0s autopkgtest [20:00:36]: starting date and time: 2024-11-29 20:00:36+0000 0s autopkgtest [20:00:36]: git checkout: be626eda Fix armhf LXD image generation for plucky 0s autopkgtest [20:00:36]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cbr7awnb/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:openssl --apt-upgrade htslib --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=openssl/3.4.0-1ubuntu1 -- lxd -r lxd-armhf-10.145.243.27 lxd-armhf-10.145.243.27:autopkgtest/ubuntu/plucky/armhf 59s autopkgtest [20:01:35]: testbed dpkg architecture: armhf 62s autopkgtest [20:01:38]: testbed apt version: 2.9.14ubuntu1 68s autopkgtest [20:01:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 71s autopkgtest [20:01:47]: testbed release detected to be: None 83s autopkgtest [20:01:59]: updating testbed package index (apt update) 86s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 86s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [213 kB] 86s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 87s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 87s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [62.8 kB] 87s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [837 kB] 87s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.4 kB] 87s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 87s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [85.5 kB] 87s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [928 B] 87s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [636 kB] 87s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [6440 B] 87s Get:13 http://ftpmaster.internal/ubuntu plucky/universe Sources [20.7 MB] 87s Get:14 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [298 kB] 87s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1377 kB] 87s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1353 kB] 87s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [14.6 MB] 88s Get:18 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [174 kB] 91s Fetched 40.5 MB in 5s (7859 kB/s) 92s Reading package lists... 101s autopkgtest [20:02:17]: upgrading testbed (apt dist-upgrade and autopurge) 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 105s Starting 2 pkgProblemResolver with broken count: 0 105s Done 105s Entering ResolveByKeep 106s 106s The following NEW packages will be installed: 106s openssl-provider-legacy 106s The following packages will be upgraded: 106s fwupd libfwupd3 libssl3t64 openssl python3-software-properties 106s software-properties-common 106s 6 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 8135 kB of archives. 106s After this operation, 494 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf openssl-provider-legacy armhf 3.4.0-1ubuntu1 [29.3 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libssl3t64 armhf 3.4.0-1ubuntu1 [1756 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf openssl armhf 3.4.0-1ubuntu1 [1159 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 2.0.2-2 [5020 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd3 armhf 2.0.2-2 [124 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf software-properties-common all 0.107 [16.5 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf python3-software-properties all 0.107 [30.4 kB] 107s Fetched 8135 kB in 1s (10.5 MB/s) 107s (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 ... 59970 files and directories currently installed.) 107s Preparing to unpack .../libssl3t64_3.4.0-1ubuntu1_armhf.deb ... 107s Unpacking libssl3t64:armhf (3.4.0-1ubuntu1) over (3.3.1-2ubuntu2) ... 107s Selecting previously unselected package openssl-provider-legacy. 107s Preparing to unpack .../openssl-provider-legacy_3.4.0-1ubuntu1_armhf.deb ... 107s Unpacking openssl-provider-legacy (3.4.0-1ubuntu1) ... 108s Setting up libssl3t64:armhf (3.4.0-1ubuntu1) ... 108s Setting up openssl-provider-legacy (3.4.0-1ubuntu1) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59973 files and directories currently installed.) 108s Preparing to unpack .../openssl_3.4.0-1ubuntu1_armhf.deb ... 108s Unpacking openssl (3.4.0-1ubuntu1) over (3.3.1-2ubuntu2) ... 108s Preparing to unpack .../fwupd_2.0.2-2_armhf.deb ... 108s Unpacking fwupd (2.0.2-2) over (2.0.2-1) ... 108s Preparing to unpack .../libfwupd3_2.0.2-2_armhf.deb ... 108s Unpacking libfwupd3:armhf (2.0.2-2) over (2.0.2-1) ... 108s Preparing to unpack .../software-properties-common_0.107_all.deb ... 108s Unpacking software-properties-common (0.107) over (0.105) ... 108s Preparing to unpack .../python3-software-properties_0.107_all.deb ... 108s Unpacking python3-software-properties (0.107) over (0.105) ... 108s Setting up libfwupd3:armhf (2.0.2-2) ... 108s Setting up python3-software-properties (0.107) ... 108s Setting up openssl (3.4.0-1ubuntu1) ... 108s Installing new version of config file /etc/ssl/openssl.cnf ... 108s Setting up fwupd (2.0.2-2) ... 109s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 109s fwupd.service is a disabled or a static unit not running, not starting it. 109s Setting up software-properties-common (0.107) ... 109s Processing triggers for libc-bin (2.40-1ubuntu3) ... 109s Processing triggers for man-db (2.13.0-1) ... 110s Processing triggers for dbus (1.14.10-4ubuntu5) ... 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s autopkgtest [20:02:34]: rebooting testbed after setup commands that affected boot 196s autopkgtest [20:03:52]: testbed running kernel: Linux 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 18:12:14 UTC 2 247s autopkgtest [20:04:43]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 283s Get:1 http://ftpmaster.internal/ubuntu plucky/universe htslib 1.20+ds-2 (dsc) [2090 B] 283s Get:2 http://ftpmaster.internal/ubuntu plucky/universe htslib 1.20+ds-2 (tar) [1531 kB] 283s Get:3 http://ftpmaster.internal/ubuntu plucky/universe htslib 1.20+ds-2 (diff) [21.3 kB] 283s gpgv: Signature made Thu Oct 31 17:36:10 2024 UTC 283s gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 283s gpgv: Can't check signature: No public key 283s dpkg-source: warning: cannot verify inline signature for ./htslib_1.20+ds-2.dsc: no acceptable signature found 284s autopkgtest [20:05:20]: testing package htslib version 1.20+ds-2 287s autopkgtest [20:05:23]: build not needed 292s autopkgtest [20:05:28]: test run-unit-test: preparing testbed 294s Reading package lists... 294s Building dependency tree... 294s Reading state information... 294s Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 295s The following NEW packages will be installed: 295s autoconf automake autopoint autotools-dev build-essential comerr-dev cpp 295s cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 295s debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-14 295s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 295s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext htslib-test 295s intltool-debian krb5-multidev libarchive-zip-perl libasan8 libbrotli-dev 295s libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 295s libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64 295s libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl 295s libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgomp1 295s libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs-dev libhtscodecs2 295s libidn2-dev libisl23 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 295s libkrb5-dev libldap-dev liblzma-dev libmpc3 libnghttp2-dev libp11-kit-dev 295s libpkgconf3 libpsl-dev librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev 295s libtasn1-6-dev libtool libubsan1 libunbound8 libzstd-dev linux-libc-dev m4 295s nettle-dev pkgconf pkgconf-bin po-debconf rpcsvc-proto tabix zlib1g-dev 296s 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. 296s Need to get 70.2 MB of archives. 296s After this operation, 205 MB of additional disk space will be used. 296s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB] 296s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 296s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 296s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 296s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB] 296s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB] 296s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB] 296s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-5 [119 kB] 296s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 296s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB] 296s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 296s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 296s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB] 297s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B] 297s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B] 297s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB] 297s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB] 297s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 297s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB] 297s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB] 297s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB] 297s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB] 297s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB] 297s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B] 297s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B] 297s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB] 297s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB] 298s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB] 298s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B] 298s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B] 298s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 298s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 298s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-8 [166 kB] 298s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 298s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 298s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 298s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B] 298s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB] 298s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 298s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB] 298s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 298s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 298s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB] 298s Get:44 http://ftpmaster.internal/ubuntu plucky/universe armhf htslib-test all 1.20+ds-2 [1145 kB] 298s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf comerr-dev armhf 2.1-1.47.1-1ubuntu1 [43.9 kB] 298s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libgssrpc4t64 armhf 1.21.3-3 [51.5 kB] 298s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libkadm5clnt-mit12 armhf 1.21.3-3 [35.1 kB] 298s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libkdb5-10t64 armhf 1.21.3-3 [35.1 kB] 298s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libkadm5srv-mit12 armhf 1.21.3-3 [45.6 kB] 298s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf krb5-multidev armhf 1.21.3-3 [125 kB] 298s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libbrotli-dev armhf 1.1.0-2build3 [337 kB] 298s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 298s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10 [127 kB] 298s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libunbound8 armhf 1.20.0-1ubuntu2.1 [416 kB] 298s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls-dane0t64 armhf 3.8.8-2ubuntu1 [34.7 kB] 298s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls-openssl27t64 armhf 3.8.8-2ubuntu1 [34.9 kB] 298s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libidn2-dev armhf 2.3.7-2build2 [115 kB] 298s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libp11-kit-dev armhf 0.25.5-2ubuntu1 [22.7 kB] 298s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libtasn1-6-dev armhf 4.19.0-3build1 [86.0 kB] 298s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2ubuntu7 [9124 B] 298s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2ubuntu7 [290 kB] 298s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf nettle-dev armhf 3.10-1 [1173 kB] 298s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls28-dev armhf 3.8.8-2ubuntu1 [1018 kB] 298s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libkrb5-dev armhf 1.21.3-3 [11.9 kB] 298s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-dev armhf 2.6.8+dfsg-1~exp4ubuntu3 [287 kB] 298s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 298s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 298s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 298s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf libnghttp2-dev armhf 1.64.0-1 [106 kB] 298s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf libpsl-dev armhf 0.21.2-1.1build1 [75.6 kB] 298s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 298s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2build7 [62.9 kB] 298s Get:73 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libssl-dev armhf 3.4.0-1ubuntu1 [2327 kB] 298s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libssh2-1-dev armhf 1.11.1-1 [270 kB] 298s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libzstd-dev armhf 1.5.6+dfsg-1 [331 kB] 298s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl4-gnutls-dev armhf 8.11.0-1ubuntu2 [451 kB] 298s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 298s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.22-1 [45.0 kB] 298s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 298s Get:80 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.20+ds-2 [394 kB] 298s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.3-1 [166 kB] 298s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts-dev armhf 1.20+ds-2 [1752 kB] 298s Get:83 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs-dev armhf 1.6.1-1 [2958 kB] 298s Get:84 http://ftpmaster.internal/ubuntu plucky/universe armhf tabix armhf 1.20+ds-2 [429 kB] 299s Fetched 70.2 MB in 3s (23.1 MB/s) 299s Selecting previously unselected package m4. 299s (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 ... 59975 files and directories currently installed.) 299s Preparing to unpack .../00-m4_1.4.19-4build1_armhf.deb ... 299s Unpacking m4 (1.4.19-4build1) ... 299s Selecting previously unselected package autoconf. 299s Preparing to unpack .../01-autoconf_2.72-3_all.deb ... 299s Unpacking autoconf (2.72-3) ... 299s Selecting previously unselected package autotools-dev. 299s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 299s Unpacking autotools-dev (20220109.1) ... 299s Selecting previously unselected package automake. 299s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 299s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 299s Selecting previously unselected package autopoint. 299s Preparing to unpack .../04-autopoint_0.22.5-2_all.deb ... 299s Unpacking autopoint (0.22.5-2) ... 299s Selecting previously unselected package libc-dev-bin. 299s Preparing to unpack .../05-libc-dev-bin_2.40-1ubuntu3_armhf.deb ... 299s Unpacking libc-dev-bin (2.40-1ubuntu3) ... 299s Selecting previously unselected package linux-libc-dev:armhf. 299s Preparing to unpack .../06-linux-libc-dev_6.11.0-8.8_armhf.deb ... 299s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ... 299s Selecting previously unselected package libcrypt-dev:armhf. 299s Preparing to unpack .../07-libcrypt-dev_1%3a4.4.36-5_armhf.deb ... 299s Unpacking libcrypt-dev:armhf (1:4.4.36-5) ... 299s Selecting previously unselected package rpcsvc-proto. 299s Preparing to unpack .../08-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 299s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 300s Selecting previously unselected package libc6-dev:armhf. 300s Preparing to unpack .../09-libc6-dev_2.40-1ubuntu3_armhf.deb ... 300s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ... 