tabix 407s Suggested packages: 407s cwltool 407s Recommended packages: 407s libio-pty-perl 407s The following NEW packages will be installed: 407s autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 samtools samtools-test 407s tabix 407s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 407s Need to get 4486 kB/4486 kB of archives. 407s After this operation, 25.1 MB of additional disk space will be used. 407s Get:1 /tmp/autopkgtest.uaKpTi/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 407s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 407s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 407s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 408s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 408s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools-test all 1.19.2-1 [2401 kB] 408s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el tabix ppc64el 1.18+ds-1 [692 kB] 411s Fetched 4486 kB in 2s (2373 kB/s) 411s Selecting previously unselected package libdeflate0:ppc64el. 411s (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 ... 69712 files and directories currently installed.) 411s Preparing to unpack .../0-libdeflate0_1.19-1_ppc64el.deb ... 411s Unpacking libdeflate0:ppc64el (1.19-1) ... 411s Selecting previously unselected package libhtscodecs2:ppc64el. 411s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_ppc64el.deb ... 411s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 411s Selecting previously unselected package libhts3:ppc64el. 411s Preparing to unpack .../2-libhts3_1.18+ds-1_ppc64el.deb ... 411s Unpacking libhts3:ppc64el (1.18+ds-1) ... 411s Selecting previously unselected package samtools. 411s Preparing to unpack .../3-samtools_1.19.2-1_ppc64el.deb ... 411s Unpacking samtools (1.19.2-1) ... 411s Selecting previously unselected package samtools-test. 411s Preparing to unpack .../4-samtools-test_1.19.2-1_all.deb ... 411s Unpacking samtools-test (1.19.2-1) ... 411s Selecting previously unselected package tabix. 411s Preparing to unpack .../5-tabix_1.18+ds-1_ppc64el.deb ... 411s Unpacking tabix (1.18+ds-1) ... 411s Selecting previously unselected package autopkgtest-satdep. 411s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 411s Unpacking autopkgtest-satdep (0) ... 411s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 411s Setting up libdeflate0:ppc64el (1.19-1) ... 411s Setting up samtools-test (1.19.2-1) ... 411s Setting up tabix (1.18+ds-1) ... 411s Setting up libhts3:ppc64el (1.18+ds-1) ... 411s Setting up samtools (1.19.2-1) ... 411s Setting up autopkgtest-satdep (0) ... 411s Processing triggers for man-db (2.12.0-3) ... 411s Processing triggers for libc-bin (2.39-0ubuntu6) ... 414s (Reading database ... 70552 files and directories currently installed.) 414s Removing autopkgtest-satdep (0) ... 416s autopkgtest [18:18:32]: test run-unit-test: [----------------------- 416s test_reference: 416s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reference test/reference/mpileup.1.tmp.cram 416s .. ok 416s 416s test_reference: 416s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reference -e test/reference/mpileup.1.tmp.cram 416s .. ok 416s 416s test_reference: 416s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 416s .. ok 416s 416s test_reference: 416s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 416s .. ok 416s 416s test_reference: 416s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram 416s .. ok 416s 416s test_reference: 416s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram 416s .. ok 416s 416s test_reference: 416s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 416s .. ok 416s 416s test_reference: 416s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 417s .. ok 417s 417s bgzip -c -b 65272 -s 5 /tmp/gBHGK_11C4/bgzip.dat.gz 417s .. ok 417s 417s bgzip -c -b 979200 -s 6 /tmp/gBHGK_11C4/bgzip.dat.gz 417s .. ok 417s 417s bgzip -c -b 652804 -s 6 /tmp/gBHGK_11C4/bgzip.dat.gz 417s .. ok 417s 417s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools faidx /tmp/gBHGK_11C4/faidx.fa 3:11-13 | grep -v '^>' 417s .. ok 417s 417s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools faidx /tmp/gBHGK_11C4/faidx.fa.gz 3:11-13 | grep -v '^>' 417s .. ok 417s 417s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools faidx /tmp/gBHGK_11C4/faidx.fa 2:998-1003 | grep -v '^>' 417s .. ok 417s 417s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools faidx /tmp/gBHGK_11C4/faidx.fa.gz 2:998-1003 | grep -v '^>' 417s .. ok 417s 417s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools faidx /tmp/gBHGK_11C4/faidx.fa 1:100-104 | grep -v '^>' 417s .. ok 417s 417s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools faidx /tmp/gBHGK_11C4/faidx.fa.gz 1:100-104 | grep -v '^>' 417s .. ok 417s 417s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools faidx /tmp/gBHGK_11C4/faidx.fa 1:99998-100007 | grep -v '^>' 417s .. ok 417s 417s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools faidx /tmp/gBHGK_11C4/faidx.fa.gz 1:99998-100007 | grep -v '^>' 417s .. ok 417s 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fqidx /tmp/gBHGK_11C4/fqidx.fq 3:11-13 418s .. ok 418s 418s .. ok 418s 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fqidx /tmp/gBHGK_11C4/fqidx.fq.gz 3:11-13 418s .. ok 418s 418s .. ok 418s 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fqidx /tmp/gBHGK_11C4/fqidx.fq 2:998-1003 418s .. ok 418s 418s .. ok 418s 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fqidx /tmp/gBHGK_11C4/fqidx.fq.gz 2:998-1003 418s .. ok 418s 418s .. ok 418s 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fqidx /tmp/gBHGK_11C4/fqidx.fq 1:100-104 418s .. ok 418s 418s .. ok 418s 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fqidx /tmp/gBHGK_11C4/fqidx.fq.gz 1:100-104 418s .. ok 418s 418s .. ok 418s 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fqidx /tmp/gBHGK_11C4/fqidx.fq 1:99998-100007 418s .. ok 418s 418s .. ok 418s 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fqidx /tmp/gBHGK_11C4/fqidx.fq.gz 1:99998-100007 418s .. ok 418s 418s .. ok 418s 418s test_dict: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/dict.fa 418s .. ok 418s 418s test_dict: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/gBHGK_11C4/dict.fa.gz 418s .. ok 418s 418s test_dict: 418s cat /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/dict.fa | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz 418s .. ok 418s 418s test_dict: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools dict -AH < /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/dict.alias.fa 418s .. ok 418s 418s test_dict: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools dict -H -l /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/dict.alt < /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/dict.alias.fa 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view /tmp/gBHGK_11C4/large_chrom.bam ref2 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view /tmp/gBHGK_11C4/large_chrom.bam ref2:1-541556283 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/gBHGK_11C4/test_input_1_b.bam.bai ref2 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/gBHGK_11C4/test_input_1_b.bam.bai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -O sam - -X -cp -R ref2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/gBHGK_11C4/test_input_1_b.bam.bai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/gBHGK_11C4/test_input_1_b_opt.bam.bai ref2 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/gBHGK_11C4/auto_indexed.csi && cat /tmp/gBHGK_11C4/auto_indexed.csi 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/gBHGK_11C4/auto_indexed.crai && cat /tmp/gBHGK_11C4/auto_indexed.crai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/gBHGK_11C4/auto_indexed.csi && cat /tmp/gBHGK_11C4/auto_indexed.csi 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -@ 2 /tmp/gBHGK_11C4/large_chrom.bam ref2 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -@ 2 /tmp/gBHGK_11C4/large_chrom.bam ref2:1-541556283 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/gBHGK_11C4/test_input_1_b.bam.bai