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-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n18heg04/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-18.secgroup --name adt-plucky-amd64-htslib-20241129-200036-juju-7f2275-prod-proposed-migration-environment-20-4ea8cef6-5839-4420-9de3-dce6d7b6b2de --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 58s autopkgtest [20:01:34]: testbed dpkg architecture: amd64 58s autopkgtest [20:01:34]: testbed apt version: 2.9.14ubuntu1 59s autopkgtest [20:01:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 59s autopkgtest [20:01:35]: testbed release detected to be: None 59s autopkgtest [20:01:35]: updating testbed package index (apt update) 60s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [837 kB] 60s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 60s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.4 kB] 60s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [62.8 kB] 60s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [82.1 kB] 60s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [124 kB] 60s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.6 kB] 60s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2572 B] 60s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [275 kB] 60s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [710 kB] 60s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [20.8 kB] 60s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [6036 B] 61s Fetched 2259 kB in 1s (2407 kB/s) 61s Reading package lists... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Calculating upgrade... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 63s autopkgtest [20:01:39]: upgrading testbed (apt dist-upgrade and autopurge) 63s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 64s Starting 2 pkgProblemResolver with broken count: 0 64s Done 65s Entering ResolveByKeep 65s 65s The following NEW packages will be installed: 65s openssl-provider-legacy 65s The following packages will be upgraded: 65s libssl3t64 openssl 65s 2 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 65s Need to get 3557 kB of archives. 65s After this operation, 936 kB of additional disk space will be used. 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 openssl-provider-legacy amd64 3.4.0-1ubuntu1 [39.0 kB] 65s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libssl3t64 amd64 3.4.0-1ubuntu1 [2332 kB] 66s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 openssl amd64 3.4.0-1ubuntu1 [1186 kB] 66s Fetched 3557 kB in 1s (5283 kB/s) 66s (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 ... 75952 files and directories currently installed.) 66s Preparing to unpack .../libssl3t64_3.4.0-1ubuntu1_amd64.deb ... 66s Unpacking libssl3t64:amd64 (3.4.0-1ubuntu1) over (3.3.1-2ubuntu2) ... 66s Selecting previously unselected package openssl-provider-legacy. 66s Preparing to unpack .../openssl-provider-legacy_3.4.0-1ubuntu1_amd64.deb ... 66s Unpacking openssl-provider-legacy (3.4.0-1ubuntu1) ... 66s Setting up libssl3t64:amd64 (3.4.0-1ubuntu1) ... 66s Setting up openssl-provider-legacy (3.4.0-1ubuntu1) ... 66s (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 ... 75955 files and directories currently installed.) 66s Preparing to unpack .../openssl_3.4.0-1ubuntu1_amd64.deb ... 66s Unpacking openssl (3.4.0-1ubuntu1) over (3.3.1-2ubuntu2) ... 67s Setting up openssl (3.4.0-1ubuntu1) ... 67s Installing new version of config file /etc/ssl/openssl.cnf ... 67s Processing triggers for man-db (2.13.0-1) ... 67s Processing triggers for libc-bin (2.40-1ubuntu3) ... 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Starting pkgProblemResolver with broken count: 0 68s Starting 2 pkgProblemResolver with broken count: 0 68s Done 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [20:01:47]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 71s autopkgtest [20:01:47]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 74s Get:1 http://ftpmaster.internal/ubuntu plucky/universe htslib 1.20+ds-2 (dsc) [2090 B] 74s Get:2 http://ftpmaster.internal/ubuntu plucky/universe htslib 1.20+ds-2 (tar) [1531 kB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky/universe htslib 1.20+ds-2 (diff) [21.3 kB] 74s gpgv: Signature made Thu Oct 31 17:36:10 2024 UTC 74s gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 74s gpgv: Can't check signature: No public key 74s dpkg-source: warning: cannot verify inline signature for ./htslib_1.20+ds-2.dsc: no acceptable signature found 75s autopkgtest [20:01:51]: testing package htslib version 1.20+ds-2 75s autopkgtest [20:01:51]: build not needed 76s autopkgtest [20:01:52]: test run-unit-test: preparing testbed 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s Starting pkgProblemResolver with broken count: 0 77s Starting 2 pkgProblemResolver with broken count: 0 77s Done 77s The following NEW packages will be installed: 77s autoconf automake autopoint autotools-dev build-essential comerr-dev cpp 77s cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper debugedit 77s dh-autoreconf dh-strip-nondeterminism dwz g++ g++-14 g++-14-x86-64-linux-gnu 77s g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu 77s gettext htslib-test intltool-debian krb5-multidev libarchive-zip-perl 77s libasan8 libbrotli-dev libbz2-dev libcc1-0 libcurl4-gnutls-dev 77s libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64 77s libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl 77s libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgomp1 77s libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs-dev libhtscodecs2 77s libhwasan0 libidn2-dev libisl23 libitm1 libkadm5clnt-mit12 libkadm5srv-mit12 77s libkdb5-10t64 libkrb5-dev libldap-dev liblsan0 liblzma-dev libmpc3 77s libnghttp2-dev libp11-kit-dev libpkgconf3 libpsl-dev libquadmath0 77s librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev libtasn1-6-dev libtool 77s libtsan2 libubsan1 libunbound8 libzstd-dev m4 nettle-dev pkgconf pkgconf-bin 77s po-debconf tabix zlib1g-dev 77s 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 91.9 MB of archives. 77s After this operation, 308 MB of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 78s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 78s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 78s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 78s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 78s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 78s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 78s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 78s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 78s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 78s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 78s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 78s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 78s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 78s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 78s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 78s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 78s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 78s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 78s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 79s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 79s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 79s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 79s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 79s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 79s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 79s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 80s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 80s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 80s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 80s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 80s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 80s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-8 [166 kB] 80s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 80s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 80s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 80s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 80s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 80s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 80s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 80s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 80s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 80s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 80s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 htslib-test all 1.20+ds-2 [1145 kB] 80s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 comerr-dev amd64 2.1-1.47.1-1ubuntu1 [44.5 kB] 80s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libgssrpc4t64 amd64 1.21.3-3 [57.5 kB] 80s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [40.0 kB] 80s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libkdb5-10t64 amd64 1.21.3-3 [40.6 kB] 80s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [52.8 kB] 80s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 krb5-multidev amd64 1.21.3-3 [125 kB] 80s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli-dev amd64 1.1.0-2build3 [381 kB] 80s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 80s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [144 kB] 80s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libunbound8 amd64 1.20.0-1ubuntu2.1 [447 kB] 80s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-dane0t64 amd64 3.8.8-2ubuntu1 [24.3 kB] 80s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2ubuntu1 [24.5 kB] 