300s Selecting previously unselected package libisl23:armhf. 300s Preparing to unpack .../10-libisl23_0.27-1_armhf.deb ... 300s Unpacking libisl23:armhf (0.27-1) ... 300s Selecting previously unselected package libmpc3:armhf. 300s Preparing to unpack .../11-libmpc3_1.3.1-1build2_armhf.deb ... 300s Unpacking libmpc3:armhf (1.3.1-1build2) ... 300s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 300s Preparing to unpack .../12-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 300s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 300s Selecting previously unselected package cpp-14. 300s Preparing to unpack .../13-cpp-14_14.2.0-8ubuntu1_armhf.deb ... 300s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 300s Selecting previously unselected package cpp-arm-linux-gnueabihf. 300s Preparing to unpack .../14-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 300s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 300s Selecting previously unselected package cpp. 300s Preparing to unpack .../15-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ... 300s Unpacking cpp (4:14.1.0-2ubuntu1) ... 300s Selecting previously unselected package libcc1-0:armhf. 300s Preparing to unpack .../16-libcc1-0_14.2.0-8ubuntu1_armhf.deb ... 300s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ... 300s Selecting previously unselected package libgomp1:armhf. 300s Preparing to unpack .../17-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 300s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 300s Selecting previously unselected package libasan8:armhf. 300s Preparing to unpack .../18-libasan8_14.2.0-8ubuntu1_armhf.deb ... 300s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ... 300s Selecting previously unselected package libubsan1:armhf. 300s Preparing to unpack .../19-libubsan1_14.2.0-8ubuntu1_armhf.deb ... 300s Unpacking libubsan1:armhf (14.2.0-8ubuntu1) ... 300s Selecting previously unselected package libgcc-14-dev:armhf. 300s Preparing to unpack .../20-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ... 300s Unpacking libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 300s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 300s Preparing to unpack .../21-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 300s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 301s Selecting previously unselected package gcc-14. 301s Preparing to unpack .../22-gcc-14_14.2.0-8ubuntu1_armhf.deb ... 301s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 301s Selecting previously unselected package gcc-arm-linux-gnueabihf. 301s Preparing to unpack .../23-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 301s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 301s Selecting previously unselected package gcc. 301s Preparing to unpack .../24-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ... 301s Unpacking gcc (4:14.1.0-2ubuntu1) ... 301s Selecting previously unselected package libstdc++-14-dev:armhf. 301s Preparing to unpack .../25-libstdc++-14-dev_14.2.0-8ubuntu1_armhf.deb ... 301s Unpacking libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 301s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 301s Preparing to unpack .../26-g++-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 301s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 301s Selecting previously unselected package g++-14. 301s Preparing to unpack .../27-g++-14_14.2.0-8ubuntu1_armhf.deb ... 301s Unpacking g++-14 (14.2.0-8ubuntu1) ... 301s Selecting previously unselected package g++-arm-linux-gnueabihf. 301s Preparing to unpack .../28-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 301s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 301s Selecting previously unselected package g++. 301s Preparing to unpack .../29-g++_4%3a14.1.0-2ubuntu1_armhf.deb ... 301s Unpacking g++ (4:14.1.0-2ubuntu1) ... 301s Selecting previously unselected package build-essential. 301s Preparing to unpack .../30-build-essential_12.10ubuntu1_armhf.deb ... 301s Unpacking build-essential (12.10ubuntu1) ... 301s Selecting previously unselected package libdebhelper-perl. 301s Preparing to unpack .../31-libdebhelper-perl_13.20ubuntu1_all.deb ... 301s Unpacking libdebhelper-perl (13.20ubuntu1) ... 301s Selecting previously unselected package libtool. 301s Preparing to unpack .../32-libtool_2.4.7-8_all.deb ... 301s Unpacking libtool (2.4.7-8) ... 301s Selecting previously unselected package dh-autoreconf. 301s Preparing to unpack .../33-dh-autoreconf_20_all.deb ... 301s Unpacking dh-autoreconf (20) ... 302s Selecting previously unselected package libarchive-zip-perl. 302s Preparing to unpack .../34-libarchive-zip-perl_1.68-1_all.deb ... 302s Unpacking libarchive-zip-perl (1.68-1) ... 302s Selecting previously unselected package libfile-stripnondeterminism-perl. 302s Preparing to unpack .../35-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 302s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 302s Selecting previously unselected package dh-strip-nondeterminism. 302s Preparing to unpack .../36-dh-strip-nondeterminism_1.14.0-1_all.deb ... 302s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 302s Selecting previously unselected package debugedit. 302s Preparing to unpack .../37-debugedit_1%3a5.1-1_armhf.deb ... 302s Unpacking debugedit (1:5.1-1) ... 302s Selecting previously unselected package dwz. 302s Preparing to unpack .../38-dwz_0.15-1build6_armhf.deb ... 302s Unpacking dwz (0.15-1build6) ... 302s Selecting previously unselected package gettext. 302s Preparing to unpack .../39-gettext_0.22.5-2_armhf.deb ... 302s Unpacking gettext (0.22.5-2) ... 302s Selecting previously unselected package intltool-debian. 302s Preparing to unpack .../40-intltool-debian_0.35.0+20060710.6_all.deb ... 302s Unpacking intltool-debian (0.35.0+20060710.6) ... 302s Selecting previously unselected package po-debconf. 302s Preparing to unpack .../41-po-debconf_1.0.21+nmu1_all.deb ... 302s Unpacking po-debconf (1.0.21+nmu1) ... 302s Selecting previously unselected package debhelper. 302s Preparing to unpack .../42-debhelper_13.20ubuntu1_all.deb ... 302s Unpacking debhelper (13.20ubuntu1) ... 302s Selecting previously unselected package htslib-test. 302s Preparing to unpack .../43-htslib-test_1.20+ds-2_all.deb ... 302s Unpacking htslib-test (1.20+ds-2) ... 302s Selecting previously unselected package comerr-dev:armhf. 302s Preparing to unpack .../44-comerr-dev_2.1-1.47.1-1ubuntu1_armhf.deb ... 302s Unpacking comerr-dev:armhf (2.1-1.47.1-1ubuntu1) ... 302s Selecting previously unselected package libgssrpc4t64:armhf. 302s Preparing to unpack .../45-libgssrpc4t64_1.21.3-3_armhf.deb ... 302s Unpacking libgssrpc4t64:armhf (1.21.3-3) ... 302s Selecting previously unselected package libkadm5clnt-mit12:armhf. 302s Preparing to unpack .../46-libkadm5clnt-mit12_1.21.3-3_armhf.deb ... 302s Unpacking libkadm5clnt-mit12:armhf (1.21.3-3) ... 302s Selecting previously unselected package libkdb5-10t64:armhf. 302s Preparing to unpack .../47-libkdb5-10t64_1.21.3-3_armhf.deb ... 302s Unpacking libkdb5-10t64:armhf (1.21.3-3) ... 302s Selecting previously unselected package libkadm5srv-mit12:armhf. 302s Preparing to unpack .../48-libkadm5srv-mit12_1.21.3-3_armhf.deb ... 302s Unpacking libkadm5srv-mit12:armhf (1.21.3-3) ... 302s Selecting previously unselected package krb5-multidev:armhf. 302s Preparing to unpack .../49-krb5-multidev_1.21.3-3_armhf.deb ... 302s Unpacking krb5-multidev:armhf (1.21.3-3) ... 302s Selecting previously unselected package libbrotli-dev:armhf. 302s Preparing to unpack .../50-libbrotli-dev_1.1.0-2build3_armhf.deb ... 302s Unpacking libbrotli-dev:armhf (1.1.0-2build3) ... 302s Selecting previously unselected package libbz2-dev:armhf. 302s Preparing to unpack .../51-libbz2-dev_1.0.8-6_armhf.deb ... 302s Unpacking libbz2-dev:armhf (1.0.8-6) ... 302s Selecting previously unselected package libevent-2.1-7t64:armhf. 302s Preparing to unpack .../52-libevent-2.1-7t64_2.1.12-stable-10_armhf.deb ... 302s Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10) ... 302s Selecting previously unselected package libunbound8:armhf. 302s Preparing to unpack .../53-libunbound8_1.20.0-1ubuntu2.1_armhf.deb ... 302s Unpacking libunbound8:armhf (1.20.0-1ubuntu2.1) ... 302s Selecting previously unselected package libgnutls-dane0t64:armhf. 302s Preparing to unpack .../54-libgnutls-dane0t64_3.8.8-2ubuntu1_armhf.deb ... 302s Unpacking libgnutls-dane0t64:armhf (3.8.8-2ubuntu1) ... 302s Selecting previously unselected package libgnutls-openssl27t64:armhf. 302s Preparing to unpack .../55-libgnutls-openssl27t64_3.8.8-2ubuntu1_armhf.deb ... 302s Unpacking libgnutls-openssl27t64:armhf (3.8.8-2ubuntu1) ... 302s Selecting previously unselected package libidn2-dev:armhf. 302s Preparing to unpack .../56-libidn2-dev_2.3.7-2build2_armhf.deb ... 302s Unpacking libidn2-dev:armhf (2.3.7-2build2) ... 302s Selecting previously unselected package libp11-kit-dev:armhf. 302s Preparing to unpack .../57-libp11-kit-dev_0.25.5-2ubuntu1_armhf.deb ... 302s Unpacking libp11-kit-dev:armhf (0.25.5-2ubuntu1) ... 302s Selecting previously unselected package libtasn1-6-dev:armhf. 303s Preparing to unpack .../58-libtasn1-6-dev_4.19.0-3build1_armhf.deb ... 303s Unpacking libtasn1-6-dev:armhf (4.19.0-3build1) ... 303s Selecting previously unselected package libgmpxx4ldbl:armhf. 303s Preparing to unpack .../59-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_armhf.deb ... 303s Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2ubuntu7) ... 303s Selecting previously unselected package libgmp-dev:armhf. 303s Preparing to unpack .../60-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_armhf.deb ... 303s Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-2ubuntu7) ... 303s Selecting previously unselected package nettle-dev:armhf. 303s Preparing to unpack .../61-nettle-dev_3.10-1_armhf.deb ... 303s Unpacking nettle-dev:armhf (3.10-1) ... 303s Selecting previously unselected package libgnutls28-dev:armhf. 303s Preparing to unpack .../62-libgnutls28-dev_3.8.8-2ubuntu1_armhf.deb ... 303s Unpacking libgnutls28-dev:armhf (3.8.8-2ubuntu1) ... 303s Selecting previously unselected package libkrb5-dev:armhf. 303s Preparing to unpack .../63-libkrb5-dev_1.21.3-3_armhf.deb ... 303s Unpacking libkrb5-dev:armhf (1.21.3-3) ... 303s Selecting previously unselected package libldap-dev:armhf. 303s Preparing to unpack .../64-libldap-dev_2.6.8+dfsg-1~exp4ubuntu3_armhf.deb ... 303s Unpacking libldap-dev:armhf (2.6.8+dfsg-1~exp4ubuntu3) ... 303s Selecting previously unselected package libpkgconf3:armhf. 303s Preparing to unpack .../65-libpkgconf3_1.8.1-4_armhf.deb ... 303s Unpacking libpkgconf3:armhf (1.8.1-4) ... 303s Selecting previously unselected package pkgconf-bin. 303s Preparing to unpack .../66-pkgconf-bin_1.8.1-4_armhf.deb ... 303s Unpacking pkgconf-bin (1.8.1-4) ... 303s Selecting previously unselected package pkgconf:armhf. 303s Preparing to unpack .../67-pkgconf_1.8.1-4_armhf.deb ... 303s Unpacking pkgconf:armhf (1.8.1-4) ... 303s Selecting previously unselected package libnghttp2-dev:armhf. 303s Preparing to unpack .../68-libnghttp2-dev_1.64.0-1_armhf.deb ... 303s Unpacking libnghttp2-dev:armhf (1.64.0-1) ... 303s Selecting previously unselected package libpsl-dev:armhf. 303s Preparing to unpack .../69-libpsl-dev_0.21.2-1.1build1_armhf.deb ... 303s Unpacking libpsl-dev:armhf (0.21.2-1.1build1) ... 303s Selecting previously unselected package zlib1g-dev:armhf. 303s Preparing to unpack .../70-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 303s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 303s Selecting previously unselected package librtmp-dev:armhf. 303s Preparing to unpack .../71-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_armhf.deb ... 303s Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2build7) ... 303s Selecting previously unselected package libssl-dev:armhf. 303s Preparing to unpack .../72-libssl-dev_3.4.0-1ubuntu1_armhf.deb ... 303s Unpacking libssl-dev:armhf (3.4.0-1ubuntu1) ... 303s Selecting previously unselected package libssh2-1-dev:armhf. 303s Preparing to unpack .../73-libssh2-1-dev_1.11.1-1_armhf.deb ... 303s Unpacking libssh2-1-dev:armhf (1.11.1-1) ... 303s Selecting previously unselected package libzstd-dev:armhf. 303s Preparing to unpack .../74-libzstd-dev_1.5.6+dfsg-1_armhf.deb ... 303s Unpacking libzstd-dev:armhf (1.5.6+dfsg-1) ... 303s Selecting previously unselected package libcurl4-gnutls-dev:armhf. 303s Preparing to unpack .../75-libcurl4-gnutls-dev_8.11.0-1ubuntu2_armhf.deb ... 303s Unpacking libcurl4-gnutls-dev:armhf (8.11.0-1ubuntu2) ... 303s Selecting previously unselected package libdeflate0:armhf. 303s Preparing to unpack .../76-libdeflate0_1.22-1_armhf.deb ... 303s Unpacking libdeflate0:armhf (1.22-1) ... 303s Selecting previously unselected package libdeflate-dev:armhf. 303s Preparing to unpack .../77-libdeflate-dev_1.22-1_armhf.deb ... 303s Unpacking libdeflate-dev:armhf (1.22-1) ... 303s Selecting previously unselected package libhtscodecs2:armhf. 303s Preparing to unpack .../78-libhtscodecs2_1.6.1-1_armhf.deb ... 303s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 303s Selecting previously unselected package libhts3t64:armhf. 303s Preparing to unpack .../79-libhts3t64_1.20+ds-2_armhf.deb ... 303s Unpacking libhts3t64:armhf (1.20+ds-2) ... 303s Selecting previously unselected package liblzma-dev:armhf. 303s Preparing to unpack .../80-liblzma-dev_5.6.3-1_armhf.deb ... 303s Unpacking liblzma-dev:armhf (5.6.3-1) ... 303s Selecting previously unselected package libhts-dev:armhf. 304s Preparing to unpack .../81-libhts-dev_1.20+ds-2_armhf.deb ... 304s Unpacking libhts-dev:armhf (1.20+ds-2) ... 304s Selecting previously unselected package libhtscodecs-dev:armhf. 304s Preparing to unpack .../82-libhtscodecs-dev_1.6.1-1_armhf.deb ... 304s Unpacking libhtscodecs-dev:armhf (1.6.1-1) ... 304s Selecting previously unselected package tabix. 304s Preparing to unpack .../83-tabix_1.20+ds-2_armhf.deb ... 304s Unpacking tabix (1.20+ds-2) ... 304s Setting up libhtscodecs2:armhf (1.6.1-1) ... 304s Setting up libgnutls-openssl27t64:armhf (3.8.8-2ubuntu1) ... 304s Setting up libzstd-dev:armhf (1.5.6+dfsg-1) ... 304s Setting up libarchive-zip-perl (1.68-1) ... 304s Setting up htslib-test (1.20+ds-2) ... 304s Setting up libdebhelper-perl (13.20ubuntu1) ... 304s Setting up libdeflate0:armhf (1.22-1) ... 304s Setting up linux-libc-dev:armhf (6.11.0-8.8) ... 304s Setting up m4 (1.4.19-4build1) ... 304s Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10) ... 304s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 304s Setting up libpsl-dev:armhf (0.21.2-1.1build1) ... 304s Setting up libhtscodecs-dev:armhf (1.6.1-1) ... 304s Setting up autotools-dev (20220109.1) ... 304s Setting up libunbound8:armhf (1.20.0-1ubuntu2.1) ... 304s Setting up libpkgconf3:armhf (1.8.1-4) ... 304s Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2ubuntu7) ... 304s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 304s Setting up libgnutls-dane0t64:armhf (3.8.8-2ubuntu1) ... 304s Setting up libgssrpc4t64:armhf (1.21.3-3) ... 304s Setting up libldap-dev:armhf (2.6.8+dfsg-1~exp4ubuntu3) ... 304s Setting up libssl-dev:armhf (3.4.0-1ubuntu1) ... 304s Setting up libmpc3:armhf (1.3.1-1build2) ... 304s Setting up autopoint (0.22.5-2) ... 304s Setting up pkgconf-bin (1.8.1-4) ... 304s Setting up libidn2-dev:armhf (2.3.7-2build2) ... 304s Setting up autoconf (2.72-3) ... 304s Setting up liblzma-dev:armhf (5.6.3-1) ... 304s Setting up libubsan1:armhf (14.2.0-8ubuntu1) ... 304s Setting up dwz (0.15-1build6) ... 304s Setting up libcrypt-dev:armhf (1:4.4.36-5) ... 304s Setting up libasan8:armhf (14.2.0-8ubuntu1) ... 304s Setting up debugedit (1:5.1-1) ... 304s Setting up libhts3t64:armhf (1.20+ds-2) ... 304s Setting up libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 304s Setting up libisl23:armhf (0.27-1) ... 304s Setting up libc-dev-bin (2.40-1ubuntu3) ... 