ref2 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/gBHGK_11C4/test_input_1_b.bam.bai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -O sam - -X -cp -R ref2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/gBHGK_11C4/test_input_1_b.bam.bai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/gBHGK_11C4/test_input_1_b_opt.bam.bai ref2 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -@ 2 -M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/gBHGK_11C4/auto_indexed.csi && cat /tmp/gBHGK_11C4/auto_indexed.csi 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/gBHGK_11C4/auto_indexed.crai && cat /tmp/gBHGK_11C4/auto_indexed.crai 418s .. ok 418s 418s test_index: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/gBHGK_11C4/auto_indexed.csi && cat /tmp/gBHGK_11C4/auto_indexed.csi 418s .. ok 418s 418s test_mpileup: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools mpileup -b /tmp/gBHGK_11C4/mpileup.bam.list -f /tmp/gBHGK_11C4/mpileup.ref.fa.gz -r17:100-150 418s .. ok 418s 418s test_mpileup: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools mpileup -b /tmp/gBHGK_11C4/mpileup.cram.list -f /tmp/gBHGK_11C4/mpileup.ref.fa.gz -r17:100-150 418s .. ok 418s 418s test_mpileup: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools mpileup -b /tmp/gBHGK_11C4/mpileup.bam.urllist -f /tmp/gBHGK_11C4/mpileup.ref.fa.gz -r17:100-150 418s .. ok 418s 418s test_mpileup: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools mpileup -b /tmp/gBHGK_11C4/mpileup.cram.urllist -f /tmp/gBHGK_11C4/mpileup.ref.fa.gz -r17:100-150 418s .. ok 418s 418s test_mpileup: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/gBHGK_11C4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/gBHGK_11C4/mpileup.1.bam | grep -v mpileup 418s .. ok 418s 418s test_mpileup: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/gBHGK_11C4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/gBHGK_11C4/mpileup.1.cram | grep -v mpileup 418s .. ok 418s 418s test_mpileup: 418s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools mpileup /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/mpileup/overlap.bam | grep 128814202 418s .. ok 418s 418s test_usage: 418s samtools 418s test_view: 418s Generating test data file ./test/test.pl: no IO::Pty module or can't open pty; skipping usage tests 420s .................. done 420s 1: SAM -> BAM -> SAM .. ok 420s 420s 2: SAM -> uncompressed BAM .. ok 420s 420s 3: uncompressed BAM -> SAM and compare .. ok 420s 420s 4: SAM -> fast compressed BAM .. ok 420s 420s 5: fast compressed BAM -> SAM and compare .. ok 420s 421s 6: SAM -> CRAM -> SAM (UR header tags) .. ok 421s 421s 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 421s 422s 8: BAM -> CRAM with UR -> SAM .. ok 422s 423s 9: SAM -> BAM (M5 header tags) .. ok 423s 423s 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 423s 423s 11: CRAM -> BAM with UR .. ok 423s 423s 12: CRAM -> BAM with M5 .. ok 423s 423s 13: SAM -> SAM via stdout .. ok 423s 423s 14: SAM -> BAM via stdout .. ok 423s 424s 15: SAM -> CRAM via stdout .. ok 425s 425s 16: SAM from stdin -> SAM .. ok 425s 425s 17: BAM from stdin -> SAM .. ok 425s 425s 18: CRAM from stdin -> SAM .. ok 425s 425s 19: samtools view -H (SAM input) .. ok 425s 425s 20: samtools view -H (BAM input) .. ok 425s 425s 21: samtools view -H (CRAM input) .. ok 425s 425s 22: No headers (SAM input) .. ok 425s 425s 23: No headers (BAM input) .. ok 425s 426s 24: No headers (CRAM input) .. ok 426s 426s 25: Filter -f 128 (SAM input) .. ok 426s 426s 26: Count -f 128 (SAM input) .. ok 426s 426s 27: Filter -f 128 (BAM input) .. ok 426s 426s 28: Count -f 128 (BAM input) .. ok 426s 426s 29: Filter -f 128 (CRAM input) .. ok 426s 426s 30: Count -f 128 (CRAM input) .. ok 426s 426s 31: Filter -F 128 (SAM input) .. ok 426s 426s 32: Count -F 128 (SAM input) .. ok 426s 426s 33: Filter -F 128 (BAM input) .. ok 426s 426s 34: Count -F 128 (BAM input) .. ok 426s 427s 35: Filter -F 128 (CRAM input) .. ok 427s 427s 36: Count -F 128 (CRAM input) .. ok 427s 427s 37: Filter -F 128 -f 2 (SAM input) .. ok 427s 427s 38: Count -F 128 -f 2 (SAM input) .. ok 427s 427s 39: Filter -F 128 -f 2 (BAM input) .. ok 427s 427s 40: Count -F 128 -f 2 (BAM input) .. ok 427s 427s 41: Filter -F 128 -f 2 (CRAM input) .. ok 427s 428s 42: Count -F 128 -f 2 (CRAM input) .. ok 428s 428s 43: Filter -r grp2 (SAM input) .. ok 428s 428s 44: Count -r grp2 (SAM input) .. ok 428s 428s 45: Filter -r grp2 (BAM input) .. ok 428s 428s 46: Count -r grp2 (BAM input) .. ok 428s 428s 47: Filter -r grp2 (CRAM input) .. ok 428s 428s 48: Count -r grp2 (CRAM input) .. ok 428s 428s 49: Filter -R /tmp/gBHGK_11C4/view.001.fogn (SAM input) .. ok 428s 428s 50: Count -R /tmp/gBHGK_11C4/view.001.fogn (SAM input) .. ok 428s 428s 51: Filter -R /tmp/gBHGK_11C4/view.001.fogn (BAM input) .. ok 428s 428s 52: Count -R /tmp/gBHGK_11C4/view.001.fogn (BAM input) .. ok 428s 430s 53: Filter -R /tmp/gBHGK_11C4/view.001.fogn (CRAM input) .. ok 430s 430s 54: Count -R /tmp/gBHGK_11C4/view.001.fogn (CRAM input) .. ok 430s 430s 55: Filter -R /tmp/gBHGK_11C4/view.001.fogn -r grp2 (SAM input).. ok 430s 430s 56: Count -R /tmp/gBHGK_11C4/view.001.fogn -r grp2 (SAM input).. ok 430s 430s 57: Filter -R /tmp/gBHGK_11C4/view.001.fogn -r grp2 (BAM input).. ok 430s 430s 58: Count -R /tmp/gBHGK_11C4/view.001.fogn -r grp2 (BAM input).. ok 430s 430s 59: Filter -R /tmp/gBHGK_11C4/view.001.fogn -r grp2 (CRAM input).. ok 430s 430s 60: Count -R /tmp/gBHGK_11C4/view.001.fogn -r grp2 (CRAM input).. ok 430s 430s 61: Filter -r grp2 -R /tmp/gBHGK_11C4/view.001.fogn (SAM input).. ok 430s 430s 62: Count -r grp2 -R /tmp/gBHGK_11C4/view.001.fogn (SAM input).. ok 430s 430s 63: Filter -r grp2 -R /tmp/gBHGK_11C4/view.001.fogn (BAM input).. ok 430s 430s 64: Count -r grp2 -R /tmp/gBHGK_11C4/view.001.fogn (BAM input).. ok 430s 430s 65: Filter -r grp2 -R /tmp/gBHGK_11C4/view.001.fogn (CRAM input).. ok 430s 430s 66: Count -r grp2 -R /tmp/gBHGK_11C4/view.001.fogn (CRAM input).. ok 430s 430s 67: Filter -N /tmp/gBHGK_11C4/view.001.forn (SAM input) .. ok 430s 430s 68: Count -N /tmp/gBHGK_11C4/view.001.forn (SAM input) .. ok 430s 430s 69: Filter -N /tmp/gBHGK_11C4/view.001.forn (BAM input) .. ok 430s 430s 70: Count -N /tmp/gBHGK_11C4/view.001.forn (BAM input) .. ok 430s 430s 71: Filter -N /tmp/gBHGK_11C4/view.001.forn (CRAM input) .. ok 430s 430s 72: Count -N /tmp/gBHGK_11C4/view.001.forn (CRAM input) .. ok 430s 430s 73: Filter -d BC (SAM input) .. ok 430s 430s 74: Count -d BC (SAM input) .. ok 430s 430s 75: Filter -d BC (BAM input) .. ok 430s 430s 76: Count -d BC (BAM input) .. ok 430s 431s 77: Filter -d BC (CRAM input) .. ok 431s 431s 78: Count -d BC (CRAM input) .. ok 431s 431s 79: Filter -d BC:TGCA (SAM input) .. ok 431s 431s 80: Count -d BC:TGCA (SAM input) .. ok 431s 431s 81: Filter -d BC:TGCA (BAM input) .. ok 431s 431s 82: Count -d BC:TGCA (BAM input) .. ok 431s 432s 83: Filter -d BC:TGCA (CRAM input) .. ok 432s 432s 84: Count -d BC:TGCA (CRAM input) .. ok 432s 432s 85: Filter -D BC:/tmp/gBHGK_11C4/view.001.fobc (SAM input) .. ok 432s 432s 86: Count -D BC:/tmp/gBHGK_11C4/view.001.fobc (SAM input) .. ok 432s 432s 87: Filter -D BC:/tmp/gBHGK_11C4/view.001.fobc (BAM input) .. ok 432s 432s 88: Count -D BC:/tmp/gBHGK_11C4/view.001.fobc (BAM input) .. ok 432s 432s 89: Filter -D BC:/tmp/gBHGK_11C4/view.001.fobc (CRAM input) .. ok 432s 432s 90: Count -D BC:/tmp/gBHGK_11C4/view.001.fobc (CRAM input) .. ok 432s 432s 91: Filter -D BC:/tmp/gBHGK_11C4/view.001.fobc -d BC:TGCA (SAM input).. ok 432s 432s 92: Count -D BC:/tmp/gBHGK_11C4/view.001.fobc -d BC:TGCA (SAM input).. ok 432s 432s 93: Filter -D BC:/tmp/gBHGK_11C4/view.001.fobc -d BC:TGCA (BAM input).. ok 432s 432s 94: Count -D BC:/tmp/gBHGK_11C4/view.001.fobc -d BC:TGCA (BAM input).. ok 432s 433s 95: Filter -D BC:/tmp/gBHGK_11C4/view.001.fobc -d BC:TGCA (CRAM input).. ok 433s 433s 96: Count -D BC:/tmp/gBHGK_11C4/view.001.fobc -d BC:TGCA (CRAM input).. ok 433s 433s 97: Filter -d BC:TGCA -D BC:/tmp/gBHGK_11C4/view.001.fobc (SAM input).. ok 433s 433s 98: Count -d BC:TGCA -D BC:/tmp/gBHGK_11C4/view.001.fobc (SAM input).. ok 433s 433s 99: Filter -d