0s autopkgtest [23:03:45]: starting date and time: 2025-03-15 23:03:45+0000 0s autopkgtest [23:03:45]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:03:45]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bum906lb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade samtools --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@lcy02-7.secgroup --name adt-plucky-amd64-samtools-20250315-230345-juju-7f2275-prod-proposed-migration-environment-20-60aaaada-46e5-4ac5-9bc5-eff8f02280a6 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 43s autopkgtest [23:04:28]: testbed dpkg architecture: amd64 44s autopkgtest [23:04:29]: testbed apt version: 2.9.31ubuntu1 44s autopkgtest [23:04:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 44s autopkgtest [23:04:29]: testbed release detected to be: None 44s autopkgtest [23:04:29]: updating testbed package index (apt update) 44s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 44s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 44s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 44s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 44s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 44s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 44s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 44s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 44s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 44s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 44s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 44s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 44s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 44s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 44s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 44s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 44s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 44s Fetched 1265 kB in 0s (7710 kB/s) 45s Reading package lists... 46s Reading package lists... 46s Building dependency tree... 46s Reading state information... 46s Calculating upgrade... 47s Calculating upgrade... 47s The following package was automatically installed and is no longer required: 47s libnl-genl-3-200 47s Use 'sudo apt autoremove' to remove it. 47s The following NEW packages will be installed: 47s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 47s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 47s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 47s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 47s The following packages will be upgraded: 47s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 47s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 47s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 47s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 47s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 47s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 47s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 47s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 47s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 47s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 47s linux-headers-generic linux-headers-virtual linux-image-generic 47s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 47s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 47s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 47s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 47s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 47s python3.13-minimal rsync rsyslog strace xz-utils 47s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 47s Need to get 807 MB of archives. 47s After this operation, 326 MB of additional disk space will be used. 47s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 47s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 47s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 47s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 47s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 47s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 47s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 47s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 47s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 47s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 47s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 47s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 47s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 47s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 47s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 47s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 47s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 47s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 47s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 47s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 47s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 47s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 47s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 47s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 47s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 47s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 47s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 47s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 47s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 47s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 47s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 47s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 47s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 47s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 47s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 47s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 47s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 47s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 47s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 47s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 47s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 47s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 47s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 47s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 47s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 47s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 47s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 47s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 47s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 47s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 47s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 47s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 47s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 47s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 47s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 47s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 47s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 47s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 47s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 47s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 47s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 47s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 47s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 47s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 47s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 47s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 47s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 47s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 47s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 47s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 47s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 47s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 47s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 47s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 47s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 47s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 47s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 47s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 51s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 52s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 52s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 53s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 53s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 53s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 53s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 53s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 53s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 53s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 53s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 53s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 53s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 53s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 53s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 53s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 53s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 53s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 53s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 53s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 53s Preconfiguring packages ... 53s Fetched 807 MB in 6s (135 MB/s) 54s (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 ... 109138 files and directories currently installed.) 54s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 54s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 54s Setting up ncurses-bin (6.5+20250216-2) ... 54s (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 ... 109138 files and directories currently installed.) 54s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 54s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 54s Setting up ncurses-base (6.5+20250216-2) ... 54s (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 ... 109138 files and directories currently installed.) 54s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 54s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 55s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 55s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 55s Setting up liblz4-1:amd64 (1.10.0-4) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 55s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 55s Setting up liblzma5:amd64 (5.6.4-1) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 55s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 55s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 55s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 55s Setting up apt (2.9.33) ... 56s (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 ... 109138 files and directories currently installed.) 56s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 56s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 56s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 56s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 56s Setting up python3-minimal (3.13.2-2) ... 56s (Reading database ... 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Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 73s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 73s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 73s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 73s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 73s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 73s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 73s Setting up media-types (13.0.0) ... 73s Installing new version of config file /etc/mime.types ... 