304s Setting up libtasn1-6-dev:armhf (4.19.0-3build1) ... 304s Setting up libdeflate-dev:armhf (1.22-1) ... 304s Setting up tabix (1.20+ds-2) ... 304s Setting up libcc1-0:armhf (14.2.0-8ubuntu1) ... 304s Setting up libbrotli-dev:armhf (1.1.0-2build3) ... 304s Setting up libp11-kit-dev:armhf (0.25.5-2ubuntu1) ... 304s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 304s Setting up libkadm5clnt-mit12:armhf (1.21.3-3) ... 304s Setting up automake (1:1.16.5-1.3ubuntu1) ... 304s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 304s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 304s Setting up gettext (0.22.5-2) ... 304s Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2ubuntu7) ... 304s Setting up nettle-dev:armhf (3.10-1) ... 304s Setting up libkdb5-10t64:armhf (1.21.3-3) ... 304s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 304s Setting up pkgconf:armhf (1.8.1-4) ... 304s Setting up intltool-debian (0.35.0+20060710.6) ... 304s Setting up cpp-14 (14.2.0-8ubuntu1) ... 304s Setting up dh-strip-nondeterminism (1.14.0-1) ... 304s Setting up libkadm5srv-mit12:armhf (1.21.3-3) ... 304s Setting up libc6-dev:armhf (2.40-1ubuntu3) ... 304s Setting up libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 304s Setting up cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 304s Setting up libbz2-dev:armhf (1.0.8-6) ... 304s Setting up gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 304s Setting up libgnutls28-dev:armhf (3.8.8-2ubuntu1) ... 304s Setting up libnghttp2-dev:armhf (1.64.0-1) ... 304s Setting up g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 304s Setting up po-debconf (1.0.21+nmu1) ... 304s Setting up gcc-14 (14.2.0-8ubuntu1) ... 304s Setting up comerr-dev:armhf (2.1-1.47.1-1ubuntu1) ... 304s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 304s Setting up cpp (4:14.1.0-2ubuntu1) ... 304s Setting up g++-14 (14.2.0-8ubuntu1) ... 304s Setting up krb5-multidev:armhf (1.21.3-3) ... 304s Setting up g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 304s Setting up libtool (2.4.7-8) ... 304s Setting up gcc (4:14.1.0-2ubuntu1) ... 304s Setting up dh-autoreconf (20) ... 304s Setting up libkrb5-dev:armhf (1.21.3-3) ... 304s Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2build7) ... 304s Setting up libssh2-1-dev:armhf (1.11.1-1) ... 304s Setting up g++ (4:14.1.0-2ubuntu1) ... 304s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 304s Setting up build-essential (12.10ubuntu1) ... 304s Setting up debhelper (13.20ubuntu1) ... 304s Setting up libcurl4-gnutls-dev:armhf (8.11.0-1ubuntu2) ... 304s Setting up libhts-dev:armhf (1.20+ds-2) ... 304s Processing triggers for install-info (7.1.1-1) ... 304s Processing triggers for libc-bin (2.40-1ubuntu3) ... 304s Processing triggers for man-db (2.13.0-1) ... 325s autopkgtest [20:06:01]: test run-unit-test: [----------------------- 328s + pkg=htslib 328s + '[' /tmp/autopkgtest.QPWU3q/autopkgtest_tmp = '' ']' 328s + cp -aL /usr/share/htslib-test/Makefile /usr/share/htslib-test/annot-tsv.c /usr/share/htslib-test/bcf_sr_sort.c /usr/share/htslib-test/bcf_sr_sort.h /usr/share/htslib-test/bgzf.c /usr/share/htslib-test/bgzip.c /usr/share/htslib-test/config.h /usr/share/htslib-test/config.mk /usr/share/htslib-test/config_vars.h /usr/share/htslib-test/cram /usr/share/htslib-test/errmod.c /usr/share/htslib-test/faidx.c /usr/share/htslib-test/fuzz_settings.h /usr/share/htslib-test/header.c /usr/share/htslib-test/header.h /usr/share/htslib-test/hfile.c /usr/share/htslib-test/hfile_gcs.c /usr/share/htslib-test/hfile_internal.h /usr/share/htslib-test/hfile_libcurl.c /usr/share/htslib-test/hfile_s3.c /usr/share/htslib-test/hfile_s3_write.c /usr/share/htslib-test/hts.c /usr/share/htslib-test/hts_expr.c /usr/share/htslib-test/hts_internal.h /usr/share/htslib-test/hts_os.c /usr/share/htslib-test/hts_time_funcs.h /usr/share/htslib-test/htscodecs.mk /usr/share/htslib-test/htscodecs_bundled.mk /usr/share/htslib-test/htscodecs_external.mk /usr/share/htslib-test/htsfile.c /usr/share/htslib-test/htslib.mk /usr/share/htslib-test/htslib_static.mk /usr/share/htslib-test/htslib_vars.mk /usr/share/htslib-test/kfunc.c /usr/share/htslib-test/kstring.c /usr/share/htslib-test/md5.c /usr/share/htslib-test/multipart.c /usr/share/htslib-test/os /usr/share/htslib-test/plugin.c /usr/share/htslib-test/probaln.c /usr/share/htslib-test/realn.c /usr/share/htslib-test/regidx.c /usr/share/htslib-test/region.c /usr/share/htslib-test/sam.c /usr/share/htslib-test/sam_internal.h /usr/share/htslib-test/sam_mods.c /usr/share/htslib-test/synced_bcf_reader.c /usr/share/htslib-test/tabix.c /usr/share/htslib-test/tbx.c /usr/share/htslib-test/test /usr/share/htslib-test/textutils.c /usr/share/htslib-test/textutils_internal.h /usr/share/htslib-test/thread_pool.c /usr/share/htslib-test/thread_pool_internal.h /usr/share/htslib-test/vcf.c /usr/share/htslib-test/vcf_sweep.c /usr/share/htslib-test/vcfutils.c /usr/share/htslib-test/version.h /usr/share/htslib-test/version.sh /tmp/autopkgtest.QPWU3q/autopkgtest_tmp 328s + cp -aL htslib.pc.in /tmp/autopkgtest.QPWU3q/autopkgtest_tmp 328s + cp -aL htslib.map /tmp/autopkgtest.QPWU3q/autopkgtest_tmp 328s + cd /tmp/autopkgtest.QPWU3q/autopkgtest_tmp 328s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 328s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 328s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 328s + grep sse /proc/cpuinfo 328s + export CFLAGS 328s + make -e check 328s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kfunc.o kfunc.c 328s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kstring.o kstring.c 328s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bcf_sr_sort.o bcf_sr_sort.c 329s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzf.o bgzf.c 330s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o errmod.o errmod.c 330s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o faidx.o faidx.c 331s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o header.o header.c 332s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hfile.o hfile.c 333s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts.o hts.c 336s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_expr.o hts_expr.c 336s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_os.o hts_os.c 336s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o md5.o md5.c 337s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o multipart.o multipart.c 337s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o probaln.o probaln.c 337s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o realn.o realn.c 337s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o regidx.o regidx.c 338s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o region.o region.c 338s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam.o sam.c 342s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_mods.o sam_mods.c 342s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o synced_bcf_reader.o synced_bcf_reader.c 343s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf_sweep.o vcf_sweep.c 344s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tbx.o tbx.c 344s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o textutils.o textutils.c 344s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o thread_pool.o thread_pool.c 344s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf.o vcf.c 349s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcfutils.o vcfutils.c 351s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_codecs.o cram/cram_codecs.c 352s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_decode.o cram/cram_decode.c 354s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_encode.o cram/cram_encode.c 357s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_external.o cram/cram_external.c 357s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_index.o cram/cram_index.c 357s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_io.o cram/cram_io.c 360s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_stats.o cram/cram_stats.c 360s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/mFILE.o cram/mFILE.c 360s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/open_trace_file.o cram/open_trace_file.c 360s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/pooled_alloc.o cram/pooled_alloc.c 360s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/string_alloc.o cram/string_alloc.c 360s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c 361s ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o 361s ranlib libhts.a 361s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kfunc.pico kfunc.c 361s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kstring.pico kstring.c 361s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c 362s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bgzf.pico bgzf.c 363s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o errmod.pico errmod.c 363s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o faidx.pico faidx.c 364s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o header.pico header.c 365s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile.pico hfile.c 366s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts.pico hts.c 369s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_expr.pico hts_expr.c 369s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_os.pico hts_os.c 369s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o md5.pico md5.c 369s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o multipart.pico multipart.c 370s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o probaln.pico probaln.c 370s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o realn.pico realn.c 370s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o regidx.pico regidx.c 371s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o region.pico region.c 371s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam.pico sam.c 375s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam_mods.pico sam_mods.c 375s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c 376s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 377s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o tbx.pico tbx.c 377s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o textutils.pico textutils.c 377s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o thread_pool.pico thread_pool.c 378s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf.pico vcf.c 382s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcfutils.pico vcfutils.c 384s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c 385s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c 387s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c 390s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_external.pico cram/cram_external.c 390s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_index.pico cram/cram_index.c 391s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_io.pico cram/cram_io.c 393s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c 393s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/mFILE.pico cram/mFILE.c 393s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c 393s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c 393s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c 393s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c 394s gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 394s ln -sf libhts.so libhts.so.3 394s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o annot-tsv.o annot-tsv.c 394s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 394s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzip.o bgzip.c 395s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 395s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o htsfile.o htsfile.c 395s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 395s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tabix.o tabix.c 395s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 396s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 396s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread 396s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 396s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 397s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3.pico hfile_s3.c 397s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread 398s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c 398s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread 398s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hts_endian.o test/hts_endian.c 398s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm 398s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fieldarith.o test/fieldarith.c 398s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 399s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hfile.o test/hfile.c 399s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 399s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup.o test/pileup.c 399s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 399s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup_mod.o test/pileup_mod.c 399s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 399s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/plugins-dlhts.o test/plugins-dlhts.c 399s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm 399s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/sam.o test/sam.c 400s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 401s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_bgzf.o test/test_bgzf.c 401s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 401s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_expr.o test/test_expr.c 401s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 401s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_faidx.o test/test_faidx.c 401s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 402s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kfunc.o test/test_kfunc.c 402s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 402s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kstring.o test/test_kstring.c 402s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 402s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_mod.o test/test_mod.c 402s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 402s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_realn.o test/test_realn.c 402s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 402s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-regidx.o test/test-regidx.c 402s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 403s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_str2int.o test/test_str2int.c 403s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 403s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_time_funcs.o test/test_time_funcs.c 403s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o 403s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_view.o test/test_view.c 403s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 403s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_index.o test/test_index.c 403s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 403s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-api.o test/test-vcf-api.c 404s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 404s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c 404s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 404s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-sr.o test/test-bcf-sr.c 404s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 404s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c 404s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-translate.o test/test-bcf-translate.c 404s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 404s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-parse-reg.o test/test-parse-reg.c 405s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 405s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_introspection.o test/test_introspection.c 405s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 405s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c 410s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 410s sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 410s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 410s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 410s test/hts_endian 410s test/test_expr 410s test/test_kfunc 410s test/test_kstring 410s test/test_str2int 410s test/test_time_funcs 411s test/fieldarith test/fieldarith.sam 411s test/hfile 411s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 411s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 411s fi 411s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 411s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 411s fi 411s test/test_bgzf test/bgziptest.txt 412s test/test-parse-reg -t test/colons.bam 412s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 412s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 412s Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" 412s Expected error: [E::hts_parse_region] Unexpected string "x" after region 412s Expected error: [E::hts_parse_region] Unexpected string "y" after region 412s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 412s cd test/faidx && ./test-faidx.sh faidx.tst 412s Testing faidx... 