BC:TGCA -D BC:/tmp/gBHGK_11C4/view.001.fobc (BAM input).. ok 433s 433s 100: Count -d BC:TGCA -D BC:/tmp/gBHGK_11C4/view.001.fobc (BAM input).. ok 433s 434s 101: Filter -d BC:TGCA -D BC:/tmp/gBHGK_11C4/view.001.fobc (CRAM input).. ok 434s 434s 102: Count -d BC:TGCA -D BC:/tmp/gBHGK_11C4/view.001.fobc (CRAM input).. ok 434s 434s 103: Filter -D RG:/tmp/gBHGK_11C4/view.001.fogn (SAM input) .. ok 434s 434s 104: Count -D RG:/tmp/gBHGK_11C4/view.001.fogn (SAM input) .. ok 434s 434s 105: Filter -D RG:/tmp/gBHGK_11C4/view.001.fogn (BAM input) .. ok 434s 434s 106: Count -D RG:/tmp/gBHGK_11C4/view.001.fogn (BAM input) .. ok 434s 434s 107: Filter -D RG:/tmp/gBHGK_11C4/view.001.fogn (CRAM input).. ok 434s 434s 108: Count -D RG:/tmp/gBHGK_11C4/view.001.fogn (CRAM input) .. ok 434s 434s 109: Filter -d NE:TGCA (SAM input) .. ok 434s 434s 110: Count -d NE:TGCA (SAM input) .. ok 434s 434s 111: Filter -d NE:TGCA (BAM input) .. ok 434s 434s 112: Count -d NE:TGCA (BAM input) .. ok 434s 435s 113: Filter -d NE:TGCA (CRAM input) .. ok 435s 435s 114: Count -d NE:TGCA (CRAM input) .. ok 435s 435s 115: Filter -d TGCA (SAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test115.sam -h -d TGCA /tmp/gBHGK_11C4/view.001.sam --no-PG 435s 435s 435s .. expected failure 435s 435s 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" 435s samtools view: Invalid "tag:value" option: "TGCA" 435s Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -d TGCA /tmp/gBHGK_11C4/view.001.sam --no-PG 435s 435s 435s .. expected failure 435s 435s 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 435s Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test117.sam -h -d TGCA /tmp/gBHGK_11C4/view.test001.bam --no-PG 435s 435s 435s .. expected failure 435s 435s 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 435s Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -d TGCA /tmp/gBHGK_11C4/view.test001.bam --no-PG 435s 435s 435s .. expected failure 435s 435s 119: Filter -d TGCA (CRAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test119.sam -h -d TGCA /tmp/gBHGK_11C4/view.test006.cram --no-PG 435s 435s 435s .. expected failure 435s 435s 120: Count -d TGCA (CRAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -d TGCA /tmp/gBHGK_11C4/view.test006.cram --no-PG 435s 435s 435s .. expected failure 435s 435s 121: Filter -D BClong:/tmp/gBHGK_11C4/view.001.fobc (SAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test121.sam -h -D BClong:/tmp/gBHGK_11C4/view.001.fobc /tmp/gBHGK_11C4/view.001.sam --no-PG 435s 435s 435s .. expected failure 435s 435s 122: Count -D BClong:/tmp/gBHGK_11C4/view.001.fobc (SAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -D BClong:/tmp/gBHGK_11C4/view.001.fobc /tmp/gBHGK_11C4/view.001.sam --no-PG 435s 435s 435s .. expected failure 435s 435s 123: Filter -D BClong:/tmp/gBHGK_11C4/view.001.fobc (BAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test123.sam -h -D BClong:/tmp/gBHGK_11C4/view.001.fobc /tmp/gBHGK_11C4/view.test001.bam --no-PG 435s 435s 435s .. expected failure 435s 435s 124: Count -D BClong:/tmp/gBHGK_11C4/view.001.fobc (BAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -D BClong:/tmp/gBHGK_11C4/view.001.fobc /tmp/gBHGK_11C4/view.test001.bam --no-PG 435s 435s 435s .. expected failure 435s 435s 125: Filter -D BClong:/tmp/gBHGK_11C4/view.001.fobc (CRAM input)samtools view: Invalid "tag:value" option: "TGCA" 435s samtools view: Invalid "tag:value" option: "TGCA" 435s samtools view: Invalid "tag:file" option: "BClong:/tmp/gBHGK_11C4/view.001.fobc" 435s samtools view: Invalid "tag:file" option: "BClong:/tmp/gBHGK_11C4/view.001.fobc" 435s samtools view: Invalid "tag:file" option: "BClong:/tmp/gBHGK_11C4/view.001.fobc" 435s samtools view: Invalid "tag:file" option: "BClong:/tmp/gBHGK_11C4/view.001.fobc" 435s samtools view: Invalid "tag:file" option: "BClong:/tmp/gBHGK_11C4/view.001.fobc" 435s Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test125.sam -h -D BClong:/tmp/gBHGK_11C4/view.001.fobc /tmp/gBHGK_11C4/view.test006.cram --no-PG 435s 435s 435s .. expected failure 435s 435s 126: Count -D BClong:/tmp/gBHGK_11C4/view.001.fobc (CRAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -D BClong:/tmp/gBHGK_11C4/view.001.fobc /tmp/gBHGK_11C4/view.test006.cram --no-PG 435s 435s 435s .. expected failure 435s 435s 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/gBHGK_11C4/view.001.sam --no-PG 435s 435s 435s .. expected failure 435s 435s 128: Count -d BC:ACGT -d RG:grp2 (SAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/gBHGK_11C4/view.001.sam --no-PG 435s 435s 435s .. expected failure 435s 435s 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/gBHGK_11C4/view.test001.bam --no-PG 435s 435s 435s .. expected failure 435s 435s 130: Count -d BC:ACGT -d RG:grp2 (BAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/gBHGK_11C4/view.test001.bam --no-PG 435s 435s 435s .. expected failure 435s 435s 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -o /tmp/gBHGK_11C4/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/gBHGK_11C4/view.test006.cram --no-PG 435s 435s 435s .. expected failure 435s 435s 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Invalid "tag:file" option: "BClong:/tmp/gBHGK_11C4/view.001.fobc" 435s samtools view: Different tag "BC" was specified before: "RG:grp2" 435s samtools view: Different tag "BC" was specified before: "RG:grp2" 435s samtools view: Different tag "BC" was specified before: "RG:grp2" 435s samtools view: Different tag "BC" was specified before: "RG:grp2" 435s samtools view: Different tag "BC" was specified before: "RG:grp2" 435s samtools view: Different tag "BC" was specified before: "RG:grp2" 435s Failed command: 435s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/gBHGK_11C4/view.test006.cram --no-PG 435s 435s 435s .. expected failure 435s 435s 133: Filter -d NM:13 (SAM input) .. ok 435s 435s 134: Count -d NM:13 (SAM input) .. ok 435s 435s 135: Filter -d NM:13 (BAM input) .. ok 435s 435s 136: Count -d NM:13 (BAM input) .. ok 435s 435s 137: Filter -d NM:13 (CRAM input) .. ok 435s 436s 138: Count -d NM:13 (CRAM input) .. ok 436s 436s 139: Filter -d ab:z (SAM input) .. ok 436s 436s 140: Count -d ab:z (SAM input) .. ok 436s 436s 141: Filter -d ab:z (BAM input) .. ok 436s 436s 142: Count -d ab:z (BAM input) .. ok 436s 437s 143: Filter -d ab:z (CRAM input) .. ok 437s 437s 144: Count -d ab:z (CRAM input) .. ok 437s 437s 145: Filter -l Library 2 (SAM input) .. ok 437s 437s 146: Count -l Library 2 (SAM input) .. ok 437s 437s 147: Filter -l Library 2 (BAM input) .. ok 437s 437s 148: Count -l Library 2 (BAM input) .. ok 437s 437s 149: Filter -l Library 2 (CRAM input) .. ok 437s 437s 150: Count -l Library 2 (CRAM input) .. ok 437s 437s 151: Filter -l Library 3 (SAM input) .. ok 437s 437s 152: Count -l Library 3 (SAM input) .. ok 437s 437s 153: Filter -l Library 3 (BAM input) .. ok 437s 437s 154: Count -l Library 3 (BAM input) .. ok 437s 438s 155: Filter -l Library 3 (CRAM input) .. ok 438s 438s 156: Count -l Library 3 (CRAM input) .. ok 438s 438s 157: Filter -q 50 (SAM input) .. ok 438s 438s 158: Count -q 50 (SAM input) .. ok 438s 438s 159: Filter -q 50 (BAM input) .. ok 438s 438s 160: Count -q 50 (BAM input) .. ok 438s 439s 161: Filter -q 50 (CRAM input) .. ok 439s 439s 162: Count -q 50 (CRAM input) .. ok 439s 439s 163: Filter -q 99 (SAM input) .. ok 439s 439s 164: Count -q 99 (SAM input) .. ok 439s 439s 165: Filter -q 99 (BAM input) .. ok 439s 439s 166: Count -q 99 (BAM input) .. ok 439s 439s 167: Filter -q 99 (CRAM input) .. ok 439s 439s 168: Count -q 99 (CRAM input) .. ok 439s 439s 169: Filter -q 100 (SAM input) .. ok 439s 439s 170: Count -q 100 (SAM input) .. ok 439s 439s 171: Filter -q 100 (BAM input) .. ok 439s 439s 172: Count -q 100 (BAM input) .. ok 439s 440s 173: Filter -q 100 (CRAM input) .. ok 440s 440s 174: Count -q 100 (CRAM input) .. ok 440s 440s 175: Filter -x fa (SAM input) .. ok 440s 440s 176: Count -x fa (SAM input) .. ok 440s 440s 177: Filter -x fa (BAM input) .. ok 440s 440s 178: Count -x fa (BAM input) .. ok 440s 440s 179: Filter -x fa (CRAM input) .. ok 440s 440s 180: Count -x fa (CRAM input) .. ok 440s 440s 181: Filter -x fa -x ha (SAM input) .. ok 440s 440s 182: Count -x fa -x ha (SAM input) .. ok 440s 440s 183: Filter -x fa -x ha (BAM input) .. ok 440s 440s 184: Count -x fa -x ha (BAM input) .. ok 440s 441s 185: Filter -x fa -x ha (CRAM input) .. ok 441s 441s 186: Count -x fa -x ha (CRAM input) .. ok 441s 441s 187: Filter -x fa,ha (SAM input) .. ok 441s 441s 188: Count -x fa,ha (SAM input) .. ok 441s 441s 189: Filter -x fa,ha (BAM input) .. ok 441s 441s 190: Count -x fa,ha (BAM input) .. ok 441s 441s 191: Filter -x fa,ha (CRAM input) .. ok 441s 441s 192: Count -x fa,ha (CRAM input) .. ok 441s 441s 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 441s 441s 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 441s 441s 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 441s 441s 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 441s 442s 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 442s 442s 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 442s 442s 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 442s 442s 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 442s 442s 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 442s 442s 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 442s 442s 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 442s 442s 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 442s 442s 205: Filter -x fa -r grp2 (SAM input) .. ok 442s 442s 206: Count -x fa -r grp2 (SAM input) .. ok 442s 442s 207: Filter -x fa -r grp2 (BAM input) .. ok 442s 442s 208: Count -x fa -r grp2 (BAM input) .. ok 442s 443s 209: Filter -x fa -r grp2 (CRAM input) .. ok 443s 443s 210: Count -x fa -r grp2 (CRAM input) .. ok 443s 443s 211: Filter -x RG -r grp2 (SAM input) .. ok 443s 443s 212: Count -x RG -r grp2 (SAM input) .. ok 443s 443s 213: Filter -x RG -r grp2 (BAM input) .. ok 443s 443s 214: Count -x RG -r grp2 (BAM input) .. ok 443s 445s 215: Filter -x RG -r grp2 (CRAM input) .. ok 445s 445s 216: Count -x RG -r grp2 (CRAM input) .. ok 445s 445s 217: Filter -m 10 (SAM input) .. ok 445s 445s 218: Count -m 10 (SAM input) .. ok 445s 445s 219: Filter -m 10 (BAM input) .. ok 445s 445s 220: Count -m 10 (BAM input) .. ok 445s 445s 221: Filter -m 10 (CRAM input) .. ok 445s 445s 222: Count -m 10 (CRAM input) .. ok 445s 445s 223: Filter -m 11 (SAM input) .. ok 445s 445s 224: Count -m 11 (SAM input) .. ok 445s 445s 225: Filter -m 11 (BAM input) .. ok 445s 445s 226: Count -m 11 (BAM input) .. ok 445s 446s 227: Filter -m 11 (CRAM input) .. ok 446s 446s 228: Count -m 11 (CRAM input) .. ok 446s 446s 229: Filter -m 15 (SAM input) .. ok 446s 446s 230: Count -m 15 (SAM input) .. ok 446s 446s 231: Filter -m 15 (BAM input) .. ok 446s 446s 232: Count -m 15 (BAM input) .. ok 446s 447s 233: Filter -m 15 (CRAM input) .. ok 447s 447s 234: Count -m 15 (CRAM input) .. ok 447s 447s 235: Filter -m 16 (SAM input) .. ok 447s 447s 236: Count -m 16 (SAM input) .. ok 447s 447s 237: Filter -m 16 (BAM input) .. ok 447s 447s 238: Count -m 16 (BAM input) .. ok 447s 448s 239: Filter -m 16 (CRAM input) .. ok 448s 449s 240: Count -m 16 (CRAM input) .. ok 449s 449s 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 449s 449s 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 449s 449s 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 449s 449s 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 449s 449s 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 449s 450s 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 450s 450s 247: Filter -e [BC] (SAM input) .. ok 450s 450s 248: Count -e [BC] (SAM input) .. ok 450s 450s 249: Filter -e [BC] (BAM input) .. ok 450s 450s 250: Count -e [BC] (BAM input) .. ok 450s 450s 251: Filter -e [BC] (CRAM input) .. ok 450s 451s 252: Count -e [BC] (CRAM input) .. ok 451s 451s 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 451s 451s 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 451s 451s 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 451s 451s 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 451s 452s 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 452s 452s 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 452s 452s 259: Filter -e mapq >= 50 (SAM input) .. ok 452s 452s 260: Count -e mapq >= 50 (SAM input) .. ok 452s 452s 261: Filter -e mapq >= 50 (BAM input) .. ok 452s 452s 262: Count -e mapq >= 50 (BAM input) .. ok 452s 453s 263: Filter -e mapq >= 50 (CRAM input) .. ok 453s 454s 264: Count -e mapq >= 50 (CRAM input) .. ok 454s 454s 265: Filter -e mapq >= 99 (SAM input) .. ok 454s 454s 266: Count -e mapq >= 99 (SAM input) .. ok 454s 454s 267: Filter -e mapq >= 99 (BAM input) .. ok 454s 454s 268: Count -e mapq >= 99 (BAM input) .. ok 454s 454s 269: Filter -e mapq >= 99 (CRAM input) .. ok 454s 455s 270: Count -e mapq >= 99 (CRAM input) .. ok 455s 455s 271: Filter -e mapq >= 100 (SAM input) .. ok 455s 455s 272: Count -e mapq >= 100 (SAM input) .. ok 455s 455s 273: Filter -e mapq >= 100 (BAM input) .. ok 455s 455s 274: Count -e mapq >= 100 (BAM input) .. ok 455s 456s 275: Filter -e mapq >= 100 (CRAM input) .. ok 456s 456s 276: Count -e mapq >= 100 (CRAM input) .. ok 456s 456s 277: 1bp reads file SAM -> BAM -> SAM .. ok 456s 457s 278: 1bp reads file SAM -> CRAM -> SAM .. ok 458s 458s 278: Region Z (BAM input) .. ok 458s 458s 279: Count Z (BAM input) .. ok 458s 458s 280: Region Z (CRAM input) .. ok 458s 458s 281: Count Z (CRAM input) .. ok 458s 458s 282: Region Z:30 (BAM input) .. ok 458s 458s 283: Count Z:30 (BAM input) .. ok 458s 459s 284: Region Z:30 (CRAM input) .. ok 459s 459s 285: Count Z:30 (CRAM input) .. ok 459s 459s 286: Region Z:20-40 (BAM input) .. ok 459s 459s 287: Count Z:20-40 (BAM input) .. ok 459s 459s 288: Region Z:20-40 (CRAM input) .. ok 459s 459s 289: Count Z:20-40 (CRAM input) .. ok 459s 459s 290: Region ref1 (BAM input) .. ok 459s 459s 291: Count ref1 (BAM input) .. ok 459s 460s 292: Region ref1 (CRAM input) .. ok 460s 460s 293: Count ref1 (CRAM input) .. ok 460s 460s 294: Region ref1:15 (BAM input) .. ok 460s 460s 295: Count ref1:15 (BAM input) .. ok 460s 460s 296: Region ref1:15 (CRAM input) .. ok 460s 460s 297: Count ref1:15 (CRAM input) .. ok 460s 460s 298: Region ref1:15-45 (BAM input) .. ok 460s 460s 299: Count ref1:15-45 (BAM input) .. ok 460s 461s 300: Region ref1:15-45 (CRAM input) .. ok 461s 461s 301: Count ref1:15-45 (CRAM input) .. ok 461s 461s 302: Region ref1:15-45 ref2 (BAM input) .. ok 461s 461s 303: Count ref1:15-45 ref2 (BAM input) .. ok 461s 463s 304: Region ref1:15-45 ref2 (CRAM input) .. ok 463s 463s 305: Count ref1:15-45 ref2 (CRAM input) .. ok 463s 463s 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 463s 463s 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 463s 463s 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 463s 463s 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 463s 463s 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 463s 463s 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 463s 463s 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 463s 463s 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 463s 463s 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 463s 463s 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 463s 463s 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 463s 463s 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 463s 463s 318: Region -f 128 ref1 (BAM input) .. ok 463s 464s 319: Count -f 128 ref1 (BAM input) .. ok 464s 464s 320: Region -f 128 ref1 (CRAM input) .. ok 464s 464s 321: Count -f 128 ref1 (CRAM input) .. ok 464s 464s 322: Region -q 50 ref1:15-45 (BAM input) .. ok 464s 464s 323: Count -q 50 ref1:15-45 (BAM input) .. ok 464s 465s 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 465s 465s 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 465s 465s 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 465s 465s 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 465s 465s 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 465s 465s 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 465s 465s 330: Region * (BAM input) .. ok 465s 465s 331: Count * (BAM input) .. ok 