73s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 73s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 73s Setting up pci.ids (0.0~2025.03.09-1) ... 73s Setting up apt-utils (2.9.33) ... 73s Setting up libdebuginfod-common (0.192-4) ... 73s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 73s Setting up bpftool (7.6.0+6.14.0-10.10) ... 73s Setting up libestr0:amd64 (0.1.11-2) ... 73s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 73s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 73s Setting up dosfstools (4.2-1.2) ... 73s Setting up rsyslog (8.2412.0-2ubuntu2) ... 73s info: The user `syslog' is already a member of `adm'. 74s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 74s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 74s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 74s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 74s Setting up linux-headers-generic (6.14.0-10.10) ... 74s Setting up libjemalloc2:amd64 (5.3.0-3) ... 74s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 74s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 74s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 74s Installing new version of config file /etc/apparmor.d/openvpn ... 75s Reloading AppArmor profiles 76s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 76s No schema files found: doing nothing. 76s Setting up libglib2.0-data (2.84.0-1) ... 76s Setting up libncurses6:amd64 (6.5+20250216-2) ... 76s Setting up strace (6.13+ds-1ubuntu1) ... 76s Setting up xz-utils (5.6.4-1) ... 76s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 76s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 78s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 78s Setting up libpci3:amd64 (1:3.13.0-2) ... 78s Setting up python-apt-common (2.9.9build1) ... 78s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 78s Setting up pnp.ids (0.393-3) ... 78s Setting up libnl-3-200:amd64 (3.7.0-1) ... 78s Setting up python3.13-minimal (3.13.2-2) ... 79s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 79s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 79s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 79s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 79s Setting up rsync (3.4.1+ds1-3) ... 79s rsync.service is a disabled or a static unit not running, not starting it. 79s Setting up python3.13-gdbm (3.13.2-2) ... 79s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 79s Setting up ncurses-term (6.5+20250216-2) ... 79s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 79s Setting up libpython3.13:amd64 (3.13.2-2) ... 79s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 79s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 79s Setting up linux-headers-virtual (6.14.0-10.10) ... 79s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 79s Setting up python3.13 (3.13.2-2) ... 80s Setting up htop (3.4.0-2) ... 80s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 82s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 82s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 82s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 82s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 82s Setting up libfwupd3:amd64 (2.0.6-4) ... 82s Setting up python3 (3.13.2-2) ... 83s Setting up python3-markupsafe (2.1.5-1build4) ... 83s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 85s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 85s Setting up hwdata (0.393-3) ... 85s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 85s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 85s Setting up linux-perf (6.14.0-10.10) ... 85s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 85s Setting up python3-gi (3.50.0-4build1) ... 85s Setting up pciutils (1:3.13.0-2) ... 85s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 85s Setting up curl (8.12.1-3ubuntu1) ... 85s Setting up linux-image-virtual (6.14.0-10.10) ... 85s Setting up linux-tools-common (6.14.0-10.10) ... 85s Setting up fwupd (2.0.6-4) ... 86s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 86s fwupd.service is a disabled or a static unit not running, not starting it. 86s Setting up python3-systemd (235-1build6) ... 86s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 86s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 86s Setting up linux-image-generic (6.14.0-10.10) ... 86s Setting up python3-dbus (1.3.2-5build5) ... 86s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 86s Setting up linux-generic (6.14.0-10.10) ... 86s Setting up python3-apt (2.9.9build1) ... 86s Setting up python3-yaml (6.0.2-1build2) ... 86s Setting up python3-lazr.uri (1.0.6-6) ... 86s Setting up binutils (2.44-3ubuntu1) ... 86s Setting up cloud-init-base (25.1-0ubuntu3) ... 88s Setting up linux-virtual (6.14.0-10.10) ... 88s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 88s Setting up cloud-init (25.1-0ubuntu3) ... 88s Processing triggers for systemd (257.3-1ubuntu3) ... 88s Processing triggers for man-db (2.13.0-1) ... 90s Processing triggers for dbus (1.16.2-1ubuntu1) ... 90s Processing triggers for libc-bin (2.41-1ubuntu1) ... 90s Processing triggers for initramfs-tools (0.146ubuntu1) ... 90s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 90s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 101s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 101s /etc/kernel/postinst.d/initramfs-tools: 101s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 101s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 112s /etc/kernel/postinst.d/zz-update-grub: 112s Sourcing file `/etc/default/grub' 112s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 112s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 112s Generating grub configuration file ... 112s Found linux image: /boot/vmlinuz-6.14.0-10-generic 112s Found initrd image: /boot/initrd.img-6.14.0-10-generic 112s Found linux image: /boot/vmlinuz-6.12.0-16-generic 112s Found initrd image: /boot/initrd.img-6.12.0-16-generic 112s Found linux image: /boot/vmlinuz-6.11.0-8-generic 112s Found initrd image: /boot/initrd.img-6.11.0-8-generic 112s Warning: os-prober will not be executed to detect other bootable partitions. 112s Systems on them will not be added to the GRUB boot configuration. 112s Check GRUB_DISABLE_OS_PROBER documentation entry. 112s Adding boot menu entry for UEFI Firmware Settings ... 112s done 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Solving dependencies... 114s The following packages will be REMOVED: 114s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 114s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 114s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 114s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 114s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 114s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 114s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 114s linux-tools-6.12.0-16-generic* 115s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 115s After this operation, 545 MB disk space will be freed. 115s (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 ... 148643 files and directories currently installed.) 115s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 115s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 115s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 115s Removing libpython3.12t64:amd64 (3.12.9-1) ... 115s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 115s Removing libnsl2:amd64 (1.3.0-3build3) ... 115s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 115s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 116s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 118s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 118s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 120s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 121s /etc/kernel/postrm.d/initramfs-tools: 121s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 121s /etc/kernel/postrm.d/zz-update-grub: 121s Sourcing file `/etc/default/grub' 121s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 121s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 121s Generating grub configuration file ... 121s Found linux image: /boot/vmlinuz-6.14.0-10-generic 121s Found initrd image: /boot/initrd.img-6.14.0-10-generic 121s Found linux image: /boot/vmlinuz-6.12.0-16-generic 121s Found initrd image: /boot/initrd.img-6.12.0-16-generic 121s Warning: os-prober will not be executed to detect other bootable partitions. 121s Systems on them will not be added to the GRUB boot configuration. 121s Check GRUB_DISABLE_OS_PROBER documentation entry. 121s Adding boot menu entry for UEFI Firmware Settings ... 121s done 121s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 122s W: Removing the running kernel 122s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 122s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 122s /etc/kernel/postrm.d/initramfs-tools: 122s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 122s /etc/kernel/postrm.d/zz-update-grub: 122s Sourcing file `/etc/default/grub' 122s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 122s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 122s Generating grub configuration file ... 122s Found linux image: /boot/vmlinuz-6.14.0-10-generic 122s Found initrd image: /boot/initrd.img-6.14.0-10-generic 122s Warning: os-prober will not be executed to detect other bootable partitions. 122s Systems on them will not be added to the GRUB boot configuration. 122s Check GRUB_DISABLE_OS_PROBER documentation entry. 122s Adding boot menu entry for UEFI Firmware Settings ... 122s done 122s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 122s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 124s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 124s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 124s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 124s Processing triggers for libc-bin (2.41-1ubuntu1) ... 124s (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 ... 76972 files and directories currently installed.) 124s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 124s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 124s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 124s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 124s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 124s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 124s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 124s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 124s autopkgtest [23:05:49]: upgrading testbed (apt dist-upgrade and autopurge) 124s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 125s Starting 2 pkgProblemResolver with broken count: 0 125s Done 126s Entering ResolveByKeep 126s 126s Calculating upgrade... 126s The following packages will be upgraded: 126s libc-bin libc-dev-bin libc6 libc6-dev locales 126s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Need to get 10.5 MB of archives. 126s After this operation, 1024 B of additional disk space will be used. 126s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 126s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 126s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 127s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 127s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 127s Preconfiguring packages ... 127s Fetched 10.5 MB in 0s (43.4 MB/s) 127s (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 ... 76968 files and directories currently installed.) 