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 412s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 412s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 412s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 412s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 412s 412s Expected passes: 25 412s Unexpected passes: 0 412s Expected failures: 0 412s Unexpected failures: 0 412s cd test/sam_filter && ./filter.sh filter.tst 412s Testing sam_filter... 412s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 412s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 412s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 412s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 412s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 412s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 412s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 412s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 412s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 412s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 412s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 412s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 412s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 413s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 413s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 413s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 413s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 413s PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' 413s 413s Expected passes: 18 413s Unexpected passes: 0 413s Expected failures: 0 413s Unexpected failures: 0 413s cd test/tabix && ./test-tabix.sh tabix.tst 413s Testing tabix... 413s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 413s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 413s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 413s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 413s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 413s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 413s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 413s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 413s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 413s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 413s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 413s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 413s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 413s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 413s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 413s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 413s 413s Expected passes: 16 413s Unexpected passes: 0 413s Expected failures: 0 413s Unexpected failures: 0 413s cd test/mpileup && ./test-pileup.sh mpileup.tst 413s Testing (m)pileup... 413s PASS : $pileup mp_D.sam 413s PASS : $pileup -m mp_D.sam 413s PASS : $pileup mp_DI.sam 413s PASS : $pileup -m mp_DI.sam 413s PASS : $pileup mp_I.sam 413s PASS : $pileup -m mp_I.sam 413s PASS : $pileup mp_P.sam 413s PASS : $pileup -m mp_P.sam 413s PASS : $pileup mp_ID.sam 413s PASS : $pileup -m mp_ID.sam 413s PASS : $pileup mp_N.sam 413s PASS : $pileup -m mp_N.sam 413s PASS : $pileup mp_N2.sam 413s PASS : $pileup -m mp_N2.sam 413s PASS : $pileup c1#pad1.sam 413s PASS : $pileup -m c1#pad1.sam 413s PASS : $pileup c1#pad2.sam 413s PASS : $pileup -m c1#pad2.sam 413s PASS : $pileup c1#pad3.sam 413s PASS : $pileup -m c1#pad3.sam 413s PASS : $pileup -m small.bam 413s PASS : $pileup -m mp_overlap1.sam 413s PASS : $pileup -m mp_overlap2.sam 413s 413s Expected passes: 23 413s Unexpected passes: 0 413s Expected failures: 0 413s Unexpected failures: 0 413s cd test/fastq && ./test-fastq.sh 413s Testing fastq support 413s PASS : $tview minimal.fq 413s PASS : $tview minimal.fa 413s PASS : $tview multiline.fq 413s PASS : $tview multiline.fa 413s PASS : $tview -i fastq_aux longline.fq 413s PASS : $tview single.fq 413s PASS : $tview single.fa 413s PASS : $tview -i fastq_aux single.fq 413s PASS : $tview -i fastq_aux single.fa 413s PASS : $tview interleaved.fq 413s PASS : $tview interleaved.fa 413s PASS : $tview -i fastq_aux interleaved.fq 413s PASS : $tview -i fastq_aux interleaved.fa 413s PASS : $tview -i fastq_casava interleaved_casava.fq 413s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 413s PASS : $tview -i fastq_casava interleaved_casava.fa 413s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 413s PASS : $tview -i fastq_casava filter_casava.fq 413s PASS : $tview -i fastq_casava filter_casava.fa 413s PASS : $tview -i fastq_aux r1.fq 413s PASS : $tview -i fastq_aux r2.fq 413s PASS : $tview -i fastq_aux r1.fa 413s PASS : $tview -i fastq_aux r2.fa 413s PASS : $tview -i fastq_name2 name2.fq 413s PASS : $tview -i fastq_name2 name2.fa 413s PASS : $tview -f minimal.sam 413s PASS : $tview -F minimal.sam 413s PASS : $tview -f -o fastq_aux single_aux.sam 413s PASS : $tview -F -o fastq_aux single_aux.sam 413s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 413s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 413s PASS : $tview -f -o fastq_casava inter_casava.sam 413s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 413s PASS : $tview -F -o fastq_casava inter_casava.sam 413s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 413s PASS : $tview -f -o fastq_casava filter_casava.sam 413s PASS : $tview -F -o fastq_casava filter_casava.sam 413s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 413s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 413s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 413s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 413s 413s Expected passes: 41 413s Unexpected passes: 0 413s Expected failures: 0 413s Unexpected failures: 0 413s cd test/base_mods && ./base-mods.sh base-mods.tst 413s Testing base-modifications... 413s PASS : $test_mod MM-chebi.sam 413s PASS : $test_mod MM-double.sam 413s PASS : $test_mod MM-multi.sam 413s PASS : $test_mod MM-explicit.sam 413s PASS : $test_mod -x MM-explicit.sam 413s PASS : $test_mod -f 1 MM-explicit.sam 414s PASS : $test_mod MM-not-all-modded.sam 414s PASS : $pileup_mod < MM-pileup.sam 414s PASS : $pileup_mod < MM-pileup2.sam 414s PASS : $pileup_mod < MM-MNp.sam 414s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 414s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 414s PASS : $test_mod < MM-MNf1.sam (must exit non-zero) 414s PASS : $test_mod < MM-MNf2.sam (must exit non-zero) 414s PASS : $test_mod < MM-bounds+.sam (must exit non-zero) 414s PASS : $test_mod < MM-bounds-.sam (must exit non-zero) 414s 414s Expected passes: 16 414s Unexpected passes: 0 414s Expected failures: 0 414s Unexpected failures: 0 414s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 414s (Expect trailing 'x' message for " -1,001x") 414s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 414s (Expect trailing 'k' message for "1.5e+3k") 414s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 414s (Expect dropped fraction message for "12.3456k") 414s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 414s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 414s (Expect invalid numeric message for "A") 414s [W::hts_parse_decimal] Invalid numeric value A[truncated] 414s (Expect invalid numeric message for "G") 414s [W::hts_parse_decimal] Invalid numeric value G[truncated] 414s (Expect invalid numeric message for " +/-") 414s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 414s (Expect invalid numeric message for " -.e+9999") 414s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 414s test/test-regidx 414s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 414s bgzip round-trip no threads: .. ok 414s 414s bgzip text mode round-trip no threads: .. ok 414s 414s bgzip -b no threads: .. ok 414s 414s bgzip -b -I no threads: .. ok 414s 415s bgzip multifile no threads: .. ok 415s 415s bgzip --output no threads: .. ok 415s 415s bgzip round-trip 4 threads: .. ok 415s 415s bgzip text mode round-trip 4 threads: .. ok 415s 415s bgzip -b 4 threads: .. ok 415s 415s bgzip -b -I 4 threads: .. ok 415s 415s bgzip multifile 4 threads: .. ok 415s 415s bgzip --output 4 threads: .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/Y45xkKEikS/index.bam.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.bam 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.bam 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/Y45xkKEikS/index.bam.bai /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.bam 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -b /tmp/Y45xkKEikS/index.bam 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/Y45xkKEikS/index.sam.gz.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.sam.gz 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.sam.gz 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/Y45xkKEikS/index.sam.gz.bai /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.sam.gz 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -b /tmp/Y45xkKEikS/index.sam.gz 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/Y45xkKEikS/index.sam.gz.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index_dos.sam > /tmp/Y45xkKEikS/index.sam.gz 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.sam.gz 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/Y45xkKEikS/index.sam.gz.bai /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index_dos.sam > /tmp/Y45xkKEikS/index.sam.gz 415s .. ok 415s 415s test_index: 415s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -b /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/Y45xkKEikS/index.cram.crai /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.cram 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index /tmp/Y45xkKEikS/index.cram 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/Y45xkKEikS/index.bcf.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.vcf > /tmp/Y45xkKEikS/index.bcf 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.bcf 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/Y45xkKEikS/index.vcf.gz.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.vcf > /tmp/Y45xkKEikS/index.vcf.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.vcf.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/Y45xkKEikS/index.vcf.gz.tbi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.vcf > /tmp/Y45xkKEikS/index.vcf.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -t /tmp/Y45xkKEikS/index.vcf.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/tabix /tmp/Y45xkKEikS/index.vcf.gz##idx##/tmp/Y45xkKEikS/index.vcf.gz.tbi 1:10000060-10000060 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/Y45xkKEikS/index2.bam 1:1000000-1000000 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/Y45xkKEikS/index2.bam 1:2000000-2000000 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/Y45xkKEikS/index2.bam 2:1000000-1000000 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/Y45xkKEikS/index2.bam 2:2000000-2000000 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Y45xkKEikS/index.bam.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.bam 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.bam 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/Y45xkKEikS/index.bam.bai /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.bam 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -b /tmp/Y45xkKEikS/index.bam 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Y45xkKEikS/index.sam.gz.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Y45xkKEikS/index.sam.gz.bai /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -b /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Y45xkKEikS/index.sam.gz.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index_dos.sam > /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Y45xkKEikS/index.sam.gz.bai /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index_dos.sam > /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -b /tmp/Y45xkKEikS/index.sam.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/Y45xkKEikS/index.cram.crai /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.sam > /tmp/Y45xkKEikS/index.cram 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index /tmp/Y45xkKEikS/index.cram 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Y45xkKEikS/index.bcf.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.vcf > /tmp/Y45xkKEikS/index.bcf 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.bcf 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Y45xkKEikS/index.vcf.gz.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.vcf > /tmp/Y45xkKEikS/index.vcf.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c /tmp/Y45xkKEikS/index.vcf.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Y45xkKEikS/index.vcf.gz.tbi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/index.vcf > /tmp/Y45xkKEikS/index.vcf.