465s 465s 332: Region * (CRAM input) .. ok 465s 465s 333: Count * (CRAM input) .. ok 465s 465s 334: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 465s 465s 335: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 465s 466s 336: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 466s 466s 337: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 466s 466s 338: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 466s 466s 339: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 466s 468s 340: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 468s 468s 341: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 468s 468s 342: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 468s 468s 343: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 468s 468s 344: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 468s 468s 345: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 468s 468s 346: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 468s 468s 347: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 468s 468s 348: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 468s 468s 349: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 468s 468s 350: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 468s 468s 351: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 468s 468s 352: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 468s 468s 353: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 468s 468s 354: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 468s 468s 355: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 468s 468s 356: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 468s 468s 357: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 468s 468s 358: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 468s 468s 359: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 468s 469s 360: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 469s 469s 361: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 469s 469s 362: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 469s 469s 363: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 469s 470s 364: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 470s 470s 365: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 470s 470s 366: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 470s 470s 367: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 470s 470s 368: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 470s 470s 369: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 470s 470s 370: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 470s 470s 371: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 470s 471s 372: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 471s 471s 373: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 471s 471s 374: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 471s 471s 375: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 471s 471s 376: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 471s 471s 377: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 471s 471s 378: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 471s 471s 379: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 471s 472s 380: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 472s 472s 381: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 472s 472s 382: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 472s 472s 383: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 472s 472s 384: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 472s 472s 385: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 472s 472s 386: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 472s 472s 387: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 472s 473s 388: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 473s 473s 389: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 473s 473s 390: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 473s 473s 391: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 473s 474s 392: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 474s 474s 393: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 474s 474s 394: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 474s 474s 395: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 474s 474s 396: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 474s 474s 397: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 474s 474s 398: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 474s 474s 399: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 474s 475s 400: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 475s 475s 401: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 475s 475s 402: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 475s 475s 403: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 475s 476s 404: Region -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 476s 476s 405: Count -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 476s 476s 406: Make BAM with no M5/UR tags .. ok 476s 476s 407: Add @SQ with -t (SAM -> SAM) .. ok 476s 476s 408: Add @SQ with -T (SAM -> SAM) .. ok 476s 476s 409: Add @SQ with -t (BAM -> SAM) .. ok 476s 476s 410: Add @SQ with -T (BAM -> SAM) .. ok 476s 476s 411: Add @SQ with -t (SAM -> BAM) .. ok 476s 476s 412: Add @SQ with -T (SAM -> BAM) .. ok 476s 476s 413: Add @SQ with -t (BAM -> BAM) .. ok 476s 476s 414: Add @SQ with -T (BAM -> BAM) .. ok 476s 476s 415: Add @SQ with -t (SAM -> CRAM) .. ok 476s 477s 416: Add @SQ with -T (SAM -> CRAM) .. ok 477s 477s 417: Add @SQ with -t (BAM -> CRAM) .. ok 477s 478s 418: Add @SQ with -T (BAM -> CRAM) .. ok 478s 478s 419: Make CRAM with no UR field .. ok 478s 478s 420: Decoding CRAM with no UR field via -T .. ok 478s 478s 421: CIGAR B-operator removal .. ok 478s 479s 422: Big SAM -> BAM .. ok 479s 479s 423: Big SAM -> BAM (2 threads) .. ok 479s 479s 424: Big SAM -> BAM (4 threads) .. ok 479s 482s 425: Big SAM -> CRAM .. ok 482s 483s 426: Big SAM -> CRAM (2 threads) .. ok 483s 485s 427: Big SAM -> CRAM (4 threads) .. ok 485s 487s 428: Subsample 0.2 (SAM input) ............ ok 487s 489s 429: Subsample 0.5 (SAM input) ............ ok 489s 491s 430: Subsample 0.8 (SAM input) ............ ok 491s 491s 431: Subsample 0.2 (BAM input) ............ ok 491s 492s 432: Subsample 0.5 (BAM input) ............ ok 492s 494s 433: Subsample 0.8 (BAM input) ............ ok 494s 500s 434: Subsample 0.2 (CRAM input) ............ ok 500s 507s 435: Subsample 0.5 (CRAM input) ............ ok 507s 514s 436: Subsample 0.8 (CRAM input) ............ ok 514s 514s 437: SAM add PG .. ok 514s 514s 438: Unset dup flag, remove dt and do tags .. ok 514s 514s 439: Unmap dup flagged reads. .. ok 514s 514s 440: Unmap dup flagged reads. .. ok 514s 514s 441: fetch pairs .. ok 514s 514s 442: fetch pairs .. ok 514s 514s 443: fetch pairs .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -h 0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -h 1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -h 5 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -h 29 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -h 30 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -n 0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -n 1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -n 5 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_head: 514s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools head -h 5 -n 5 < /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.sam 514s .. ok 514s 514s test_cat: 514s Generating test data file .................. done 514s Generate BAM file #1 .. ok 514s 515s Generate CRAM file #1 .. ok 515s 515s Generating test data file .................. done 515s Generate BAM file #2 .. ok 515s 515s Generate CRAM file #2 .. ok 515s 516s Generating test data file .................. done 516s Generate BAM file #3 .. ok 516s 516s Generate CRAM file #3 .. ok 516s 516s Generating test data file .................. done 516s Generate BAM file #4 .. ok 516s 517s Generate CRAM file #4 .. ok 517s 517s 1: cat BAM files .. ok 517s 517s 2: cat recompressed BAM files .. ok 517s 518s 3: cat CRAM files .. ok 518s 518s 4: cat BAM files to stdout .. ok 518s 518s 5: cat recompressed BAM files to stdout .. ok 518s 518s 6: cat CRAM files to stdout .. ok 518s 518s 7: cat BAM files with new header .. ok 518s 518s 8: cat recompressed BAM files with new header .. ok 518s 519s 9: cat CRAM files with new header .