80s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn2-dev amd64 2.3.7-2build2 [120 kB] 80s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit-dev amd64 0.25.5-2ubuntu1 [22.7 kB] 80s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6-dev amd64 4.19.0-3build1 [90.5 kB] 80s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2ubuntu7 [10.0 kB] 80s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2ubuntu7 [341 kB] 80s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 nettle-dev amd64 3.10-1 [1172 kB] 80s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls28-dev amd64 3.8.8-2ubuntu1 [1108 kB] 80s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libkrb5-dev amd64 1.21.3-3 [11.9 kB] 80s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libldap-dev amd64 2.6.8+dfsg-1~exp4ubuntu3 [308 kB] 80s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 80s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 80s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 80s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libnghttp2-dev amd64 1.64.0-1 [123 kB] 80s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libpsl-dev amd64 0.21.2-1.1build1 [76.4 kB] 80s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 80s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2build7 [66.7 kB] 80s Get:73 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libssl-dev amd64 3.4.0-1ubuntu1 [2871 kB] 80s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libssh2-1-dev amd64 1.11.1-1 [292 kB] 80s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [371 kB] 80s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4-gnutls-dev amd64 8.11.0-1ubuntu2 [512 kB] 80s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 80s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.22-1 [72.2 kB] 80s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 80s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 80s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.3-1 [189 kB] 80s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts-dev amd64 1.20+ds-2 [6298 kB] 81s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs-dev amd64 1.6.1-1 [3027 kB] 81s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 tabix amd64 1.20+ds-2 [640 kB] 81s Fetched 91.9 MB in 3s (26.3 MB/s) 81s Selecting previously unselected package m4. 81s (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 ... 75957 files and directories currently installed.) 81s Preparing to unpack .../00-m4_1.4.19-4build1_amd64.deb ... 81s Unpacking m4 (1.4.19-4build1) ... 81s Selecting previously unselected package autoconf. 81s Preparing to unpack .../01-autoconf_2.72-3_all.deb ... 81s Unpacking autoconf (2.72-3) ... 81s Selecting previously unselected package autotools-dev. 81s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 81s Unpacking autotools-dev (20220109.1) ... 81s Selecting previously unselected package automake. 81s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 81s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 81s Selecting previously unselected package autopoint. 81s Preparing to unpack .../04-autopoint_0.22.5-2_all.deb ... 81s Unpacking autopoint (0.22.5-2) ... 81s Selecting previously unselected package libisl23:amd64. 81s Preparing to unpack .../05-libisl23_0.27-1_amd64.deb ... 81s Unpacking libisl23:amd64 (0.27-1) ... 81s Selecting previously unselected package libmpc3:amd64. 81s Preparing to unpack .../06-libmpc3_1.3.1-1build2_amd64.deb ... 81s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 81s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 81s Preparing to unpack .../07-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 81s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package cpp-14. 82s Preparing to unpack .../08-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package cpp-x86-64-linux-gnu. 82s Preparing to unpack .../09-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 82s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 82s Selecting previously unselected package cpp. 82s Preparing to unpack .../10-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 82s Unpacking cpp (4:14.1.0-2ubuntu1) ... 82s Selecting previously unselected package libcc1-0:amd64. 82s Preparing to unpack .../11-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package libgomp1:amd64. 82s Preparing to unpack .../12-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package libitm1:amd64. 82s Preparing to unpack .../13-libitm1_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package libasan8:amd64. 82s Preparing to unpack .../14-libasan8_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package liblsan0:amd64. 82s Preparing to unpack .../15-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package libtsan2:amd64. 82s Preparing to unpack .../16-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package libubsan1:amd64. 82s Preparing to unpack .../17-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package libhwasan0:amd64. 82s Preparing to unpack .../18-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package libquadmath0:amd64. 82s Preparing to unpack .../19-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package libgcc-14-dev:amd64. 82s Preparing to unpack .../20-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 82s Preparing to unpack .../21-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package gcc-14. 82s Preparing to unpack .../22-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 82s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 82s Selecting previously unselected package gcc-x86-64-linux-gnu. 83s Preparing to unpack .../23-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 83s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 83s Selecting previously unselected package gcc. 83s Preparing to unpack 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83s Unpacking g++ (4:14.1.0-2ubuntu1) ... 83s Selecting previously unselected package build-essential. 83s Preparing to unpack .../30-build-essential_12.10ubuntu1_amd64.deb ... 83s Unpacking build-essential (12.10ubuntu1) ... 83s Selecting previously unselected package libdebhelper-perl. 83s Preparing to unpack .../31-libdebhelper-perl_13.20ubuntu1_all.deb ... 83s Unpacking libdebhelper-perl (13.20ubuntu1) ... 83s Selecting previously unselected package libtool. 83s Preparing to unpack .../32-libtool_2.4.7-8_all.deb ... 83s Unpacking libtool (2.4.7-8) ... 83s Selecting previously unselected package dh-autoreconf. 83s Preparing to unpack .../33-dh-autoreconf_20_all.deb ... 83s Unpacking dh-autoreconf (20) ... 83s Selecting previously unselected package libarchive-zip-perl. 83s Preparing to unpack .../34-libarchive-zip-perl_1.68-1_all.deb ... 83s Unpacking libarchive-zip-perl (1.68-1) ... 83s Selecting previously unselected package libfile-stripnondeterminism-perl. 83s Preparing to unpack .../35-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 83s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 83s Selecting previously unselected package dh-strip-nondeterminism. 83s Preparing to unpack .../36-dh-strip-nondeterminism_1.14.0-1_all.deb ... 83s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 83s Selecting previously unselected package debugedit. 83s Preparing to unpack .../37-debugedit_1%3a5.1-1_amd64.deb ... 83s Unpacking debugedit (1:5.1-1) ... 83s Selecting previously unselected package dwz. 83s Preparing to unpack .../38-dwz_0.15-1build6_amd64.deb ... 83s Unpacking dwz (0.15-1build6) ... 83s Selecting previously unselected package gettext. 83s Preparing to unpack .../39-gettext_0.22.5-2_amd64.deb ... 83s Unpacking gettext (0.22.5-2) ... 83s Selecting previously unselected package intltool-debian. 83s Preparing to unpack .../40-intltool-debian_0.35.0+20060710.6_all.deb ... 83s Unpacking intltool-debian (0.35.0+20060710.6) ... 83s Selecting previously unselected package po-debconf. 83s Preparing to unpack .../41-po-debconf_1.0.21+nmu1_all.deb ... 83s Unpacking po-debconf (1.0.21+nmu1) ... 83s Selecting previously unselected package debhelper. 83s Preparing to unpack .../42-debhelper_13.20ubuntu1_all.deb ... 83s Unpacking debhelper (13.20ubuntu1) ... 83s Selecting previously unselected package htslib-test. 83s Preparing to unpack .../43-htslib-test_1.20+ds-2_all.deb ... 83s Unpacking htslib-test (1.20+ds-2) ... 84s Selecting previously unselected package comerr-dev:amd64. 84s Preparing to unpack .../44-comerr-dev_2.1-1.47.1-1ubuntu1_amd64.deb ... 84s Unpacking comerr-dev:amd64 (2.1-1.47.1-1ubuntu1) ... 84s Selecting previously unselected package libgssrpc4t64:amd64. 84s Preparing to unpack .../45-libgssrpc4t64_1.21.3-3_amd64.deb ... 84s Unpacking libgssrpc4t64:amd64 (1.21.3-3) ... 84s Selecting previously unselected package libkadm5clnt-mit12:amd64. 84s Preparing to unpack .../46-libkadm5clnt-mit12_1.21.3-3_amd64.deb ... 84s Unpacking libkadm5clnt-mit12:amd64 (1.21.3-3) ... 84s Selecting previously unselected package libkdb5-10t64:amd64. 84s Preparing to unpack .../47-libkdb5-10t64_1.21.3-3_amd64.deb ... 84s Unpacking libkdb5-10t64:amd64 (1.21.3-3) ... 84s Selecting previously unselected package libkadm5srv-mit12:amd64. 84s Preparing to unpack .../48-libkadm5srv-mit12_1.21.3-3_amd64.deb ... 84s Unpacking libkadm5srv-mit12:amd64 (1.21.3-3) ... 84s Selecting previously unselected package krb5-multidev:amd64. 84s Preparing to unpack .../49-krb5-multidev_1.21.3-3_amd64.deb ... 84s Unpacking krb5-multidev:amd64 (1.21.3-3) ... 84s Selecting previously unselected package libbrotli-dev:amd64. 84s Preparing to unpack .../50-libbrotli-dev_1.1.0-2build3_amd64.deb ... 84s Unpacking libbrotli-dev:amd64 (1.1.0-2build3) ... 84s Selecting previously unselected package libbz2-dev:amd64. 