127s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 127s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 127s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 127s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 127s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 127s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 128s Setting up libc6:amd64 (2.41-1ubuntu2) ... 128s (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 ... 76968 files and directories currently installed.) 128s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 128s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 128s Setting up libc-bin (2.41-1ubuntu2) ... 128s (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 ... 76968 files and directories currently installed.) 128s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 128s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 128s Setting up locales (2.41-1ubuntu2) ... 129s Generating locales (this might take a while)... 130s en_US.UTF-8... done 130s Generation complete. 130s Setting up libc-dev-bin (2.41-1ubuntu2) ... 130s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 130s Processing triggers for man-db (2.13.0-1) ... 131s Processing triggers for systemd (257.3-1ubuntu3) ... 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s Starting pkgProblemResolver with broken count: 0 133s Starting 2 pkgProblemResolver with broken count: 0 133s Done 133s Solving dependencies... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s autopkgtest [23:05:58]: rebooting testbed after setup commands that affected boot 137s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 148s autopkgtest [23:06:13]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 149s autopkgtest [23:06:14]: @@@@@@@@@@@@@@@@@@@@ apt-source samtools 150s Get:1 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (dsc) [2281 B] 150s Get:2 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (tar) [5683 kB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (diff) [22.1 kB] 151s gpgv: Signature made Thu Feb 6 21:19:50 2025 UTC 151s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 151s gpgv: issuer "emollier@debian.org" 151s gpgv: Can't check signature: No public key 151s dpkg-source: warning: cannot verify inline signature for ./samtools_1.21-1.dsc: no acceptable signature found 151s autopkgtest [23:06:16]: testing package samtools version 1.21-1 151s autopkgtest [23:06:16]: build not needed 151s autopkgtest [23:06:16]: test run-unit-test: preparing testbed 151s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Starting pkgProblemResolver with broken count: 0 152s Starting 2 pkgProblemResolver with broken count: 0 152s Done 152s The following NEW packages will be installed: 152s libdeflate0 libhts3t64 libhtscodecs2 samtools samtools-test tabix 152s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 152s Need to get 4420 kB of archives. 152s After this operation, 23.7 MB of additional disk space will be used. 152s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 153s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 153s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 153s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.21-1 [655 kB] 153s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools-test all 1.21-1 [2413 kB] 153s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 tabix amd64 1.21+ds-1 [642 kB] 153s Fetched 4420 kB in 0s (13.6 MB/s) 153s Selecting previously unselected package libdeflate0:amd64. 153s (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 ... 76968 files and directories currently installed.) 153s Preparing to unpack .../0-libdeflate0_1.23-1_amd64.deb ... 153s Unpacking libdeflate0:amd64 (1.23-1) ... 153s Selecting previously unselected package libhtscodecs2:amd64. 153s Preparing to unpack .../1-libhtscodecs2_1.6.1-2_amd64.deb ... 153s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 153s Selecting previously unselected package libhts3t64:amd64. 153s Preparing to unpack .../2-libhts3t64_1.21+ds-1_amd64.deb ... 153s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 153s Selecting previously unselected package samtools. 153s Preparing to unpack .../3-samtools_1.21-1_amd64.deb ... 153s Unpacking samtools (1.21-1) ... 154s Selecting previously unselected package samtools-test. 154s Preparing to unpack .../4-samtools-test_1.21-1_all.deb ... 154s Unpacking samtools-test (1.21-1) ... 154s Selecting previously unselected package tabix. 154s Preparing to unpack .../5-tabix_1.21+ds-1_amd64.deb ... 154s Unpacking tabix (1.21+ds-1) ... 154s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 154s Setting up libdeflate0:amd64 (1.23-1) ... 154s Setting up libhts3t64:amd64 (1.21+ds-1) ... 154s Setting up samtools-test (1.21-1) ... 154s Setting up tabix (1.21+ds-1) ... 154s Setting up samtools (1.21-1) ... 154s Processing triggers for man-db (2.13.0-1) ... 155s Processing triggers for libc-bin (2.41-1ubuntu2) ... 155s autopkgtest [23:06:20]: test run-unit-test: [----------------------- 155s test_reference: 155s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reference test/reference/mpileup.1.tmp.cram 155s .. ok 155s 155s test_reference: 155s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reference -e test/reference/mpileup.1.tmp.cram 155s .. ok 155s 155s test_reference: 155s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 155s .. ok 155s 155s test_reference: 155s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 155s .. ok 155s 155s test_reference: 155s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram 155s .. ok 155s 155s test_reference: 155s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram 155s .. ok 155s 156s test_reference: 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram 156s .. ok 156s 156s test_reference: 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram 156s .. ok 156s 156s bgzip -c -b 65272 -s 5 /tmp/cLhFSIrin1/bgzip.dat.gz 156s .. ok 156s 156s bgzip -c -b 979200 -s 6 /tmp/cLhFSIrin1/bgzip.dat.gz 156s .. ok 156s 156s bgzip -c -b 652804 -s 6 /tmp/cLhFSIrin1/bgzip.dat.gz 156s .. ok 156s 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools faidx /tmp/cLhFSIrin1/faidx.fa 3:11-13 | grep -v '^>' 156s .. ok 156s 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools faidx /tmp/cLhFSIrin1/faidx.fa.gz 3:11-13 | grep -v '^>' 156s .. ok 156s 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools faidx /tmp/cLhFSIrin1/faidx.fa 2:998-1003 | grep -v '^>' 156s .. ok 156s 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools faidx /tmp/cLhFSIrin1/faidx.fa.gz 2:998-1003 | grep -v '^>' 156s .. ok 156s 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools faidx /tmp/cLhFSIrin1/faidx.fa 1:100-104 | grep -v '^>' 156s .. ok 156s 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools faidx /tmp/cLhFSIrin1/faidx.fa.gz 1:100-104 | grep -v '^>' 156s .. ok 156s 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools faidx /tmp/cLhFSIrin1/faidx.fa 1:99998-100007 | grep -v '^>' 156s .. ok 156s 156s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools faidx /tmp/cLhFSIrin1/faidx.fa.gz 1:99998-100007 | grep -v '^>' 156s .. ok 156s 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fqidx /tmp/cLhFSIrin1/fqidx.fq 3:11-13 157s .. ok 157s 157s .. ok 157s 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fqidx /tmp/cLhFSIrin1/fqidx.fq.gz 3:11-13 157s .. ok 157s 157s .. ok 157s 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fqidx /tmp/cLhFSIrin1/fqidx.fq 2:998-1003 157s .. ok 157s 157s .. ok 157s 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fqidx /tmp/cLhFSIrin1/fqidx.fq.gz 2:998-1003 157s .. ok 157s 157s .. ok 157s 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fqidx /tmp/cLhFSIrin1/fqidx.fq 1:100-104 157s .. ok 157s 157s .. ok 157s 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fqidx /tmp/cLhFSIrin1/fqidx.fq.gz 1:100-104 157s .. ok 157s 157s .. ok 157s 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fqidx /tmp/cLhFSIrin1/fqidx.fq 1:99998-100007 157s .. ok 157s 157s .. ok 157s 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fqidx /tmp/cLhFSIrin1/fqidx.fq.gz 1:99998-100007 157s .. ok 157s 157s .. ok 157s 157s test_dict: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/dict.fa 157s .. ok 157s 157s test_dict: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/cLhFSIrin1/dict.fa.gz 157s .. ok 157s 157s test_dict: 157s cat /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/dict.fa | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz 157s .. ok 157s 157s test_dict: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools dict -AH < /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/dict.alias.fa 157s .. ok 157s 157s test_dict: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools dict -H -l /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/dict.alt < /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/dict.alias.fa 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view /tmp/cLhFSIrin1/large_chrom.bam ref2 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view /tmp/cLhFSIrin1/large_chrom.bam ref2:1-541556283 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/cLhFSIrin1/test_input_1_b.bam.bai ref2 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/cLhFSIrin1/test_input_1_b.bam.bai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -O sam - -X -cp -R ref2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/cLhFSIrin1/test_input_1_b.bam.bai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/cLhFSIrin1/test_input_1_b_opt.bam.bai ref2 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/cLhFSIrin1/auto_indexed.csi && cat /tmp/cLhFSIrin1/auto_indexed.csi 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/cLhFSIrin1/auto_indexed.crai && cat /tmp/cLhFSIrin1/auto_indexed.crai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/cLhFSIrin1/auto_indexed.csi && cat /tmp/cLhFSIrin1/auto_indexed.csi 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -@ 2 /tmp/cLhFSIrin1/large_chrom.bam ref2 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -@ 2 /tmp/cLhFSIrin1/large_chrom.bam ref2:1-541556283 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/cLhFSIrin1/test_input_1_b.bam.bai ref2 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/cLhFSIrin1/test_input_1_b.bam.bai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -O sam - -X -cp -R ref2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/cLhFSIrin1/test_input_1_b.bam.bai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/cLhFSIrin1/test_input_1_b_opt.bam.bai ref2 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -@ 2 -M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/cLhFSIrin1/auto_indexed.csi && cat /tmp/cLhFSIrin1/auto_indexed.csi 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/cLhFSIrin1/auto_indexed.crai && cat /tmp/cLhFSIrin1/auto_indexed.crai 157s .. ok 157s 157s test_index: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/cLhFSIrin1/auto_indexed.csi && cat /tmp/cLhFSIrin1/auto_indexed.csi 157s .. ok 157s 157s test_mpileup: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools mpileup -b /tmp/cLhFSIrin1/mpileup.bam.list -f /tmp/cLhFSIrin1/mpileup.ref.fa.gz -r17:100-150 157s .. ok 157s 157s test_mpileup: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools mpileup -b /tmp/cLhFSIrin1/mpileup.cram.list -f /tmp/cLhFSIrin1/mpileup.ref.fa.gz -r17:100-150 157s .. ok 157s 157s test_mpileup: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools mpileup -b /tmp/cLhFSIrin1/mpileup.bam.urllist -f /tmp/cLhFSIrin1/mpileup.ref.fa.gz -r17:100-150 157s .. ok 157s 157s test_mpileup: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools mpileup -b /tmp/cLhFSIrin1/mpileup.cram.urllist -f /tmp/cLhFSIrin1/mpileup.ref.fa.gz -r17:100-150 157s .. ok 157s 157s test_mpileup: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/cLhFSIrin1/mpileup.ref.fa.gz -r17:1050-1060 /tmp/cLhFSIrin1/mpileup.1.bam | grep -v mpileup 157s .. ok 157s 157s test_mpileup: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/cLhFSIrin1/mpileup.ref.fa.gz -r17:1050-1060 /tmp/cLhFSIrin1/mpileup.1.cram | grep -v mpileup 157s .. ok 157s 157s test_mpileup: 157s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools mpileup /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/mpileup/overlap.bam | grep 128814202 157s .. ok 157s 157s test_usage: 157s samtools 157s test_view: 157s Generating test data file ./test/test.pl: no IO::Pty module or can't open pty; skipping usage tests 158s .................. done 158s 1: SAM -> BAM -> SAM .. ok 158s 158s 2: SAM -> uncompressed BAM .. ok 158s 158s 3: uncompressed BAM -> SAM and compare .. ok 158s 158s 4: SAM -> fast compressed BAM .. ok 158s 158s 5: fast compressed BAM -> SAM and compare .. ok 158s 159s 6: SAM -> CRAM -> SAM (UR header tags) .. ok 159s 159s 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 159s 159s 8: BAM -> CRAM with UR -> SAM .. ok 159s 159s 9: SAM -> BAM (M5 header tags) .. ok 159s 159s 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 159s 159s 11: CRAM -> BAM with UR .. ok 159s 159s 12: CRAM -> BAM with M5 .. ok 159s 159s 13: SAM -> SAM via stdout .. ok 159s 159s 14: SAM -> BAM via stdout .. ok 159s 159s 15: SAM -> CRAM via stdout .. ok 159s 159s 16: SAM from stdin -> SAM .. ok 159s 159s 17: BAM from stdin -> SAM .. ok 159s 160s 18: CRAM from stdin -> SAM .. ok 160s 160s 19: samtools view -H (SAM input) .. ok 160s 160s 20: samtools view -H (BAM input) .. ok 160s 160s 21: samtools view -H (CRAM input) .. ok 160s 160s 22: No headers (SAM input) .. ok 160s 160s 23: No headers (BAM input) .. ok 160s 160s 24: No headers (CRAM input) .. ok 160s 160s 25: Filter -f 128 (SAM input) .. ok 160s 160s 26: Count -f 128 (SAM input) .. ok 160s 160s 27: Filter -f 128 (BAM input) .. ok 160s 160s 28: Count -f 128 (BAM input) .. ok 160s 160s 29: Filter -f 128 (CRAM input) .. ok 160s 160s 30: Count -f 128 (CRAM input) .. ok 160s 160s 31: Filter -F 128 (SAM input) .. ok 160s 160s 32: Count -F 128 (SAM input) .. ok 160s 160s 33: Filter -F 128 (BAM input) .. ok 160s 160s 34: Count -F 128 (BAM input) .. ok 160s 160s 35: Filter -F 128 (CRAM input) .. ok 160s 160s 36: Count -F 128 (CRAM input) .. ok 160s 160s 37: Filter -F 128 -f 2 (SAM input) .. ok 160s 160s 38: Count -F 128 -f 2 (SAM input) .. ok 160s 160s 39: Filter -F 128 -f 2 (BAM input) .. ok 160s 160s 40: Count -F 128 -f 2 (BAM input) .. ok 160s 160s 41: Filter -F 128 -f 2 (CRAM input) .. ok 160s 160s 42: Count -F 128 -f 2 (CRAM input) .. ok 160s 160s 43: Filter -r grp2 (SAM input) .. ok 160s 160s 44: Count -r grp2 (SAM input) .. ok 160s 160s 45: Filter -r grp2 (BAM input) .. ok 160s 160s 46: Count -r grp2 (BAM input) .. ok 160s 160s 47: Filter -r grp2 (CRAM input) .. ok 160s 160s 48: Count -r grp2 (CRAM input) .. ok 160s 160s 49: Filter -R /tmp/cLhFSIrin1/view.001.fogn (SAM input) .. ok 160s 160s 50: Count -R /tmp/cLhFSIrin1/view.001.fogn (SAM input) .. ok 160s 160s 51: Filter -R /tmp/cLhFSIrin1/view.001.fogn (BAM input) .. ok 160s 160s 52: Count -R /tmp/cLhFSIrin1/view.001.fogn (BAM input) .. ok 160s 161s 53: Filter -R /tmp/cLhFSIrin1/view.001.fogn (CRAM input) .. ok 161s 161s 54: Count -R /tmp/cLhFSIrin1/view.001.fogn (CRAM input) .. ok 161s 161s 55: Filter -R /tmp/cLhFSIrin1/view.001.fogn -r grp2 (SAM input).. ok 161s 161s 56: Count -R /tmp/cLhFSIrin1/view.001.fogn -r grp2 (SAM input).. ok 161s 161s 57: Filter -R /tmp/cLhFSIrin1/view.001.fogn -r grp2 (BAM input).. ok 161s 161s 58: Count -R /tmp/cLhFSIrin1/view.001.fogn -r grp2 (BAM input).. ok 161s 161s 59: Filter -R /tmp/cLhFSIrin1/view.001.fogn -r grp2 (CRAM input).. ok 161s 161s 60: Count -R /tmp/cLhFSIrin1/view.001.fogn -r grp2 (CRAM input).. ok 161s 161s 61: Filter -r grp2 -R /tmp/cLhFSIrin1/view.001.fogn (SAM input).. ok 161s 161s 62: Count -r grp2 -R /tmp/cLhFSIrin1/view.001.fogn (SAM input).. ok 161s 161s 63: Filter -r grp2 -R /tmp/cLhFSIrin1/view.001.fogn (BAM input).. ok 161s 161s 64: Count -r grp2 -R /tmp/cLhFSIrin1/view.001.fogn (BAM input).. ok 161s 161s 65: Filter -r grp2 -R /tmp/cLhFSIrin1/view.001.fogn (CRAM input).. ok 161s 161s 66: Count -r grp2 -R /tmp/cLhFSIrin1/view.001.fogn (CRAM input).. ok 161s 161s 67: Filter -N /tmp/cLhFSIrin1/view.001.forn (SAM input) .. ok 161s 161s 68: Count -N /tmp/cLhFSIrin1/view.001.forn (SAM input) .. ok 161s 161s 69: Filter -N /tmp/cLhFSIrin1/view.001.forn (BAM input) .. ok 161s 161s 70: Count -N /tmp/cLhFSIrin1/view.001.forn (BAM input) .. ok 161s 161s 71: Filter -N /tmp/cLhFSIrin1/view.001.forn (CRAM input) .. ok 161s 161s 72: Count -N /tmp/cLhFSIrin1/view.001.forn (CRAM input) .. ok 161s 161s 73: Filter -d BC (SAM input) .. ok 161s 161s 74: Count -d BC (SAM input) .. ok 161s 161s 75: Filter -d BC (BAM input) .. ok 161s 161s 76: Count -d BC (BAM input) .. ok 161s 161s 77: Filter -d BC (CRAM input) .. ok 161s 161s 78: Count -d BC (CRAM input) .. ok 161s 161s 79: Filter -d BC:TGCA (SAM input) .. ok 161s 161s 80: Count -d BC:TGCA (SAM input) .. ok 161s 161s 81: Filter -d BC:TGCA (BAM input) .. ok 161s 161s 82: Count -d BC:TGCA (BAM input) .. ok 161s 162s 83: Filter -d BC:TGCA (CRAM input) .. ok 162s 162s 84: Count -d BC:TGCA (CRAM input) .. ok 162s 162s 85: Filter -D BC:/tmp/cLhFSIrin1/view.001.fobc (SAM input) .. ok 162s 162s 86: Count -D BC:/tmp/cLhFSIrin1/view.001.fobc (SAM input) .. ok 162s 162s 87: Filter -D BC:/tmp/cLhFSIrin1/view.001.fobc (BAM input) .. ok 162s 162s 88: Count -D BC:/tmp/cLhFSIrin1/view.001.fobc (BAM input) .. ok 162s 162s 89: Filter -D BC:/tmp/cLhFSIrin1/view.001.fobc (CRAM input) .. ok 162s 162s 90: Count -D BC:/tmp/cLhFSIrin1/view.001.fobc (CRAM input) .. ok 162s 162s 91: Filter -D BC:/tmp/cLhFSIrin1/view.001.fobc -d BC:TGCA (SAM input).. ok 162s 162s 92: Count -D BC:/tmp/cLhFSIrin1/view.001.fobc -d BC:TGCA (SAM input).. ok 162s 162s 93: Filter -D BC:/tmp/cLhFSIrin1/view.001.fobc -d BC:TGCA (BAM input).. ok 162s 162s 94: Count -D BC:/tmp/cLhFSIrin1/view.001.fobc -d BC:TGCA (BAM input).. ok 162s 162s 95: Filter -D BC:/tmp/cLhFSIrin1/view.001.fobc -d BC:TGCA (CRAM input).. ok 162s 162s 96: Count -D BC:/tmp/cLhFSIrin1/view.001.fobc -d BC:TGCA (CRAM input).. ok 162s 162s 97: Filter -d BC:TGCA -D BC:/tmp/cLhFSIrin1/view.001.fobc (SAM input).. ok 162s 162s 98: Count -d BC:TGCA -D BC:/tmp/cLhFSIrin1/view.001.fobc (SAM input).. ok 162s 162s 99: Filter -d BC:TGCA -D BC:/tmp/cLhFSIrin1/view.001.fobc (BAM input).. ok 162s 162s 100: Count -d BC:TGCA -D BC:/tmp/cLhFSIrin1/view.001.fobc (BAM input).. ok 162s 162s 101: Filter -d BC:TGCA -D BC:/tmp/cLhFSIrin1/view.001.fobc (CRAM input).. ok 162s 162s 102: Count -d BC:TGCA -D BC:/tmp/cLhFSIrin1/view.001.fobc (CRAM input).. ok 162s 162s 103: Filter -D RG:/tmp/cLhFSIrin1/view.001.fogn (SAM input) .. ok 162s 162s 104: Count -D RG:/tmp/cLhFSIrin1/view.001.fogn (SAM input) .. ok 162s 162s 105: Filter -D RG:/tmp/cLhFSIrin1/view.001.fogn (BAM input) .. ok 162s 162s 106: Count -D RG:/tmp/cLhFSIrin1/view.001.fogn (BAM input) .. ok 162s 162s 107: Filter -D RG:/tmp/cLhFSIrin1/view.001.fogn (CRAM input).. ok 162s 162s 108: Count -D RG:/tmp/cLhFSIrin1/view.001.fogn (CRAM input) .. ok 162s 162s 109: Filter -d NE:TGCA (SAM input) .. ok 162s 162s 110: Count -d NE:TGCA (SAM input) .. ok 162s 162s 111: Filter -d NE:TGCA (BAM input) .. ok 162s 162s 112: Count -d NE:TGCA (BAM input) .. ok 162s 162s 113: Filter -d NE:TGCA (CRAM input) .. ok 162s 162s 114: Count -d NE:TGCA (CRAM input) .. ok 162s 162s 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test115.sam -h -d TGCA /tmp/cLhFSIrin1/view.001.sam --no-PG 162s 162s 162s .. expected failure 162s 162s 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -d TGCA /tmp/cLhFSIrin1/view.001.sam --no-PG 162s 162s 162s .. expected failure 162s 162s 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test117.sam -h -d TGCA /tmp/cLhFSIrin1/view.test001.bam --no-PG 162s 162s 162s .. expected failure 162s 162s 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -d TGCA /tmp/cLhFSIrin1/view.test001.bam --no-PG 162s 162s 162s .. expected failure 162s 162s 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test119.sam -h -d TGCA /tmp/cLhFSIrin1/view.test006.cram --no-PG 162s 162s 162s .. expected failure 162s 162s 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -d TGCA /tmp/cLhFSIrin1/view.test006.cram --no-PG 162s 162s 162s .. expected failure 162s 162s 121: Filter -D BClong:/tmp/cLhFSIrin1/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/cLhFSIrin1/view.001.fobc" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test121.sam -h -D BClong:/tmp/cLhFSIrin1/view.001.fobc /tmp/cLhFSIrin1/view.001.sam --no-PG 162s 162s 162s .. expected failure 162s 162s 122: Count -D BClong:/tmp/cLhFSIrin1/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/cLhFSIrin1/view.001.fobc" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -D BClong:/tmp/cLhFSIrin1/view.001.fobc /tmp/cLhFSIrin1/view.001.sam --no-PG 162s 162s 162s .. expected failure 162s 162s 123: Filter -D BClong:/tmp/cLhFSIrin1/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/cLhFSIrin1/view.001.fobc" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test123.sam -h -D BClong:/tmp/cLhFSIrin1/view.001.fobc /tmp/cLhFSIrin1/view.test001.bam --no-PG 162s 162s 162s .. expected failure 162s 162s 124: Count -D BClong:/tmp/cLhFSIrin1/view.001.fobc (BAM input) Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -D BClong:/tmp/cLhFSIrin1/view.001.fobc /tmp/cLhFSIrin1/view.test001.bam --no-PG 162s 162s 162s .. expected failure 162s 162s 125: Filter -D BClong:/tmp/cLhFSIrin1/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/cLhFSIrin1/view.001.fobc" 162s samtools view: Invalid "tag:file" option: "BClong:/tmp/cLhFSIrin1/view.001.fobc" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test125.sam -h -D BClong:/tmp/cLhFSIrin1/view.001.fobc /tmp/cLhFSIrin1/view.test006.cram --no-PG 162s 162s 162s .. expected failure 162s 162s 126: Count -D BClong:/tmp/cLhFSIrin1/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/cLhFSIrin1/view.001.fobc" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -D BClong:/tmp/cLhFSIrin1/view.001.fobc /tmp/cLhFSIrin1/view.test006.cram --no-PG 162s 162s 162s .. expected failure 162s 162s 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/cLhFSIrin1/view.001.sam --no-PG 162s 162s 162s .. expected failure 162s 162s 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/cLhFSIrin1/view.001.sam --no-PG 162s 162s 162s .. expected failure 162s 162s 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/cLhFSIrin1/view.test001.bam --no-PG 162s 162s 162s .. expected failure 162s 162s 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/cLhFSIrin1/view.test001.bam --no-PG 162s 162s 162s .. expected failure 162s 162s 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -o /tmp/cLhFSIrin1/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/cLhFSIrin1/view.test006.cram --no-PG 162s 162s 162s .. expected failure 162s 162s 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" 162s Failed command: 162s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/cLhFSIrin1/view.test006.cram --no-PG 162s 162s 162s .. expected failure 162s 162s 133: Filter -d NM:13 (SAM input) .. ok 162s 162s 134: Count -d NM:13 (SAM input) .. ok 162s 162s 135: Filter -d NM:13 (BAM input) .. ok 162s 162s 136: Count -d NM:13 (BAM