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -t /tmp/Y45xkKEikS/index.vcf.gz 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/tabix /tmp/Y45xkKEikS/index.vcf.gz##idx##/tmp/Y45xkKEikS/index.vcf.gz.tbi 1:10000060-10000060 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/Y45xkKEikS/index2.bam 1:1000000-1000000 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/Y45xkKEikS/index2.bam 1:2000000-2000000 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/Y45xkKEikS/index2.bam 2:1000000-1000000 416s .. ok 416s 416s test_index: 416s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/Y45xkKEikS/index2.bam 2:2000000-2000000 416s .. ok 416s 416s test_view testing multi-ref CRAM modes: 416s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 416s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 416s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 416s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 416s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 416s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 416s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 416s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 416s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 417s .. ok 417s 417s test_view testing multi-ref CRAM modes: 417s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 417s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 417s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 417s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 417s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 417s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 417s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 417s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 417s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 417s .. ok 417s 417s test_view testing auxf#values.sam, ref auxf.fa: 417s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 417s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 417s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 417s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 417s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 417s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 417s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 417s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 417s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 417s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 417s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 417s .. ok 417s 417s test_view testing c1#bounds.sam, ref c1.fa: 417s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 417s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 417s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 417s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 417s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 417s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 417s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 417s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 417s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 417s .. ok 417s 417s test_view testing c1#clip.sam, ref c1.fa: 417s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 417s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 417s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 417s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 417s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 417s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 417s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 417s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 417s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 417s .. ok 417s 417s test_view testing c1#noseq.sam, ref c1.fa: 417s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 417s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 417s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 417s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 417s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 417s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 417s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 417s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 417s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 417s .. ok 417s 417s test_view testing c1#pad1.sam, ref c1.fa: 417s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 417s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 417s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 417s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 417s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 417s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 417s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 417s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 417s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 417s .. ok 417s 417s test_view testing c1#pad2.sam, ref c1.fa: 417s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 417s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 417s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 417s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 418s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 418s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 418s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 418s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 418s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 418s .. ok 418s 418s test_view testing c1#pad3.sam, ref c1.fa: 418s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 418s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 418s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 418s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 418s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 418s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 418s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 418s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 418s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 418s .. ok 418s 418s test_view testing c1#unknown.sam, ref c1.fa: 418s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 418s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 418s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 418s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 418s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 418s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 418s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 418s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 418s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 418s .. ok 418s 418s test_view testing c2#pad.sam, ref c2.fa: 418s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 418s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 418s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 418s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 418s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 418s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 418s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 418s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 418s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 418s .. ok 418s 418s test_view testing ce#1.sam, ref ce.fa: 418s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 418s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 418s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 418s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 418s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 418s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 418s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 418s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 418s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 418s .. ok 418s 418s test_view testing ce#1000.sam, ref ce.fa: 418s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 418s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 418s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 418s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 418s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 418s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 418s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 418s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 418s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 418s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 418s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 418s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 418s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 418s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 418s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 418s .. ok 418s 418s test_view testing ce#2.sam, ref ce.fa: 418s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 418s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 418s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 418s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 418s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 418s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 418s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 418s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 418s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 418s .. ok 418s 418s test_view testing ce#5.sam, ref ce.fa: 418s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 418s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 419s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 419s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 419s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 419s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 419s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 419s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 419s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 419s .. ok 419s 419s test_view testing ce#5b.sam, ref ce.fa: 419s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 419s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 419s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 419s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 419s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 419s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 419s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 419s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 419s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 419s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 419s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 419s .. ok 419s 419s test_view testing ce#large_seq.sam, ref ce.fa: 419s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 419s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 419s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 419s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 419s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 419s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 419s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 419s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 419s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 419s .. ok 419s 419s test_view testing ce#supp.sam, ref ce.fa: 419s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 419s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 419s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 419s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 419s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 419s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 419s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 419s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 419s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 419s .. ok 419s 419s test_view testing ce#tag_depadded.sam, ref ce.fa: 419s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 419s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 419s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 419s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 419s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 419s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 419s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 419s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 419s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 420s .. ok 420s 420s test_view testing ce#tag_padded.sam, ref ce.fa: 420s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 420s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 420s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 420s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 420s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 420s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 420s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 420s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 420s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 420s .. ok 420s 420s test_view testing ce#unmap.sam, ref ce.fa: 420s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 420s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 420s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 420s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 420s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 420s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 420s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 420s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 420s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 420s .. ok 420s 420s test_view testing ce#unmap1.sam, ref ce.fa: 420s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 420s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 420s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 420s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 420s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 420s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 420s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 420s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 420s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 420s .. ok 420s 420s test_view testing ce#unmap2.sam, ref ce.fa: 420s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 420s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 420s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 420s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 420s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 420s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 420s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 420s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 420s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 420s .. ok 420s 420s test_view testing md#1.sam, ref md.fa: 420s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 420s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 420s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 420s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 420s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 420s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 420s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 420s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 420s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 420s .. ok 420s 420s test_view testing xx#blank.sam, ref xx.fa: 420s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 420s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 420s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 420s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 420s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 420s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 420s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 420s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 420s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 420s .. ok 420s 420s test_view testing xx#large_aux.sam, ref xx.fa: 420s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 420s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 420s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 420s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 420s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 420s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 420s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 420s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 420s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 420s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 420s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 420s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 420s .. ok 420s 420s test_view testing xx#large_aux2.sam, ref xx.fa: 420s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 421s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 421s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 421s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 421s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#MD.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 421s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 421s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 421s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 421s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#MD2.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 421s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 421s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 421s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 421s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#minimal.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 421s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 421s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 421s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 421s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#pair.