84s Preparing to unpack .../51-libbz2-dev_1.0.8-6_amd64.deb ... 84s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 84s Selecting previously unselected package libevent-2.1-7t64:amd64. 84s Preparing to unpack .../52-libevent-2.1-7t64_2.1.12-stable-10_amd64.deb ... 84s Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... 84s Selecting previously unselected package libunbound8:amd64. 84s Preparing to unpack .../53-libunbound8_1.20.0-1ubuntu2.1_amd64.deb ... 84s Unpacking libunbound8:amd64 (1.20.0-1ubuntu2.1) ... 84s Selecting previously unselected package libgnutls-dane0t64:amd64. 84s Preparing to unpack .../54-libgnutls-dane0t64_3.8.8-2ubuntu1_amd64.deb ... 84s Unpacking libgnutls-dane0t64:amd64 (3.8.8-2ubuntu1) ... 84s Selecting previously unselected package libgnutls-openssl27t64:amd64. 84s Preparing to unpack .../55-libgnutls-openssl27t64_3.8.8-2ubuntu1_amd64.deb ... 84s Unpacking libgnutls-openssl27t64:amd64 (3.8.8-2ubuntu1) ... 84s Selecting previously unselected package libidn2-dev:amd64. 84s Preparing to unpack .../56-libidn2-dev_2.3.7-2build2_amd64.deb ... 84s Unpacking libidn2-dev:amd64 (2.3.7-2build2) ... 84s Selecting previously unselected package libp11-kit-dev:amd64. 84s Preparing to unpack .../57-libp11-kit-dev_0.25.5-2ubuntu1_amd64.deb ... 84s Unpacking libp11-kit-dev:amd64 (0.25.5-2ubuntu1) ... 84s Selecting previously unselected package libtasn1-6-dev:amd64. 84s Preparing to unpack .../58-libtasn1-6-dev_4.19.0-3build1_amd64.deb ... 84s Unpacking libtasn1-6-dev:amd64 (4.19.0-3build1) ... 84s Selecting previously unselected package libgmpxx4ldbl:amd64. 84s Preparing to unpack .../59-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_amd64.deb ... 84s Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 84s Selecting previously unselected package libgmp-dev:amd64. 84s Preparing to unpack .../60-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_amd64.deb ... 84s Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 84s Selecting previously unselected package nettle-dev:amd64. 84s Preparing to unpack .../61-nettle-dev_3.10-1_amd64.deb ... 84s Unpacking nettle-dev:amd64 (3.10-1) ... 84s Selecting previously unselected package libgnutls28-dev:amd64. 84s Preparing to unpack .../62-libgnutls28-dev_3.8.8-2ubuntu1_amd64.deb ... 84s Unpacking libgnutls28-dev:amd64 (3.8.8-2ubuntu1) ... 84s Selecting previously unselected package libkrb5-dev:amd64. 84s Preparing to unpack .../63-libkrb5-dev_1.21.3-3_amd64.deb ... 84s Unpacking libkrb5-dev:amd64 (1.21.3-3) ... 84s Selecting previously unselected package libldap-dev:amd64. 84s Preparing to unpack .../64-libldap-dev_2.6.8+dfsg-1~exp4ubuntu3_amd64.deb ... 84s Unpacking libldap-dev:amd64 (2.6.8+dfsg-1~exp4ubuntu3) ... 84s Selecting previously unselected package libpkgconf3:amd64. 84s Preparing to unpack .../65-libpkgconf3_1.8.1-4_amd64.deb ... 84s Unpacking libpkgconf3:amd64 (1.8.1-4) ... 84s Selecting previously unselected package pkgconf-bin. 84s Preparing to unpack .../66-pkgconf-bin_1.8.1-4_amd64.deb ... 84s Unpacking pkgconf-bin (1.8.1-4) ... 84s Selecting previously unselected package pkgconf:amd64. 84s Preparing to unpack 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libdeflate-dev:amd64 (1.22-1) ... 85s Selecting previously unselected package libhtscodecs2:amd64. 85s Preparing to unpack .../78-libhtscodecs2_1.6.1-1_amd64.deb ... 85s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 85s Selecting previously unselected package libhts3t64:amd64. 85s Preparing to unpack .../79-libhts3t64_1.20+ds-2_amd64.deb ... 85s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 85s Selecting previously unselected package liblzma-dev:amd64. 85s Preparing to unpack .../80-liblzma-dev_5.6.3-1_amd64.deb ... 85s Unpacking liblzma-dev:amd64 (5.6.3-1) ... 85s Selecting previously unselected package libhts-dev:amd64. 85s Preparing to unpack .../81-libhts-dev_1.20+ds-2_amd64.deb ... 85s Unpacking libhts-dev:amd64 (1.20+ds-2) ... 85s Selecting previously unselected package libhtscodecs-dev:amd64. 85s Preparing to unpack .../82-libhtscodecs-dev_1.6.1-1_amd64.deb ... 85s Unpacking libhtscodecs-dev:amd64 (1.6.1-1) ... 85s Selecting previously unselected package tabix. 85s Preparing to 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libgssrpc4t64:amd64 (1.21.3-3) ... 85s Setting up libldap-dev:amd64 (2.6.8+dfsg-1~exp4ubuntu3) ... 85s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 85s Setting up comerr-dev:amd64 (2.1-1.47.1-1ubuntu1) ... 85s Setting up libssl-dev:amd64 (3.4.0-1ubuntu1) ... 85s Setting up libmpc3:amd64 (1.3.1-1build2) ... 85s Setting up autopoint (0.22.5-2) ... 85s Setting up pkgconf-bin (1.8.1-4) ... 85s Setting up libidn2-dev:amd64 (2.3.7-2build2) ... 85s Setting up autoconf (2.72-3) ... 85s Setting up liblzma-dev:amd64 (5.6.3-1) ... 85s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 85s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 85s Setting up dwz (0.15-1build6) ... 85s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 85s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 85s Setting up debugedit (1:5.1-1) ... 85s Setting up libhts3t64:amd64 (1.20+ds-2) ... 85s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 85s Setting up libisl23:amd64 (0.27-1) ... 85s Setting up libtasn1-6-dev:amd64 (4.19.0-3build1) ... 85s Setting up libdeflate-dev:amd64 (1.22-1) ... 85s Setting up tabix (1.20+ds-2) ... 85s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 85s Setting up libbrotli-dev:amd64 (1.1.0-2build3) ... 85s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 85s Setting up libp11-kit-dev:amd64 (0.25.5-2ubuntu1) ... 85s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 85s Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... 85s Setting up libbz2-dev:amd64 (1.0.8-6) ... 85s Setting up automake (1:1.16.5-1.3ubuntu1) ... 85s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 85s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 85s Setting up gettext (0.22.5-2) ... 85s Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 85s Setting up nettle-dev:amd64 (3.10-1) ... 85s Setting up libkdb5-10t64:amd64 (1.21.3-3) ... 85s Setting up pkgconf:amd64 (1.8.1-4) ... 85s Setting up intltool-debian (0.35.0+20060710.6) ... 85s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 85s Setting up libssh2-1-dev:amd64 (1.11.1-1) ... 85s Setting up cpp-14 (14.2.0-8ubuntu1) ... 85s Setting up dh-strip-nondeterminism (1.14.0-1) ... 85s Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... 85s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 85s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 85s Setting up krb5-multidev:amd64 (1.21.3-3) ... 85s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 85s Setting up libgnutls28-dev:amd64 (3.8.8-2ubuntu1) ... 85s Setting up libnghttp2-dev:amd64 (1.64.0-1) ... 85s Setting up po-debconf (1.0.21+nmu1) ... 85s Setting up libkrb5-dev:amd64 (1.21.3-3) ... 85s Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2build7) ... 85s Setting up cpp (4:14.1.0-2ubuntu1) ... 85s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 85s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 85s Setting up libcurl4-gnutls-dev:amd64 (8.11.0-1ubuntu2) ... 85s Setting up gcc-14 (14.2.0-8ubuntu1) ... 85s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 85s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 85s Setting up g++-14 (14.2.0-8ubuntu1) ... 85s Setting up libtool (2.4.7-8) ... 85s Setting up libhts-dev:amd64 (1.20+ds-2) ... 85s Setting up gcc (4:14.1.0-2ubuntu1) ... 85s Setting up dh-autoreconf (20) ... 85s Setting up g++ (4:14.1.0-2ubuntu1) ... 85s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 85s Setting up build-essential (12.10ubuntu1) ... 85s Setting up debhelper (13.20ubuntu1) ... 85s Processing triggers for install-info (7.1.1-1) ... 85s Processing triggers for libc-bin (2.40-1ubuntu3) ... 85s Processing triggers for man-db (2.13.0-1) ... 88s autopkgtest [20:02:04]: test run-unit-test: [----------------------- 88s + pkg=htslib 88s + '[' /tmp/autopkgtest.NWxfCW/autopkgtest_tmp = '' ']' 88s + 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.NWxfCW/autopkgtest_tmp 88s + cp -aL htslib.pc.in /tmp/autopkgtest.NWxfCW/autopkgtest_tmp 88s + cp -aL htslib.map /tmp/autopkgtest.NWxfCW/autopkgtest_tmp 88s + cd /tmp/autopkgtest.NWxfCW/autopkgtest_tmp 88s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 88s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 88s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 88s + grep sse /proc/cpuinfo 88s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse' 88s + export CFLAGS 88s + make -e check 88s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kfunc.o kfunc.c 88s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kstring.o kstring.c 88s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bcf_sr_sort.o bcf_sr_sort.c 89s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzf.o bgzf.c 90s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o errmod.o errmod.c 90s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o faidx.o faidx.c 90s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o header.o header.c 91s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hfile.o hfile.c 92s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts.o hts.c 93s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_expr.o hts_expr.c 94s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_os.o hts_os.c 94s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o md5.o md5.c 94s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o multipart.o multipart.c 94s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o probaln.o probaln.c 94s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o realn.o realn.c 