input) .. ok 162s 162s 137: Filter -d NM:13 (CRAM input) .. ok 162s 163s 138: Count -d NM:13 (CRAM input) .. ok 163s 163s 139: Filter -d ab:z (SAM input) .. ok 163s 163s 140: Count -d ab:z (SAM input) .. ok 163s 163s 141: Filter -d ab:z (BAM input) .. ok 163s 163s 142: Count -d ab:z (BAM input) .. ok 163s 163s 143: Filter -d ab:z (CRAM input) .. ok 163s 163s 144: Count -d ab:z (CRAM input) .. ok 163s 163s 145: Filter -l Library 2 (SAM input) .. ok 163s 163s 146: Count -l Library 2 (SAM input) .. ok 163s 163s 147: Filter -l Library 2 (BAM input) .. ok 163s 163s 148: Count -l Library 2 (BAM input) .. ok 163s 163s 149: Filter -l Library 2 (CRAM input) .. ok 163s 163s 150: Count -l Library 2 (CRAM input) .. ok 163s 163s 151: Filter -l Library 3 (SAM input) .. ok 163s 163s 152: Count -l Library 3 (SAM input) .. ok 163s 163s 153: Filter -l Library 3 (BAM input) .. ok 163s 163s 154: Count -l Library 3 (BAM input) .. ok 163s 163s 155: Filter -l Library 3 (CRAM input) .. ok 163s 163s 156: Count -l Library 3 (CRAM input) .. ok 163s 163s 157: Filter -q 50 (SAM input) .. ok 163s 163s 158: Count -q 50 (SAM input) .. ok 163s 163s 159: Filter -q 50 (BAM input) .. ok 163s 163s 160: Count -q 50 (BAM input) .. ok 163s 163s 161: Filter -q 50 (CRAM input) .. ok 163s 163s 162: Count -q 50 (CRAM input) .. ok 163s 163s 163: Filter -q 99 (SAM input) .. ok 163s 163s 164: Count -q 99 (SAM input) .. ok 163s 163s 165: Filter -q 99 (BAM input) .. ok 163s 163s 166: Count -q 99 (BAM input) .. ok 163s 163s 167: Filter -q 99 (CRAM input) .. ok 163s 163s 168: Count -q 99 (CRAM input) .. ok 163s 163s 169: Filter -q 100 (SAM input) .. ok 163s 163s 170: Count -q 100 (SAM input) .. ok 163s 163s 171: Filter -q 100 (BAM input) .. ok 163s 163s 172: Count -q 100 (BAM input) .. ok 163s 164s 173: Filter -q 100 (CRAM input) .. ok 164s 164s 174: Count -q 100 (CRAM input) .. ok 164s 164s 175: Filter -x fa (SAM input) .. ok 164s 164s 176: Count -x fa (SAM input) .. ok 164s 164s 177: Filter -x fa (BAM input) .. ok 164s 164s 178: Count -x fa (BAM input) .. ok 164s 164s 179: Filter -x fa (CRAM input) .. ok 164s 164s 180: Count -x fa (CRAM input) .. ok 164s 164s 181: Filter -x fa -x ha (SAM input) .. ok 164s 164s 182: Count -x fa -x ha (SAM input) .. ok 164s 164s 183: Filter -x fa -x ha (BAM input) .. ok 164s 164s 184: Count -x fa -x ha (BAM input) .. ok 164s 164s 185: Filter -x fa -x ha (CRAM input) .. ok 164s 164s 186: Count -x fa -x ha (CRAM input) .. ok 164s 164s 187: Filter -x fa,ha (SAM input) .. ok 164s 164s 188: Count -x fa,ha (SAM input) .. ok 164s 164s 189: Filter -x fa,ha (BAM input) .. ok 164s 164s 190: Count -x fa,ha (BAM input) .. ok 164s 164s 191: Filter -x fa,ha (CRAM input) .. ok 164s 164s 192: Count -x fa,ha (CRAM input) .. ok 164s 164s 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 164s 164s 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 164s 164s 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 164s 164s 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 164s 164s 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 164s 164s 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 164s 164s 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 164s 164s 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 164s 164s 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 164s 164s 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 164s 164s 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 164s 164s 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 164s 164s 205: Filter -x fa -r grp2 (SAM input) .. ok 164s 164s 206: Count -x fa -r grp2 (SAM input) .. ok 164s 164s 207: Filter -x fa -r grp2 (BAM input) .. ok 164s 164s 208: Count -x fa -r grp2 (BAM input) .. ok 164s 164s 209: Filter -x fa -r grp2 (CRAM input) .. ok 164s 164s 210: Count -x fa -r grp2 (CRAM input) .. ok 164s 164s 211: Filter -x RG -r grp2 (SAM input) .. ok 164s 164s 212: Count -x RG -r grp2 (SAM input) .. ok 164s 164s 213: Filter -x RG -r grp2 (BAM input) .. ok 164s 164s 214: Count -x RG -r grp2 (BAM input) .. ok 164s 165s 215: Filter -x RG -r grp2 (CRAM input) .. ok 165s 165s 216: Count -x RG -r grp2 (CRAM input) .. ok 165s 165s 217: Filter -m 10 (SAM input) .. ok 165s 165s 218: Count -m 10 (SAM input) .. ok 165s 165s 219: Filter -m 10 (BAM input) .. ok 165s 165s 220: Count -m 10 (BAM input) .. ok 165s 165s 221: Filter -m 10 (CRAM input) .. ok 165s 165s 222: Count -m 10 (CRAM input) .. ok 165s 165s 223: Filter -m 11 (SAM input) .. ok 165s 165s 224: Count -m 11 (SAM input) .. ok 165s 165s 225: Filter -m 11 (BAM input) .. ok 165s 165s 226: Count -m 11 (BAM input) .. ok 165s 165s 227: Filter -m 11 (CRAM input) .. ok 165s 165s 228: Count -m 11 (CRAM input) .. ok 165s 165s 229: Filter -m 15 (SAM input) .. ok 165s 165s 230: Count -m 15 (SAM input) .. ok 165s 165s 231: Filter -m 15 (BAM input) .. ok 165s 165s 232: Count -m 15 (BAM input) .. ok 165s 165s 233: Filter -m 15 (CRAM input) .. ok 165s 166s 234: Count -m 15 (CRAM input) .. ok 166s 166s 235: Filter -m 16 (SAM input) .. ok 166s 166s 236: Count -m 16 (SAM input) .. ok 166s 166s 237: Filter -m 16 (BAM input) .. ok 166s 166s 238: Count -m 16 (BAM input) .. ok 166s 166s 239: Filter -m 16 (CRAM input) .. ok 166s 166s 240: Count -m 16 (CRAM input) .. ok 166s 166s 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 166s 166s 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 166s 166s 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 166s 166s 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 166s 166s 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 166s 166s 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 166s 166s 247: Filter -e [BC] (SAM input) .. ok 166s 166s 248: Count -e [BC] (SAM input) .. ok 166s 166s 249: Filter -e [BC] (BAM input) .. ok 166s 166s 250: Count -e [BC] (BAM input) .. ok 166s 166s 251: Filter -e [BC] (CRAM input) .. ok 166s 166s 252: Count -e [BC] (CRAM input) .. ok 166s 166s 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 166s 166s 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 166s 166s 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 166s 166s 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 166s 166s 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 166s 166s 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 166s 166s 259: Filter -e mapq >= 50 (SAM input) .. ok 166s 166s 260: Count -e mapq >= 50 (SAM input) .. ok 166s 167s 261: Filter -e mapq >= 50 (BAM input) .. ok 167s 167s 262: Count -e mapq >= 50 (BAM input) .. ok 167s 167s 263: Filter -e mapq >= 50 (CRAM input) .. ok 167s 167s 264: Count -e mapq >= 50 (CRAM input) .. ok 167s 167s 265: Filter -e mapq >= 99 (SAM input) .. ok 167s 167s 266: Count -e mapq >= 99 (SAM input) .. ok 167s 167s 267: Filter -e mapq >= 99 (BAM input) .. ok 167s 167s 268: Count -e mapq >= 99 (BAM input) .. ok 167s 167s 269: Filter -e mapq >= 99 (CRAM input) .. ok 167s 167s 270: Count -e mapq >= 99 (CRAM input) .. ok 167s 167s 271: Filter -e mapq >= 100 (SAM input) .. ok 167s 167s 272: Count -e mapq >= 100 (SAM input) .. ok 167s 167s 273: Filter -e mapq >= 100 (BAM input) .. ok 167s 167s 274: Count -e mapq >= 100 (BAM input) .. ok 167s 167s 275: Filter -e mapq >= 100 (CRAM input) .. ok 167s 167s 276: Count -e mapq >= 100 (CRAM input) .. ok 167s 167s 277: 1bp reads file SAM -> BAM -> SAM .. ok 167s 167s 278: 1bp reads file SAM -> CRAM -> SAM .. ok 167s 168s 278: Region Z (BAM input) .. ok 168s 168s 279: Count Z (BAM input) .. ok 168s 168s 280: Region Z (CRAM input) .. ok 168s 168s 281: Count Z (CRAM input) .. ok 168s 168s 282: Region Z:30 (BAM input) .. ok 168s 168s 283: Count Z:30 (BAM input) .. ok 168s 168s 284: Region Z:30 (CRAM input) .. ok 168s 168s 285: Count Z:30 (CRAM input) .. ok 168s 168s 286: Region Z:20-40 (BAM input) .. ok 168s 168s 287: Count Z:20-40 (BAM input) .. ok 168s 168s 288: Region Z:20-40 (CRAM input) .. ok 168s 168s 289: Count Z:20-40 (CRAM input) .. ok 168s 168s 290: Region ref1 (BAM input) .. ok 168s 168s 291: Count ref1 (BAM input) .. ok 168s 168s 292: Region ref1 (CRAM input) .. ok 168s 168s 293: Count ref1 (CRAM input) .. ok 168s 168s 294: Region ref1:15 (BAM input) .. ok 168s 168s 295: Count ref1:15 (BAM input) .. ok 168s 168s 296: Region ref1:15 (CRAM input) .. ok 168s 168s 297: Count ref1:15 (CRAM input) .. ok 168s 168s 298: Region ref1:15-45 (BAM input) .. ok 168s 168s 299: Count ref1:15-45 (BAM input) .. ok 168s 168s 300: Region ref1:15-45 (CRAM input) .. ok 168s 168s 301: Count ref1:15-45 (CRAM input) .. ok 168s 168s 302: Region ref1:15-45 ref2 (BAM input) .. ok 168s 168s 303: Count ref1:15-45 ref2 (BAM input) .. ok 168s 169s 304: Region ref1:15-45 ref2 (CRAM input) .. ok 169s 169s 305: Count ref1:15-45 ref2 (CRAM input) .. ok 169s 169s 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 169s 169s 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 169s 169s 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 169s 169s 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 169s 169s 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 169s 169s 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 169s 169s 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 169s 169s 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 169s 169s 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 169s 169s 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 169s 169s 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 169s 169s 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 169s 169s 318: Region -f 128 ref1 (BAM input) .. ok 169s 169s 319: Count -f 128 ref1 (BAM input) .. ok 169s 169s 320: Region -f 128 ref1 (CRAM input) .. ok 169s 169s 321: Count -f 128 ref1 (CRAM input) .. ok 169s 169s 322: Region -q 50 ref1:15-45 (BAM input) .. ok 169s 169s 323: Count -q 50 ref1:15-45 (BAM input) .. ok 169s 169s 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 169s 169s 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 169s 169s 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 169s 169s 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 169s 170s 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 170s 170s 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 170s 170s 330: Region * (BAM input) .. ok 170s 170s 331: Count * (BAM input) .. ok 170s 170s 332: Region * (CRAM input) .. ok 170s 170s 333: Count * (CRAM input) .. ok 170s 170s 334: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 170s 170s 335: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok 170s 170s 336: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 170s 170s 337: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok 170s 170s 338: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 170s 170s 339: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok 170s 170s 340: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 170s 170s 341: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok 170s 170s 342: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 170s 170s 343: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok 170s 170s 344: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 170s 170s 345: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok 170s 170s 346: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 170s 170s 347: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok 170s 170s 348: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 170s 170s 349: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok 170s 170s 350: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 170s 170s 351: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok 170s 170s 