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 421s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 421s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 421s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 421s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#repeated.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 421s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 421s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 421s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 421s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#rg.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 421s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 421s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 421s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 421s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#tlen.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 421s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 421s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 421s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 421s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#tlen2.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 421s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 421s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 421s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 421s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 421s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 421s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 421s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 421s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 421s .. ok 421s 421s test_view testing xx#triplet.sam, ref xx.fa: 421s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 421s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 421s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 422s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 422s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 422s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 422s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 422s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 422s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 422s .. ok 422s 422s test_view testing xx#unsorted.sam, ref xx.fa: 422s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 422s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 422s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 422s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 422s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 422s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 422s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 422s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 422s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 422s .. ok 422s 422s test_view testing embed_ref=2: 422s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 422s [W::cram_get_ref] Failed to populate reference for id 0 422s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 422s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 422s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 422s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 422s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 422s .. ok 422s 422s test_view testing region queries: 422s ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 422s ./compare_sam.pl range.tmp range.out 422s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 422s ./compare_sam.pl range.tmp range.out 422s .. ok 422s 422s test_view testing BAM files with absent @SQ lines: 422s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 422s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 422s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 422s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 422s .. ok 422s 422s test_view testing large (> 2Gbases) positions: 422s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 422s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 422s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 422s test_view: 422s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 422s .. ok 422s 422s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 422s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 422s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 422s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 422s .. ok 422s 422s test_view testing auxf#values.sam, ref auxf.fa: 422s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 422s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 422s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 422s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 422s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 422s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 422s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 422s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 422s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 422s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 422s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 422s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 422s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 422s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 422s This is a technology demonstration that should not be used for archival data. 422s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 422s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 422s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 423s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 423s .. ok 423s 423s test_view testing c1#bounds.sam, ref c1.fa: 423s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 423s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 423s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 423s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 423s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 423s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 423s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 423s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 423s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 423s .. ok 423s 423s test_view testing c1#clip.sam, ref c1.fa: 423s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 423s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 423s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 423s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 423s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 423s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 423s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 423s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 423s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 423s .. ok 423s 423s test_view testing c1#noseq.sam, ref c1.fa: 423s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 423s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 423s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 423s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 423s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 423s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 423s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 423s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 423s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 423s .. ok 423s 423s test_view testing c1#pad1.sam, ref c1.fa: 423s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 423s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 423s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 423s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 423s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 423s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 423s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 423s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 423s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 423s .. ok 423s 423s test_view testing c1#pad2.sam, ref c1.fa: 423s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 423s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 423s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 423s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 423s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 423s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 423s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 423s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 423s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 423s .. ok 423s 423s test_view testing c1#pad3.sam, ref c1.fa: 423s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 423s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 423s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 423s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 424s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 424s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 424s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 424s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 424s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 424s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 424s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 424s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 424s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 424s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 424s This is a technology demonstration that should not be used for archival data. 424s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 424s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 424s .. ok 424s 424s test_view testing c1#unknown.sam, ref c1.fa: 424s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 424s ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 424s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 424s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 424s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 424s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 424s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 424s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 424s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 424s .. ok 424s 424s test_view testing c2#pad.sam, ref c2.fa: 424s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 424s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 424s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 424s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 424s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 424s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 424s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 424s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 424s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 424s .. ok 424s 424s test_view testing ce#1.sam, ref ce.fa: 424s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 424s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 424s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 424s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 424s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 424s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 424s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 424s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 424s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 424s .. ok 424s 424s test_view testing ce#1000.sam, ref ce.fa: 424s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 424s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 425s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 425s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 425s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 425s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 425s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 425s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 425s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 425s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 425s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 425s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 425s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 425s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 425s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 425s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms 425s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 425s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 425s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 425s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 425s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 425s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 425s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 425s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 425s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 425s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 426s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 426s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 426s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 426s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 426s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 426s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 426s This is a technology demonstration that should not be used for archival data. 426s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 426s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 426s .. ok 426s 426s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 426s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 426s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 426s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 426s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram 426s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 426s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 426s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram 427s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 427s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 427s .. ok 427s 427s test_view testing ce#2.sam, ref ce.fa: 427s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 427s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 427s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 427s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 427s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 427s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 427s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 427s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 427s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 427s .. ok 427s 427s test_view testing ce#5.sam, ref ce.fa: 427s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 427s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 427s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 427s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 427s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 427s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 427s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 427s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 427s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 427s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms 427s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 427s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 427s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 427s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 427s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 427s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 427s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 427s This is a technology demonstration that should not be used for archival data. 427s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 