94s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o regidx.o regidx.c 95s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o region.o region.c 98s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam.o sam.c 98s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_mods.o sam_mods.c 98s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o synced_bcf_reader.o synced_bcf_reader.c 99s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf_sweep.o vcf_sweep.c 99s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tbx.o tbx.c 99s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o textutils.o textutils.c 99s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o thread_pool.o thread_pool.c 99s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf.o vcf.c 103s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcfutils.o vcfutils.c 103s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_codecs.o cram/cram_codecs.c 104s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_decode.o cram/cram_decode.c 105s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_encode.o cram/cram_encode.c 107s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_external.o cram/cram_external.c 107s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_index.o cram/cram_index.c 107s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_io.o cram/cram_io.c 109s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_stats.o cram/cram_stats.c 109s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/mFILE.o cram/mFILE.c 109s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/open_trace_file.o cram/open_trace_file.c 109s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/pooled_alloc.o cram/pooled_alloc.c 109s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/string_alloc.o cram/string_alloc.c 109s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -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 109s 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 109s ranlib libhts.a 109s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kfunc.pico kfunc.c 109s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kstring.pico kstring.c 110s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c 110s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bgzf.pico bgzf.c 111s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o errmod.pico errmod.c 111s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o faidx.pico faidx.c 111s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o header.pico header.c 112s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile.pico hfile.c 113s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts.pico hts.c 114s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_expr.pico hts_expr.c 115s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_os.pico hts_os.c 115s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o md5.pico md5.c 115s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o multipart.pico multipart.c 115s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o probaln.pico probaln.c 115s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o realn.pico realn.c 115s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o regidx.pico regidx.c 116s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o region.pico region.c 116s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam.pico sam.c 118s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam_mods.pico sam_mods.c 118s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c 119s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 119s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o tbx.pico tbx.c 119s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o textutils.pico textutils.c 119s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o thread_pool.pico thread_pool.c 120s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf.pico vcf.c 122s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcfutils.pico vcfutils.c 123s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c 124s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c 125s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c 127s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_external.pico cram/cram_external.c 127s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_index.pico cram/cram_index.c 127s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_io.pico cram/cram_io.c 129s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c 129s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/mFILE.pico cram/mFILE.c 129s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c 129s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c 129s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c 129s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -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 129s 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 129s ln -sf libhts.so libhts.so.3 129s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o annot-tsv.o annot-tsv.c 130s 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 130s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzip.o bgzip.c 130s 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 130s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o htsfile.o htsfile.c 130s 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 130s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tabix.o tabix.c 130s 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 130s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 131s 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 131s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 131s 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 131s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3.pico hfile_s3.c 132s 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 132s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c 132s 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 132s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hts_endian.o test/hts_endian.c 132s 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 132s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fieldarith.o test/fieldarith.c 132s 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 132s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hfile.o test/hfile.c 132s 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 132s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup.o test/pileup.c 132s 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 132s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup_mod.o test/pileup_mod.c 133s 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 133s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/plugins-dlhts.o test/plugins-dlhts.c 133s 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 133s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/sam.o test/sam.c 133s 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 133s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_bgzf.o test/test_bgzf.c 134s 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 134s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_expr.o test/test_expr.c 134s 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 134s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_faidx.o test/test_faidx.c 134s 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 134s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kfunc.o test/test_kfunc.c 134s 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 134s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kstring.o test/test_kstring.c 134s 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 134s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_mod.o test/test_mod.c 134s 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 134s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_realn.o test/test_realn.c 134s 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 134s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-regidx.o test/test-regidx.c 135s 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 135s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_str2int.o test/test_str2int.c 135s 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 135s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_time_funcs.o test/test_time_funcs.c 135s 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 135s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_view.o test/test_view.c 135s 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 135s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_index.o test/test_index.c 135s 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 135s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-api.o test/test-vcf-api.c 135s 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 135s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c 135s 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 135s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-sr.o test/test-bcf-sr.c 136s 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 136s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c 136s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-translate.o test/test-bcf-translate.c 136s 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 136s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-parse-reg.o test/test-parse-reg.c 136s 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 136s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_introspection.o test/test_introspection.c 136s 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 136s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -msse -mfpmath=sse -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c 139s 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 139s sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 139s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 139s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 139s test/hts_endian 139s test/test_expr 139s test/test_kfunc 139s test/test_kstring 139s test/test_str2int 139s test/test_time_funcs 139s test/fieldarith test/fieldarith.sam 139s test/hfile 139s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 139s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 139s fi 139s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 139s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 139s fi 139s test/test_bgzf test/bgziptest.txt 140s test/test-parse-reg -t test/colons.bam 140s cd test/faidx && ./test-faidx.sh faidx.tst 140s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 140s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 140s Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" 140s Expected error: [E::hts_parse_region] Unexpected string "x" after region 140s Expected error: [E::hts_parse_region] Unexpected string "y" after region 140s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 140s Testing faidx... 