352: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 170s 170s 353: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok 170s 170s 354: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 170s 170s 355: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok 170s 171s 356: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 171s 171s 357: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok 171s 171s 358: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 171s 171s 359: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok 171s 171s 360: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 171s 171s 361: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 171s 171s 362: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 171s 171s 363: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 171s 171s 364: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 171s 171s 365: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 171s 171s 366: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 171s 171s 367: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 171s 171s 368: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 171s 171s 369: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 171s 171s 370: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 171s 171s 371: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 171s 171s 372: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 171s 171s 373: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 171s 171s 374: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 171s 171s 375: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok 171s 171s 376: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 171s 171s 377: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok 171s 171s 378: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 171s 171s 379: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 171s 171s 380: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 171s 171s 381: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 171s 171s 382: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 171s 171s 383: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 171s 172s 384: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 172s 172s 385: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 172s 172s 386: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 172s 172s 387: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok 172s 172s 388: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 172s 172s 389: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 172s 172s 390: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 172s 172s 391: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok 172s 172s 392: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 172s 172s 393: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 172s 172s 394: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 172s 172s 395: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 172s 172s 396: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 172s 172s 397: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 172s 172s 398: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 172s 172s 399: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 172s 172s 400: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 172s 172s 401: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 172s 172s 402: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 172s 172s 403: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 172s 172s 404: Region -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 172s 172s 405: Count -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 172s 172s 406: -L with nested regions .. ok 172s 172s 407: Make BAM with no M5/UR tags .. ok 172s 172s 408: Add @SQ with -t (SAM -> SAM) .. ok 172s 172s 409: Add @SQ with -T (SAM -> SAM) .. ok 172s 172s 410: Add @SQ with -t (BAM -> SAM) .. ok 172s 172s 411: Add @SQ with -T (BAM -> SAM) .. ok 172s 172s 412: Add @SQ with -t (SAM -> BAM) .. ok 172s 172s 413: Add @SQ with -T (SAM -> BAM) .. ok 172s 172s 414: Add @SQ with -t (BAM -> BAM) .. ok 172s 172s 415: Add @SQ with -T (BAM -> BAM) .. ok 172s 172s 416: Add @SQ with -t (SAM -> CRAM) .. ok 172s 172s 417: Add @SQ with -T (SAM -> CRAM) .. ok 172s 173s 418: Add @SQ with -t (BAM -> CRAM) .. ok 173s 173s 419: Add @SQ with -T (BAM -> CRAM) .. ok 173s 173s 420: Make CRAM with no UR field .. ok 173s 173s 421: Decoding CRAM with no UR field via -T .. ok 173s 173s 422: CIGAR B-operator removal .. ok 173s 173s 423: Big SAM -> BAM .. ok 173s 173s 424: Big SAM -> BAM (2 threads) .. ok 173s 173s 425: Big SAM -> BAM (4 threads) .. ok 173s 175s 426: Big SAM -> CRAM .. ok 175s 176s 427: Big SAM -> CRAM (2 threads) .. ok 176s 177s 428: Big SAM -> CRAM (4 threads) .. ok 177s 177s 429: Subsample 0.2 (SAM input) ............ ok 177s 178s 430: Subsample 0.5 (SAM input) ............ ok 178s 179s 431: Subsample 0.8 (SAM input) ............ ok 179s 180s 432: Subsample 0.2 (BAM input) ............ ok 180s 180s 433: Subsample 0.5 (BAM input) ............ ok 180s 181s 434: Subsample 0.8 (BAM input) ............ ok 181s 183s 435: Subsample 0.2 (CRAM input) ............ ok 183s 185s 436: Subsample 0.5 (CRAM input) ............ ok 185s 188s 437: Subsample 0.8 (CRAM input) ............ ok 188s 188s 438: SAM add PG .. ok 188s 188s 439: Unset dup flag, remove dt and do tags .. ok 188s 188s 440: Unmap dup flagged reads. .. ok 188s 188s 441: Unmap dup flagged reads. .. ok 188s 188s 442: fetch pairs .. ok 188s 188s 443: fetch pairs .. ok 188s 188s 444: fetch pairs .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -h 0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -h 1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -h 5 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -h 29 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -h 30 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -n 0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -n 1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -n 5 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_head: 188s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools head -h 5 -n 5 < /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.sam 188s .. ok 188s 188s test_cat: 188s Generating test data file .................. done 188s Generate BAM file #1 .. ok 188s 188s Generate BAM region file #1 .. ok 188s 188s Generate CRAM file #1 .. ok 188s 188s Generating test data file .................. done 188s Generate BAM file #2 .. ok 188s 188s Generate BAM region file #2 .. ok 188s 188s Generate CRAM file #2 .. ok 188s 188s Generating test data file .................. done 188s Generate BAM file #3 .. ok 188s 188s Generate BAM region file #3 .. ok 188s 188s Generate CRAM file #3 .. ok 188s 189s Generating test data file .................. done 189s Generate BAM file #4 .. ok 189s 189s Generate BAM region file #4 .. ok 189s 189s Generate CRAM file #4 .. ok 189s 189s 1: cat BAM files .. ok 189s 189s 2: cat recompressed BAM files .. ok 189s 189s 3: cat CRAM files .. ok 189s 190s 4: cat CRAM subregion files .. ok 190s 190s 5: cat BAM files to stdout .. ok 190s 190s 6: cat recompressed BAM files to stdout .. ok 190s 190s 7: cat CRAM files to stdout .. ok 190s 191s 8: cat CRAM subregion files to stdout .. ok 191s 191s 9: cat CRAM part 1/2 .. ok 191s 191s 9: cat CRAM part 2/2 .. ok 191s 192s 9: cat CRAM parts 1/2 + 2/2 .. ok 192s 192s 10: cat BAM files with new header .. ok 192s 192s 11: cat recompressed BAM files with new header .. ok 192s 192s 12: cat CRAM files with new header .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/0.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/0.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT,MD,ia -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/import/2.interleaved.fq -T "" 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/import/3.interleaved.fq -i 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T "*" 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T "" 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq 192s .. ok 192s 192s test_import: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ 192s .. ok 192s 192s test_bam2fq: 192s Generate BAM file .. ok 192s 192s Generate CRAM file .. ok 192s 192s 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons 192s [M::bam2fq_mainloop] processed 36 reads 192s .. ok 192s 192s 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons 192s [M::bam2fq_mainloop] processed 36 reads 192s .. ok 192s 192s 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons 192s [M::bam2fq_mainloop] processed 36 reads 192s .. ok 192s 192s 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons 192s [M::bam2fq_mainloop] processed 36 reads 192s .. ok 192s 192s 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons 192s [M::bam2fq_mainloop] processed 36 reads 192s .. ok 192s 192s 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons 192s [M::bam2fq_mainloop] processed 36 reads 192s .. ok 192s 192s test_bam2fq: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 192s .. ok 192s 192s test_bam2fq: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 192s .. ok 192s 192s test_bam2fq: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.002.sam 192s .. ok 192s 192s test_bam2fq: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.003.sam 192s .. ok 192s 192s test_bam2fq: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.004.sam 192s .. ok 192s 192s test_bam2fq: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.004.sam 192s .. ok 192s 192s test_bam2fq: 192s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.010.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -t -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -t -T MD,ia -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.004.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.703.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fasta -N -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -s /tmp/cLhFSIrin1/bam2fq.discard.s.fq -0 /tmp/cLhFSIrin1/bam2fq.discard.0.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.013.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq --index-format 'i8n1i8' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.014.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -T '' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -t -T '*' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -T '*' -d MD:10 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -T '*' -d NM:0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -N -T '*' -d ia /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -d NM:13 -d NM:14 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -D NM:test/dat/bam2fq.NM-D /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -D MD:test/dat/bam2fq.MD-D /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s Generate BAM file (2 threads) .. ok 193s 193s Generate CRAM file (2 threads) .. ok 193s 193s 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 193s [M::bam2fq_mainloop] processed 36 reads 193s .. ok 193s 193s 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 193s [M::bam2fq_mainloop] processed 36 reads 193s .. ok 193s 193s 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 193s [M::bam2fq_mainloop] processed 36 reads 193s .. ok 193s 193s 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 193s [M::bam2fq_mainloop] processed 36 reads 193s .. ok 193s 193s 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 193s [M::bam2fq_mainloop] processed 36 reads 193s .. ok 193s 193s 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons 193s [M::bam2fq_mainloop] processed 36 reads 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.002.