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import -0 test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/0.fq 519s [M::bam2fq_mainloop] discarded 0 singletons 519s [M::bam2fq_mainloop] processed 36 reads 519s [M::bam2fq_mainloop] discarded 0 singletons 519s [M::bam2fq_mainloop] processed 36 reads 519s [M::bam2fq_mainloop] discarded 0 singletons 519s [M::bam2fq_mainloop] processed 36 reads 519s [M::bam2fq_mainloop] discarded 0 singletons 519s [M::bam2fq_mainloop] processed 36 reads 519s [M::bam2fq_mainloop] discarded 0 singletons 519s [M::bam2fq_mainloop] processed 36 reads 519s [M::bam2fq_mainloop] discarded 0 singletons 519s [M::bam2fq_mainloop] processed 36 reads 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import -s test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/0.fq 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import -s test/bam2fq/5.s.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT,MD,ia -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/import/2.interleaved.fq -T "" 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/import/3.interleaved.fq -i 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/import/4.aux.fq -T "*" 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/import/4.aux.fq -T "" 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools import test/import/4.aux.fq -T XZ,XA,AA 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/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 519s .. ok 519s 519s test_import: 519s /tmp/autopkgtest.uaKpTi/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 519s .. ok 519s 519s test_bam2fq: 519s Generate BAM file .. ok 519s 519s Generate CRAM file .. ok 519s 519s 1: fastq (SAM input) .. ok 519s 519s 2: fastq -n (SAM input) .. ok 519s 519s 3: fastq (BAM input) .. ok 519s 519s 4: fastq -n (BAM input) .. ok 519s 519s 5: fastq (CRAM input) .. ok 519s 519s 6: fastq -n (CRAM input) .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.002.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.003.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.004.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.004.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.010.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -t -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -t -T MD,ia -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.004.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.703.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fasta -N -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -s /tmp/gBHGK_11C4/bam2fq.discard.s.fq -0 /tmp/gBHGK_11C4/bam2fq.discard.0.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.013.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq --index-format 'i8n1i8' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.014.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -T '' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -t -T '*' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -T '*' -d MD:10 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -T '*' -d NM:0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -N -T '*' -d ia /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 519s .. ok 519s 519s test_bam2fq: 519s Generate BAM file (2 threads) .. ok 519s 520s Generate CRAM file (2 threads) .. ok 520s 520s 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 520s [M::bam2fq_mainloop] processed 36 reads 520s .. ok 520s 520s 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 520s [M::bam2fq_mainloop] processed 36 reads 520s .. ok 520s 520s 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 520s [M::bam2fq_mainloop] processed 36 reads 520s .. ok 520s 520s 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 520s [M::bam2fq_mainloop] processed 36 reads 520s .. ok 520s 520s 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 520s [M::bam2fq_mainloop] processed 36 reads 520s .. ok 520s 520s 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 520s [M::bam2fq_mainloop] processed 36 reads 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.002.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.003.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.004.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.004.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.010.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -t -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T MD,ia -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.004.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -i --index-format 'i*i*' -s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.005.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.703.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fasta -@ 2 -N -1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -s /tmp/gBHGK_11C4/bam2fq.discard.s.fq -0 /tmp/gBHGK_11C4/bam2fq.discard.0.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.013.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.014.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -T '' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T '*' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d MD:10 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d NM:0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_bam2fq: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d ia /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/bam2fq.001.sam 520s .. ok 520s 520s test_depad: 520s Generate BAM file .. ok 520s 520s depad (SAM input) .. ok 520s 520s depad -s (SAM input) .. ok 520s 520s depad -u (SAM input) .. ok 520s 520s depad -1 (SAM input) .. ok 520s 520s depad (BAM input) .. ok 520s 520s depad -s (BAM input) .. ok 520s 520s depad -u (BAM input) .. ok 520s 520s depad -1 (BAM input) .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/1_map_cigar_large.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/4_X_cigar_full_seq.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/5_insert_cigar_large.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa -i 0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/7_supp.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/7_supp_large.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/8_secondary.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/8_secondary_large.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/10_map_cigar.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -t /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -g 4 -t /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -g 4 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/13_barcodes_ok.