427s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 427s .. ok 427s 427s test_view testing ce#5b.sam, ref ce.fa: 427s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 427s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 427s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 427s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 427s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 427s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 427s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 427s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 428s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 428s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms 428s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 428s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 428s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 428s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 428s .. ok 428s 428s test_view testing ce#large_seq.sam, ref ce.fa: 428s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 428s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 428s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 428s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 428s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 428s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 428s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 428s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 428s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 428s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 429s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 429s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 429s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 429s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 429s This is a technology demonstration that should not be used for archival data. 429s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 429s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 429s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 429s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 429s This is a technology demonstration that should not be used for archival data. 430s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 430s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 430s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 430s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 430s This is a technology demonstration that should not be used for archival data. 430s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 430s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 430s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 430s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 430s This is a technology demonstration that should not be used for archival data. 431s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 431s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 431s .. ok 431s 431s test_view testing ce#supp.sam, ref ce.fa: 431s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 431s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 431s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 431s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 431s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 431s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 431s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 431s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 431s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 431s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 431s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 431s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 431s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 431s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 431s This is a technology demonstration that should not be used for archival data. 431s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 431s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 431s .. ok 431s 431s test_view testing ce#tag_depadded.sam, ref ce.fa: 431s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 432s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 432s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 432s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 432s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 432s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 432s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 432s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 432s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 432s .. ok 432s 432s test_view testing ce#tag_padded.sam, ref ce.fa: 432s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 432s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 432s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 432s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 432s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 432s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 432s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 432s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 432s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 432s .. ok 432s 432s test_view testing ce#unmap.sam, ref ce.fa: 432s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 432s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 432s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 432s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 432s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 432s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 432s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 432s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 432s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 432s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms 432s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 432s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 432s .. ok 432s 432s test_view testing ce#unmap1.sam, ref ce.fa: 432s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 432s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 432s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 432s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 432s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 432s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 432s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 432s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 432s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 432s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms 432s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 432s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 432s .. ok 432s 432s test_view testing ce#unmap2.sam, ref ce.fa: 432s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 432s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 432s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 432s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 432s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 432s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 432s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 432s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 432s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 433s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms 433s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 433s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 433s .. ok 433s 433s test_view testing md#1.sam, ref md.fa: 433s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 433s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 433s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 433s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 433s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 433s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 433s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 433s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 433s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 433s .. ok 433s 433s test_view testing xx#blank.sam, ref xx.fa: 433s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 433s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 433s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 433s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 433s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 433s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 433s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 433s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 433s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 433s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms 433s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 433s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 433s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 433s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 433s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 433s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 433s This is a technology demonstration that should not be used for archival data. 433s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 433s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 433s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 433s .. ok 433s 433s test_view testing xx#large_aux.sam, ref xx.fa: 433s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 433s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 433s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 433s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 433s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 433s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 433s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 433s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 433s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 433s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 434s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 434s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 434s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 434s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 434s This is a technology demonstration that should not be used for archival data. 434s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 434s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 434s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 434s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 434s This is a technology demonstration that should not be used for archival data. 434s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 434s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 434s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 434s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 434s This is a technology demonstration that should not be used for archival data. 435s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 435s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 435s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 435s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 435s This is a technology demonstration that should not be used for archival data. 435s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 435s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 435s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 435s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 435s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 435s .. ok 435s 435s test_view testing xx#large_aux2.sam, ref xx.fa: 435s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 435s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 435s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 435s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 436s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 436s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 436s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 436s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 436s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 436s .. ok 436s 436s test_view testing xx#MD.sam, ref xx.fa: 436s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 436s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 436s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 436s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 436s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 436s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 436s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 436s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 436s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 436s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 436s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 436s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 436s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 436s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 436s This is a technology demonstration that should not be used for archival data. 436s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 436s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 436s .. ok 436s 436s test_view testing xx#MD2.sam, ref xx.fa: 436s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 436s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 436s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 436s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 436s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 436s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 436s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 436s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 436s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 436s .. ok 436s 436s test_view testing xx#minimal.sam, ref xx.fa: 436s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 436s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 436s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 436s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 436s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 436s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 436s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 436s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 436s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 436s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms 436s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 436s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 436s .. ok 436s 436s test_view testing xx#pair.sam, ref xx.fa: 436s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 436s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 437s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 437s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 437s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 437s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 437s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 437s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 437s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 437s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 437s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 437s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 437s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 437s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 437s This is a technology demonstration that should not be used for archival data. 437s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 437s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 437s .. ok 437s 437s test_view testing xx#repeated.sam, ref xx.fa: 437s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 437s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 437s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 437s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 437s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 437s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 