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.003.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.004.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.004.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.010.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -t -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T MD,ia -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.004.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -i --index-format 'i*i*' -s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.005.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.703.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fasta -@ 2 -N -1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -s /tmp/cLhFSIrin1/bam2fq.discard.s.fq -0 /tmp/cLhFSIrin1/bam2fq.discard.0.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.013.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.014.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -T '' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T '*' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d MD:10 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d NM:0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d ia /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -d NM:13 -d NM:14 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_bam2fq: 193s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/bam2fq.001.sam 193s .. ok 193s 193s test_depad: 193s Generate BAM file .. ok 193s 193s depad (SAM input) .. ok 193s 193s depad -s (SAM input) .. ok 193s 193s depad -u (SAM input) .. ok 193s 193s depad -1 (SAM input) .. ok 193s 193s depad (BAM input) .. ok 193s 193s depad -s (BAM input) .. ok 193s 194s depad -u (BAM input) .. ok 194s 194s depad -1 (BAM input) .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/1_map_cigar_large.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/4_X_cigar_full_seq.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/5_insert_cigar_large.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa -i 0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/7_supp.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/7_supp_large.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/8_secondary.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/8_secondary_large.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/10_map_cigar.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -t /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -g 4 -t /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -g 4 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/13_barcodes_ok.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 194s 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 194s .. expected failure 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 194s 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 194s .. expected failure 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 194s 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory 194s .. expected failure 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -I s1 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -I grp2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -I grp3 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -I Sample /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4 194s .. ok 194s 194s test_stats: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/mpileup/ce.fa /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/stat/15.big_del.sam | tail -n+4 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_c.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_c.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -s 1 -O sam -b /tmp/fiI7lJGaeT - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -r -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_c.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -cp -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -o - -s 1 -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_c.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/cLhFSIrin1/merge.tag.1.bam /tmp/cLhFSIrin1/merge.tag.2.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/cLhFSIrin1/merge.tag.3.bam /tmp/cLhFSIrin1/merge.tag.4.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge --no-PG -O SAM - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge --no-PG -O SAM -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/merge.bed - /tmp/cLhFSIrin1/merge.bed.1.bam /tmp/cLhFSIrin1/merge.bed.2.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge --no-PG -r -O SAM - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge --no-PG -O SAM --template-coordinate - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/test_template_coordinate.1.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/test_template_coordinate.2.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_c.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_c.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam -b /tmp/s1OeZPyu4M - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -r -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_c.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -cp -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -o - -s 1 -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_c.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/cLhFSIrin1/merge.tag.1.bam /tmp/cLhFSIrin1/merge.tag.2.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/cLhFSIrin1/merge.tag.3.bam /tmp/cLhFSIrin1/merge.tag.4.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/merge.bed - /tmp/cLhFSIrin1/merge.bed.1.bam /tmp/cLhFSIrin1/merge.bed.2.bam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 --no-PG -r -O SAM - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam 194s .. ok 194s 194s test_merge: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/test_template_coordinate.1.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/merge/test_template_coordinate.2.sam 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/cLhFSIrin1/sortout 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/cLhFSIrin1/sortout.bam 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/cLhFSIrin1/sorttmp 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -N -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/sort_name_input_1.sam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -t RG -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -n -t RG -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -t AS -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -t FI -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort --template-coordinate -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -M -K10 -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -M -K10 -I /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -MH -K10 -I /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/cLhFSIrin1/sortout 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/cLhFSIrin1/sortout.bam 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/cLhFSIrin1/sorttmp 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -N -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/sort_name_input_1.sam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -t RG -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -n -t RG -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -t AS -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -t FI -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 --template-coordinate -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o - 194s .. ok 194s 194s test_sort: 194s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -O SAM -o - 195s .. ok 195s 195s test_sort: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -I /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 195s .. ok 195s 195s test_sort: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -@ 2 -MH -K10 -I /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o - 195s .. ok 195s 195s test_collate: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate --output-fmt=sam -O /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam 195s .. ok 195s 195s test_collate: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam 195s .. ok 195s 195s test_collate: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/collate2.tmp 195s .. ok 195s 195s test_collate: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate --output-fmt=sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/collate3.tmp 195s .. ok 195s 195s test_collate: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate --output-fmt=sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/1_fast_collate.sam 195s .. ok 195s 195s test_collate: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate --output-fmt=sam -f -r 4 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 195s .. ok 195s 195s test_collate: 195s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -O /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam 196s .. ok 196s 196s test_collate: 196s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam 197s .. ok 197s 197s test_collate: 197s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/collate2.tmp 198s .. ok 198s 198s test_collate: 198s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/collate3.tmp 199s .. ok 199s 199s test_collate: 199s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/1_fast_collate.sam 200s .. ok 200s 200s test_collate: 200s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f -r 4 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam 200s .. ok 200s 200s test_fixmate: 200s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 200s 200s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 200s 200s .. expected failure 200s 200s test_fixmate: 200s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/5_ct.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/sanitize.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_ok+.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_ok-.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_draft.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_not_updated.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_not_updated_noML.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_not_updated_noMN.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_bad_MN.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_MN_only.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_ML_only.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_ML_wrong_len.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_noseq.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_bounds.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/1_coord_sort.sam - 201s 201s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 201s 201s .. expected failure 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/5_ct.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/6_ct_replace.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/sanitize.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_ok+.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_ok-.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_draft.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_not_updated.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_not_updated_noML.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_not_updated_noMN.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_bad_MN.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_MN_only.