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 520s 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 520s .. expected failure 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 520s 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 520s .. expected failure 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 520s 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 520s .. expected failure 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -I s1 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -I grp2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -I grp3 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -I Sample /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 520s .. ok 520s 520s test_stats: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/mpileup/ce.fa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/stat/15.big_del.sam | tail -n+4 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_c.sam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_c.bam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -s 1 -O sam -b /tmp/tY4_Qf3nol - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -r -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_c.sam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -cp -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.sam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -o - -s 1 -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_c.sam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/gBHGK_11C4/merge.tag.1.bam /tmp/gBHGK_11C4/merge.tag.2.bam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/gBHGK_11C4/merge.tag.3.bam /tmp/gBHGK_11C4/merge.tag.4.bam 520s .. ok 520s 520s test_merge: 520s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge --no-PG -O SAM - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge --no-PG -O SAM -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/merge/merge.bed - /tmp/gBHGK_11C4/merge.bed.1.bam /tmp/gBHGK_11C4/merge.bed.2.bam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge --no-PG -r -O SAM - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_c.sam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_c.bam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam -b /tmp/oJPK2bN2QE - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -r -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_c.sam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -cp -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.sam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -o - -s 1 -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_c.sam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/gBHGK_11C4/merge.tag.1.bam /tmp/gBHGK_11C4/merge.tag.2.bam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/gBHGK_11C4/merge.tag.3.bam /tmp/gBHGK_11C4/merge.tag.4.bam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/merge/merge.bed - /tmp/gBHGK_11C4/merge.bed.1.bam /tmp/gBHGK_11C4/merge.bed.2.bam 521s .. ok 521s 521s test_merge: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -@ 2 --no-PG -r -O SAM - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/gBHGK_11C4/sortout 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/gBHGK_11C4/sortout.bam 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/gBHGK_11C4/sorttmp 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -N -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -t RG -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -n -t RG -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -t AS -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -t FI -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort --template-coordinate -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -M -K10 -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -M -K10 -I /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -MH -K10 -I /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/gBHGK_11C4/sortout 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/gBHGK_11C4/sortout.bam 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/gBHGK_11C4/sorttmp 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -N -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -t RG -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -n -t RG -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -t AS -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -t FI -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 --template-coordinate -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -I /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 521s .. ok 521s 521s test_sort: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -@ 2 -MH -K10 -I /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 521s .. ok 521s 521s test_collate: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate --output-fmt=sam -O /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam 521s .. ok 521s 521s test_collate: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam 521s .. ok 521s 521s test_collate: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/collate2.tmp 521s .. ok 521s 521s test_collate: 521s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate --output-fmt=sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/collate3.tmp 522s .. ok 522s 522s test_collate: 522s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate --output-fmt=sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/1_fast_collate.sam 522s .. ok 522s 522s test_collate: 522s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate --output-fmt=sam -f -r 4 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 522s .. ok 522s 522s test_collate: 522s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -O /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam 523s .. ok 523s 523s test_collate: 523s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam 524s .. ok 524s 524s test_collate: 524s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/collate2.tmp 525s .. ok 525s 525s test_collate: 525s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/collate3.tmp 526s .. ok 526s 526s test_collate: 526s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/1_fast_collate.sam 526s .. ok 526s 526s test_collate: 526s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f -r 4 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 527s 527s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 527s 527s .. expected failure 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/5_ct.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/sanitize.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 527s 527s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 527s 527s .. expected failure 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/5_ct.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 527s .. ok 527s 527s test_fixmate: 527s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 528s .. ok 528s 528s test_fixmate: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 528s .. ok 528s 528s test_fixmate: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/fixmate/sanitize.sam - 528s .. ok 528s 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools calmd -uAr /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.ref.fa 528s .. ok 528s 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools calmd -@ 2 -uAr /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.ref.fa 528s .. ok 528s 528s test_idxstat: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam 528s .. ok 528s 528s test_idxstat: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.cram 528s .. ok 528s 528s test_idxstat: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.sam 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck -v /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 528s .. ok 528s 528s test_quickcheck: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools quickcheck -uv /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 528s .. ok 528s 528s test_reheader: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 528s .. ok 528s 528s test_reheader: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 528s .. ok 528s 528s test_reheader: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 528s .. ok 528s 528s test_reheader: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram && /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' 528s .. ok 528s 528s test_reheader: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram && /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' 528s .. ok 528s 528s test_reheader: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 528s .. ok 528s 528s test_reheader: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/1_fixup.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -O sam -m orphan_only /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -O sam -R '1#9' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/1_fixup.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/1_fixup.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/1_fixup.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/1_fixup.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m orphan_only /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -R '1#9' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/1_fixup.