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 140s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 140s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 140s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 140s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 140s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 140s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 140s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 140s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 140s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 140s 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 140s 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 140s 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 140s 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 140s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 140s 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 140s 140s Expected passes: 25 140s Unexpected passes: 0 140s Expected failures: 0 140s Unexpected failures: 0 140s cd test/sam_filter && ./filter.sh filter.tst 140s Testing sam_filter... 140s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 140s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 140s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 140s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 140s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 140s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 140s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 140s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 140s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 140s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 140s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 140s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 140s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 140s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 140s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 140s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 140s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 140s PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' 141s 141s Expected passes: 18 141s Unexpected passes: 0 141s Expected failures: 0 141s Unexpected failures: 0 141s cd test/tabix && ./test-tabix.sh tabix.tst 141s Testing tabix... 141s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 141s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 141s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 141s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 141s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 141s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 141s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 141s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 141s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 141s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 141s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 141s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 141s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 141s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 141s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 141s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 141s 141s Expected passes: 16 141s Unexpected passes: 0 141s Expected failures: 0 141s Unexpected failures: 0 141s cd test/mpileup && ./test-pileup.sh mpileup.tst 141s Testing (m)pileup... 141s PASS : $pileup mp_D.sam 141s PASS : $pileup -m mp_D.sam 141s PASS : $pileup mp_DI.sam 141s PASS : $pileup -m mp_DI.sam 141s PASS : $pileup mp_I.sam 141s PASS : $pileup -m mp_I.sam 141s PASS : $pileup mp_P.sam 141s PASS : $pileup -m mp_P.sam 141s PASS : $pileup mp_ID.sam 141s PASS : $pileup -m mp_ID.sam 141s PASS : $pileup mp_N.sam 141s PASS : $pileup -m mp_N.sam 141s PASS : $pileup mp_N2.sam 141s PASS : $pileup -m mp_N2.sam 141s PASS : $pileup c1#pad1.sam 141s PASS : $pileup -m c1#pad1.sam 141s PASS : $pileup c1#pad2.sam 141s PASS : $pileup -m c1#pad2.sam 141s PASS : $pileup c1#pad3.sam 141s PASS : $pileup -m c1#pad3.sam 141s PASS : $pileup -m small.bam 141s PASS : $pileup -m mp_overlap1.sam 141s PASS : $pileup -m mp_overlap2.sam 141s 141s Expected passes: 23 141s Unexpected passes: 0 141s Expected failures: 0 141s Unexpected failures: 0 141s cd test/fastq && ./test-fastq.sh 141s Testing fastq support 141s PASS : $tview minimal.fq 141s PASS : $tview minimal.fa 141s PASS : $tview multiline.fq 141s PASS : $tview multiline.fa 141s PASS : $tview -i fastq_aux longline.fq 141s PASS : $tview single.fq 141s PASS : $tview single.fa 141s PASS : $tview -i fastq_aux single.fq 141s PASS : $tview -i fastq_aux single.fa 141s PASS : $tview interleaved.fq 141s PASS : $tview interleaved.fa 141s PASS : $tview -i fastq_aux interleaved.fq 141s PASS : $tview -i fastq_aux interleaved.fa 141s PASS : $tview -i fastq_casava interleaved_casava.fq 141s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 141s PASS : $tview -i fastq_casava interleaved_casava.fa 141s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 141s PASS : $tview -i fastq_casava filter_casava.fq 141s PASS : $tview -i fastq_casava filter_casava.fa 141s PASS : $tview -i fastq_aux r1.fq 141s PASS : $tview -i fastq_aux r2.fq 141s PASS : $tview -i fastq_aux r1.fa 141s PASS : $tview -i fastq_aux r2.fa 141s PASS : $tview -i fastq_name2 name2.fq 141s PASS : $tview -i fastq_name2 name2.fa 141s PASS : $tview -f minimal.sam 141s PASS : $tview -F minimal.sam 141s PASS : $tview -f -o fastq_aux single_aux.sam 141s PASS : $tview -F -o fastq_aux single_aux.sam 141s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 141s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 141s PASS : $tview -f -o fastq_casava inter_casava.sam 141s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 141s PASS : $tview -F -o fastq_casava inter_casava.sam 141s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 141s PASS : $tview -f -o fastq_casava filter_casava.sam 141s PASS : $tview -F -o fastq_casava filter_casava.sam 141s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 141s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 141s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 141s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 141s 141s Expected passes: 41 141s Unexpected passes: 0 141s Expected failures: 0 141s Unexpected failures: 0 141s cd test/base_mods && ./base-mods.sh base-mods.tst 141s Testing base-modifications... 141s PASS : $test_mod MM-chebi.sam 141s PASS : $test_mod MM-double.sam 141s PASS : $test_mod MM-multi.sam 141s PASS : $test_mod MM-explicit.sam 141s PASS : $test_mod -x MM-explicit.sam 141s PASS : $test_mod -f 1 MM-explicit.sam 141s PASS : $test_mod MM-not-all-modded.sam 141s PASS : $pileup_mod < MM-pileup.sam 141s PASS : $pileup_mod < MM-pileup2.sam 141s PASS : $pileup_mod < MM-MNp.sam 141s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 141s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 141s PASS : $test_mod < MM-MNf1.sam (must exit non-zero) 141s PASS : $test_mod < MM-MNf2.sam (must exit non-zero) 141s PASS : $test_mod < MM-bounds+.sam (must exit non-zero) 141s PASS : $test_mod < MM-bounds-.sam (must exit non-zero) 141s 141s Expected passes: 16 141s Unexpected passes: 0 141s Expected failures: 0 141s Unexpected failures: 0 141s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 141s (Expect trailing 'x' message for " -1,001x") 141s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 141s (Expect trailing 'k' message for "1.5e+3k") 141s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 141s (Expect dropped fraction message for "12.3456k") 141s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 141s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 141s (Expect invalid numeric message for "A") 141s [W::hts_parse_decimal] Invalid numeric value A[truncated] 141s (Expect invalid numeric message for "G") 141s [W::hts_parse_decimal] Invalid numeric value G[truncated] 141s (Expect invalid numeric message for " +/-") 141s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 141s (Expect invalid numeric message for " -.e+9999") 141s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 141s test/test-regidx 141s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 141s bgzip round-trip no threads: .. ok 141s 142s bgzip text mode round-trip no threads: .. ok 142s 142s bgzip -b no threads: .. ok 142s 142s bgzip -b -I no threads: .. ok 142s 142s bgzip multifile no threads: .. ok 142s 142s bgzip --output no threads: .. ok 142s 142s bgzip round-trip 4 threads: .. ok 142s 142s bgzip text mode round-trip 4 threads: .. ok 142s 142s bgzip -b 4 threads: .. ok 142s 142s bgzip -b -I 4 threads: .. ok 142s 142s bgzip multifile 4 threads: .. ok 142s 143s bgzip --output 4 threads: .