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_ML_only.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_ML_wrong_len.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_noseq.sam - 201s .. ok 201s 201s test_fixmate: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/fixmate/mod_bounds.sam - 201s .. ok 201s 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools calmd -uAr /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.ref.fa 201s .. ok 201s 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools calmd -@ 2 -uAr /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.ref.fa 201s .. ok 201s 201s test_idxstat: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam 201s .. ok 201s 201s test_idxstat: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.cram 201s .. ok 201s 201s test_idxstat: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.sam 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck -v /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 201s .. ok 201s 201s test_quickcheck: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools quickcheck -uv /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' 201s .. ok 201s 201s test_reheader: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 201s .. ok 201s 201s test_reheader: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 201s .. ok 201s 201s test_reheader: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 201s .. ok 201s 201s test_reheader: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram && /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' 201s .. ok 201s 201s test_reheader: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram && /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' 201s .. ok 201s 201s test_reheader: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 201s .. ok 201s 201s test_reheader: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//' 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/1_fixup.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -O sam -m orphan_only /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -O sam -R '1#9' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/1_fixup.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/1_fixup.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/1_fixup.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/1_fixup.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m orphan_only /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -R '1#9' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/1_fixup.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/1_fixup.sam 201s .. ok 201s 201s test_addrprg: 201s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam 202s .. ok 202s 202s test_addrprg: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/addrprg/1_fixup.sam 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/1_name_sort.sam - 202s 202s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 202s 202s 202s .. expected failure 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/2_bad_order.sam - 202s 202s ERR: samtools markdup: error, not in coordinate sorted order. 202s 202s 202s .. expected failure 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 202s 202s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 202s 202s samtools markdup: error, unable to assign pair hash key. 202s 202s 202s .. expected failure 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 202s 202s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 202s 202s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 202s 202s 202s .. expected failure 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/5_markdup.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -O sam -r --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/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.N9Cu7L/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/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.N9Cu7L/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/17_read_group.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/1_name_sort.sam - 202s 202s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. 202s 202s 202s .. expected failure 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/2_bad_order.sam - 202s 202s ERR: samtools markdup: error, not in coordinate sorted order. 202s 202s 202s .. expected failure 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/3_missing_mc.sam - 202s 202s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. 202s 202s samtools markdup: error, unable to assign pair hash key. 202s 202s 202s .. expected failure 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/4_missing_ms.sam - 202s 202s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 202s 202s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. 202s 202s 202s .. expected failure 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/5_markdup.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -O sam -r --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/6_remove_dups.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/8_optical_dup.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/10_optical_chain.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/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.N9Cu7L/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/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.N9Cu7L/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/17_read_group.sam - 202s .. ok 202s 202s test_markdup: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam - 202s .. ok 202s 202s test_bedcov: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools bedcov /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bedcov/bedcov.bam 202s .. ok 202s 202s test_bedcov: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools bedcov -j /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bedcov/bedcov.bam 202s .. ok 202s 202s test_bedcov: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools bedcov -g512 -G2048 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bedcov/bedcov.bam 202s .. ok 202s 202s test_bedcov: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools bedcov -c /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/bedcov/bedcov.bam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -p 5 -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split --output-fmt sam -d RG -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split --output-fmt sam -d an -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split --output-fmt sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -d nn -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.d_nn.unk.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split_d_nn.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split --output-fmt sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.d_nn.0unk.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split_d_nn.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -p 5 -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 202s .. ok 202s 202s test_split: 202s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d RG -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 203s .. ok 203s 203s test_split: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 203s .. ok 203s 203s test_split: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.sam 203s .. ok 203s 203s test_split: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -d nn -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.d_nn.unk.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split_d_nn.sam 203s .. ok 203s 203s test_split: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -f /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split.tmp.d_nn.0unk.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/split/split_d_nn.sam 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG /tmp/cLhFSIrin1/longref.sam.gz 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG /tmp/cLhFSIrin1/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view -h --no-PG -L /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/large_pos/test.bed /tmp/cLhFSIrin1/longref.sam.gz 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/large_pos/longref_name.sam 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools merge -O sam --no-PG - /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/large_pos/longref.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/large_pos/longref2.sam 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools depth /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/large_pos/longref.sam 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools depth -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/large_pos/test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/large_pos/longref.sam 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/cLhFSIrin1/longref.sam.gz 203s .. ok 203s 203s test_large_positions: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools fixmate -O sam --no-PG - - | 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --primer-counts /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/3_multi_ref_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/3_multi_ref_data.sam 203s .. ok 203s 203s test_ampliconclip: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam 203s .. ok 203s 203s test_ampliconstats: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_hard_clipped.expected.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_soft_clipped.expected.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/1_soft_clipped_strand.expected.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' 203s .. ok 203s 203s test_ampliconstats: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 203s .. ok 203s 203s test_ampliconstats: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' 203s .. ok 203s 203s test_reset: 203s cat /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view 203s .. ok 203s 203s test_reset: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag < /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view 203s .. ok 203s 203s test_reset: 203s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools view 204s .. ok 204s 204s test_reset: 204s cat /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.bam 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/test_input_1_a.cram 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG sam_to_fixed_bam /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index --no-PG /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG" 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s test_reset: 204s /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/samtools reset /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.N9Cu7L/autopkgtest_tmp/test/reset/output 204s .. ok 204s 204s 204s Number of tests: 204s total .. 951 204s passed .. 920 204s failed .. 0 204s expected failure .. 31 204s unexpected pass .. 0 204s 204s autopkgtest [23:07:09]: test run-unit-test: -----------------------] 204s run-unit-test PASS 204s autopkgtest [23:07:09]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 205s autopkgtest [23:07:10]: @@@@@@@@@@@@@@@@@@@@ summary 205s run-unit-test PASS 220s nova [W] Skipping flock for amd64 220s Creating nova instance adt-plucky-amd64-samtools-20250315-230345-juju-7f2275-prod-proposed-migration-environment-20-60aaaada-46e5-4ac5-9bc5-eff8f02280a6 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 220s nova [W] Timed out waiting for ffe0f8ac-c494-4687-a123-225c3d8d1dd8 to get deleted.