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/1_fixup.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 528s .. ok 528s 528s test_addrprg: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/addrprg/1_fixup.sam 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/1_name_sort.sam - 528s 528s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 528s 528s 528s .. expected failure 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/2_bad_order.sam - 528s 528s ERR: samtools markdup: error, not in coordinate sorted order. 528s 528s 528s .. expected failure 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 528s 528s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 528s 528s samtools markdup: error, unable to assign pair hash key. 528s 528s 528s .. expected failure 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 528s 528s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 528s 528s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 528s 528s 528s .. expected failure 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/5_markdup.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -O sam -r --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/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.uaKpTi/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/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.uaKpTi/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/17_read_group.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/1_name_sort.sam - 528s 528s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 528s 528s 528s .. expected failure 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/2_bad_order.sam - 528s 528s ERR: samtools markdup: error, not in coordinate sorted order. 528s 528s 528s .. expected failure 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 528s 528s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 528s 528s samtools markdup: error, unable to assign pair hash key. 528s 528s 528s .. expected failure 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 528s 528s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 528s 528s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 528s 528s 528s .. expected failure 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/5_markdup.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -O sam -r --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/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.uaKpTi/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/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.uaKpTi/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/17_read_group.sam - 528s .. ok 528s 528s test_markdup: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 528s .. ok 528s 528s test_bedcov: 528s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools bedcov /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bedcov/bedcov.bam 529s .. ok 529s 529s test_bedcov: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools bedcov -j /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bedcov/bedcov.bam 529s .. ok 529s 529s test_bedcov: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools bedcov -g512 -G2048 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bedcov/bedcov.bam 529s .. ok 529s 529s test_bedcov: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools bedcov -c /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/bedcov/bedcov.bam 529s .. ok 529s 529s test_split: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.sam 529s .. ok 529s 529s test_split: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools split --output-fmt sam -d RG -u /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.sam 529s .. ok 529s 529s test_split: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools split --output-fmt sam -d an -u /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.sam 529s .. ok 529s 529s test_split: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools split --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.sam 529s .. ok 529s 529s test_split: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.sam 529s .. ok 529s 529s test_split: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d RG -u /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.sam 529s .. ok 529s 529s test_split: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -u /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.sam 529s .. ok 529s 529s test_split: 529s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/split/split.sam 531s .. ok 531s 531s autopkgtest [18:20:26]: test run-unit-test: -----------------------] 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG /tmp/gBHGK_11C4/longref.sam.gz 531s .. ok 531s 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG /tmp/gBHGK_11C4/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 531s .. ok 531s 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view -h --no-PG -L /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/large_pos/test.bed /tmp/gBHGK_11C4/longref.sam.gz 531s .. ok 531s 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/large_pos/longref_name.sam 531s .. ok 531s 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools merge -O sam --no-PG - /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/large_pos/longref.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/large_pos/longref2.sam 531s .. ok 531s 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools depth /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/large_pos/longref.sam 531s .. ok 531s 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools depth -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/large_pos/test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/large_pos/longref.sam 531s .. ok 531s 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/gBHGK_11C4/longref.sam.gz 531s .. ok 531s 531s test_large_positions: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools fixmate -O sam --no-PG - - | 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 531s .. ok 531s 531s test_ampliconclip: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 531s .. ok 531s 531s test_ampliconstats: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_hard_clipped.expected.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_soft_clipped.expected.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/1_soft_clipped_strand.expected.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' 531s .. ok 531s 531s test_ampliconstats: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 531s .. ok 531s 531s test_ampliconstats: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 531s .. ok 531s 531s test_reset: 531s cat /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset < /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools view 531s .. ok 531s 531s test_reset: 531s cat /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.bam 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/test_input_1_a.cram 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa_index /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG sam_to_fixed_bam /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa_index --no-PG /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG" 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset --reject-PG bwa /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output 531s .. ok 531s 531s test_reset: 531s /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/samtools reset /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.uaKpTi/autopkgtest_tmp/test/reset/output 531s .. ok 531s 531s 531s Number of tests: 531s total .. 894 531s passed .. 863 531s failed .. 0 531s expected failure .. 31 531s unexpected pass .. 0 531s 532s run-unit-test PASS 532s autopkgtest [18:20:28]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 532s autopkgtest [18:20:28]: @@@@@@@@@@@@@@@@@@@@ summary 532s run-unit-test PASS 661s Creating nova instance adt-noble-ppc64el-samtools-20240325-181136-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...