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/UH836QVcau/index.bam.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.bam 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.bam 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/UH836QVcau/index.bam.bai /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.bam 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -b /tmp/UH836QVcau/index.bam 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/UH836QVcau/index.sam.gz.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/UH836QVcau/index.sam.gz.bai /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -b /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/UH836QVcau/index.sam.gz.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index_dos.sam > /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/UH836QVcau/index.sam.gz.bai /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index_dos.sam > /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -b /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/UH836QVcau/index.cram.crai /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.cram 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index /tmp/UH836QVcau/index.cram 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/UH836QVcau/index.bcf.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.vcf > /tmp/UH836QVcau/index.bcf 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.bcf 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/UH836QVcau/index.vcf.gz.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.vcf > /tmp/UH836QVcau/index.vcf.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.vcf.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/UH836QVcau/index.vcf.gz.tbi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.vcf > /tmp/UH836QVcau/index.vcf.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -t /tmp/UH836QVcau/index.vcf.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/tabix /tmp/UH836QVcau/index.vcf.gz##idx##/tmp/UH836QVcau/index.vcf.gz.tbi 1:10000060-10000060 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/UH836QVcau/index2.bam 1:1000000-1000000 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/UH836QVcau/index2.bam 1:2000000-2000000 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/UH836QVcau/index2.bam 2:1000000-1000000 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/UH836QVcau/index2.bam 2:2000000-2000000 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/UH836QVcau/index.bam.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.bam 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.bam 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/UH836QVcau/index.bam.bai /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.bam 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -b /tmp/UH836QVcau/index.bam 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/UH836QVcau/index.sam.gz.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/UH836QVcau/index.sam.gz.bai /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -b /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/UH836QVcau/index.sam.gz.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index_dos.sam > /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/UH836QVcau/index.sam.gz.bai /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index_dos.sam > /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -b /tmp/UH836QVcau/index.sam.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/UH836QVcau/index.cram.crai /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.sam > /tmp/UH836QVcau/index.cram 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index /tmp/UH836QVcau/index.cram 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/UH836QVcau/index.bcf.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.vcf > /tmp/UH836QVcau/index.bcf 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.bcf 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/UH836QVcau/index.vcf.gz.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.vcf > /tmp/UH836QVcau/index.vcf.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c /tmp/UH836QVcau/index.vcf.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/UH836QVcau/index.vcf.gz.tbi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/index.vcf > /tmp/UH836QVcau/index.vcf.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -t /tmp/UH836QVcau/index.vcf.gz 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/tabix /tmp/UH836QVcau/index.vcf.gz##idx##/tmp/UH836QVcau/index.vcf.gz.tbi 1:10000060-10000060 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/UH836QVcau/index2.bam 1:1000000-1000000 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/UH836QVcau/index2.bam 1:2000000-2000000 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/UH836QVcau/index2.bam 2:1000000-1000000 143s .. ok 143s 143s test_index: 143s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/UH836QVcau/index2.bam 2:2000000-2000000 143s .. ok 143s 143s test_view testing multi-ref CRAM modes: 143s ./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 143s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 143s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 143s ./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 143s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 143s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 143s ./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 143s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 143s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 144s .. ok 144s 144s test_view testing multi-ref CRAM modes: 144s ./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 144s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 144s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 144s ./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 144s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 144s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 144s ./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 144s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 144s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 144s .. ok 144s 144s test_view testing auxf#values.sam, ref auxf.fa: 144s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 144s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 144s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 144s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 144s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 144s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 144s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 144s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 144s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 144s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 144s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 144s .. ok 144s 144s test_view testing c1#bounds.sam, ref c1.fa: 144s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 144s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 144s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 144s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 144s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 144s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 144s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 144s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 144s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 144s .. ok 144s 144s test_view testing c1#clip.sam, ref c1.fa: 144s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 144s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 144s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 144s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 144s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 144s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 144s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 144s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 144s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 144s .. ok 144s 144s test_view testing c1#noseq.sam, ref c1.fa: 144s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 144s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 144s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 144s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 144s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 144s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 144s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 144s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 144s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 144s .. ok 144s 144s test_view testing c1#pad1.sam, ref c1.fa: 144s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 144s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 144s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 144s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 144s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 144s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 144s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 144s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 144s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 144s .. ok 144s 144s test_view testing c1#pad2.sam, ref c1.fa: 144s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 144s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 144s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 