437s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 437s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 437s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 437s .. ok 437s 437s test_view testing xx#rg.sam, ref xx.fa: 437s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 437s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 437s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 437s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 437s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 437s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 437s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 437s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 437s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 437s .. ok 437s 437s test_view testing xx#tlen.sam, ref xx.fa: 437s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 437s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 437s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 437s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 437s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 437s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 437s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 437s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 437s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 437s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms 437s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 437s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 438s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 438s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 438s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 438s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 438s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 438s This is a technology demonstration that should not be used for archival data. 438s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 438s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 438s .. ok 438s 438s test_view testing xx#tlen2.sam, ref xx.fa: 438s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 438s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 438s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 438s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 438s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 438s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 438s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 438s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 438s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 438s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms 438s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 438s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 438s .. ok 438s 438s test_view testing xx#triplet.sam, ref xx.fa: 438s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 438s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 438s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 438s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 438s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 438s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 438s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 438s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 438s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 438s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms 438s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 438s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 438s .. ok 438s 438s test_view testing xx#unsorted.sam, ref xx.fa: 438s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 438s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 438s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 438s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 438s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 438s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 438s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 438s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 438s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 438s .. ok 438s 438s test_view testing embed_ref=2: 438s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 438s [W::cram_get_ref] Failed to populate reference for id 0 438s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 438s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 438s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 439s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 439s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 439s .. ok 439s 439s test_view testing region queries: 439s ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 439s ./compare_sam.pl range.tmp range.out 439s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 439s ./compare_sam.pl range.tmp range.out 439s .. ok 439s 439s test_view testing BAM files with absent @SQ lines: 439s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 439s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 439s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 439s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 439s .. ok 439s 439s test_view testing large (> 2Gbases) positions: 439s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 439s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 439s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 439s test_view: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 439s .. ok 439s 439s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 439s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 439s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 439s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 439s .. ok 439s 439s 439s test_MD testing xx#MD.sam, ref xx.fa: 439s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 439s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 439s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 439s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 439s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 439s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 439s Checking for MD/NM in xx#MD.sam 439s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 439s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 439s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 439s .. ok 439s 439s 439s test_MD testing xx#MD2.sam, ref xx.fa: 439s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 439s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 439s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 439s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 439s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 439s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 439s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 439s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 439s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 439s .. ok 439s 439s test_vcf_api: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-vcf-api /tmp/Y45xkKEikS/test-vcf-api.bcf 439s .. ok 439s 439s test_bcf2vcf: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/tabix/vcf_file.bcf 439s .. ok 439s 439s test_vcf_sweep: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-vcf-sweep /tmp/Y45xkKEikS/test-vcf-api.bcf 439s .. ok 439s 439s test_vcf_various: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 439s .. ok 439s 439s test_vcf_various: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/formatcols.vcf 439s .. ok 439s 439s test_vcf_various: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/noroundtrip.vcf 439s .. ok 439s 439s test_vcf_various: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/formatmissing.vcf 439s .. ok 439s 439s test_vcf_various: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/vcf_meta_meta.vcf 439s .. ok 439s 439s test_vcf_various: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 439s .. ok 439s 439s test-bcf-sr: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 74452500 439s .. ok 439s 439s test-bcf-sr: 439s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 34270147 440s .. ok 440s 440s test-bcf-sr: 440s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 11108528 440s .. ok 440s 440s test-bcf-sr: 440s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 42233895 440s .. ok 440s 440s test-bcf-sr: 440s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 8111117 441s .. ok 441s 441s test-bcf-sr: 441s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 85644070 441s .. ok 441s 441s test-bcf-sr: 441s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 49879942 441s .. ok 441s 441s test-bcf-sr: 441s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 47881429 441s .. ok 441s 441s test-bcf-sr: 441s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 69081244 441s .. ok 441s 441s test-bcf-sr: 441s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Y45xkKEikS -s 83459376 442s .. ok 442s 442s test_bcf_sr_no_index: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/Y45xkKEikS/no_index_1.err 442s .. ok 442s 442s test_bcf_sr_no_index: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/Y45xkKEikS/no_index_2.out 2> /tmp/Y45xkKEikS/no_index_2.err (expected fail) 442s .. ok 442s 442s test_bcf_sr_no_index: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/Y45xkKEikS/no_index_3.out 2> /tmp/Y45xkKEikS/no_index_3.err (expected fail) 442s .. ok 442s 442s test_bcf_sr_no_index: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/Y45xkKEikS/no_index_4.out 2> /tmp/Y45xkKEikS/no_index_4.err (expected fail) 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -b -p /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf -x /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_1.out.vcf -r '1' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_2.out.vcf -r '1:1-2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_4.out.vcf -r '1:1-1' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_5.out.vcf -r '{1:1}' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf (expected fail) 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_14.out.vcf -t '1' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 442s Failed to set regions 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_15.out.vcf -t '1:1-2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_17.out.vcf -t '1:1-1' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_18.out.vcf -t '{1:1}' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf 442s .. ok 442s 442s test_bcf_sr_range: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Y45xkKEikS/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/Y45xkKEikS/weird-chr-names.vcf.bcf (expected fail) 442s .. ok 442s 442s test_command: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf-translate - 442s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 442s Failed to set targets 442s .. ok 442s 442s test_convert_padded_header: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/Y45xkKEikS/headernul0.bam 442s .. ok 442s 442s test_convert_padded_header: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/Y45xkKEikS/headernul1.bam 442s .. ok 442s 442s test_convert_padded_header: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/Y45xkKEikS/headernul678.bam 442s .. ok 442s 442s test_rebgzip: Alternate zlib/deflate library detected 442s test_rebgzip: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/bgziptest.txt 442s .. ok 442s 442s test-logging: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-logging.pl 442s .. ok 442s 442s test_plugin_loading: 442s HTS_PATH=/tmp/autopkgtest.QPWU3q/autopkgtest_tmp /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn01.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn01.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn01.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02-r.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02_exp.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn02_exp-a.sam -o - 442s .. ok 442s 442s test_realn: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/realn03.sam -o - 442s .. ok 442s 442s test-bcf_set_variant_type: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/test-bcf_set_variant_type 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.1.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.2.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.3.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.3.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.3.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.3.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.3.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.3.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.4.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.4.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.4.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.4.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.4.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.4.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.5.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.5.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.5.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.5.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.5.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.5.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.6.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.6.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.6.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.6.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.6.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.6.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.7.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.7.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.7.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.7.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.7.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.7.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.8.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.8.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.8.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.8.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.8.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.8.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.9.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.9.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.9.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.9.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.9.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.9.txt 442s .. ok 442s 442s run_annot_tsv: 442s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt 442s .. ok 442s 442s run_annot_tsv: 442s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -f smpl -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -x -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -x -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -x -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -f smpl -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -f smpl -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -f smpl -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -x -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -x -s /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt 443s .. ok 443s 443s run_annot_tsv: 443s cat /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/annot-tsv -m smpl -x -t /tmp/autopkgtest.QPWU3q/autopkgtest_tmp/test/annot-tsv/dst.10.txt 443s .. ok 443s 443s 443s Number of tests: 443s total .. 293 443s passed .. 293 443s failed .. 0 443s 443s PASS 443s + echo PASS 443s autopkgtest [20:07:59]: test run-unit-test: -----------------------] 449s run-unit-test PASS 449s autopkgtest [20:08:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 455s autopkgtest [20:08:11]: @@@@@@@@@@@@@@@@@@@@ summary 455s run-unit-test PASS