144s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 144s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 144s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 144s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 144s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 144s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 144s .. ok 144s 144s test_view testing c1#pad3.sam, ref c1.fa: 144s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 144s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 144s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 144s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 144s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 144s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 144s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 144s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 144s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 144s .. ok 144s 144s test_view testing c1#unknown.sam, ref c1.fa: 144s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 144s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 144s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 144s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 144s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 145s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 145s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 145s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 145s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 145s .. ok 145s 145s test_view testing c2#pad.sam, ref c2.fa: 145s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 145s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 145s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 145s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 145s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 145s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 145s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 145s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 145s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 145s .. ok 145s 145s test_view testing ce#1.sam, ref ce.fa: 145s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 145s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 145s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 145s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 145s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 145s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 145s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 145s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 145s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 145s .. ok 145s 145s test_view testing ce#1000.sam, ref ce.fa: 145s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 145s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 145s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 145s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 145s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 145s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 145s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 145s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 145s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 145s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 145s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 145s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 145s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 145s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 145s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 145s .. ok 145s 145s test_view testing ce#2.sam, ref ce.fa: 145s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 145s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 145s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 145s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 145s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 145s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 145s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 145s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 145s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 145s .. ok 145s 145s test_view testing ce#5.sam, ref ce.fa: 145s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 145s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 145s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 145s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 145s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 145s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 145s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 145s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 145s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 145s .. ok 145s 145s test_view testing ce#5b.sam, ref ce.fa: 145s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 145s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 145s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 145s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 145s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 145s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 145s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 145s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 145s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 145s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 145s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 145s .. ok 145s 145s test_view testing ce#large_seq.sam, ref ce.fa: 145s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 145s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 145s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 146s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 146s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 146s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 146s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 146s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 146s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 146s .. ok 146s 146s test_view testing ce#supp.sam, ref ce.fa: 146s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 146s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 146s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 146s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 146s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 146s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 146s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 146s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 146s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 146s .. ok 146s 146s test_view testing ce#tag_depadded.sam, ref ce.fa: 146s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 146s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 146s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 146s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 146s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 146s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 146s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 146s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 146s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 146s .. ok 146s 146s test_view testing ce#tag_padded.sam, ref ce.fa: 146s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 146s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 146s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 146s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 146s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 146s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 146s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 146s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 146s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 146s .. ok 146s 146s test_view testing ce#unmap.sam, ref ce.fa: 146s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 146s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 146s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 146s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 146s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 146s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 146s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 146s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 146s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 146s .. ok 146s 146s test_view testing ce#unmap1.sam, ref ce.fa: 146s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 146s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 146s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 146s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 146s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 146s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 146s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 146s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 146s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 146s .. ok 146s 146s test_view testing ce#unmap2.sam, ref ce.fa: 146s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 146s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 146s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 146s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 146s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 146s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 146s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 146s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 146s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 146s .. ok 146s 146s test_view testing md#1.sam, ref md.fa: 146s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 146s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 146s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 146s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 146s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 146s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 146s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 146s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 146s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 146s .. ok 146s 146s test_view testing xx#blank.sam, ref xx.fa: 146s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 146s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 146s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 146s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 146s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 146s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 146s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 147s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#large_aux.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 147s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 147s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 147s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 147s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 147s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 147s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 147s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 147s .. ok 147s 147s test_view testing xx#large_aux2.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 147s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 147s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 147s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 147s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#MD.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 147s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 147s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 147s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 147s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#MD2.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 147s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 147s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 147s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 147s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#minimal.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 147s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 147s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 147s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 147s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#pair.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 147s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 147s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 147s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 147s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#repeated.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 147s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 147s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 147s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 147s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#rg.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 147s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 147s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 147s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 147s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#tlen.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 147s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 147s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 147s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 147s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 147s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 147s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 147s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 147s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 147s .. ok 147s 147s test_view testing xx#tlen2.sam, ref xx.fa: 147s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 147s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 147s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 148s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 148s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 148s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 148s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 148s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 148s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 148s .. ok 148s 148s test_view testing xx#triplet.sam, ref xx.fa: 148s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 148s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 148s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 148s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 148s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 148s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 148s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 148s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 148s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 148s .. ok 148s 148s test_view testing xx#unsorted.sam, ref xx.fa: 148s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 148s [W::cram_get_ref] Failed to populate reference for id 0 148s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 148s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 148s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 148s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 148s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 148s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 148s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 148s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 148s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 148s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 148s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 148s .. ok 148s 148s test_view testing embed_ref=2: 148s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 148s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 148s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 148s .. ok 148s 148s test_view testing region queries: 148s ./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 148s ./compare_sam.pl range.tmp range.out 148s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 148s ./compare_sam.pl range.tmp range.out 148s .. ok 148s 148s test_view testing BAM files with absent @SQ lines: 148s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 148s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 148s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 148s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 148s .. ok 148s 148s test_view testing large (> 2Gbases) positions: 148s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 148s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 148s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 148s test_view: 148s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 148s .. ok 148s 148s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 148s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 148s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 148s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 148s .. ok 148s 148s test_view testing auxf#values.sam, ref auxf.fa: 148s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 148s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 148s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 148s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 148s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 148s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 148s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 148s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 148s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 148s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 148s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 148s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 148s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 148s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 148s This is a technology demonstration that should not be used for archival data. 148s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 148s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 148s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 148s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 148s .. ok 148s 148s test_view testing c1#bounds.sam, ref c1.fa: 148s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 149s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 149s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 149s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 149s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 149s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 149s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 149s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 149s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 149s .. ok 149s 149s test_view testing c1#clip.sam, ref c1.fa: 149s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 149s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 149s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 149s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 149s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 149s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 149s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 149s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 149s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 149s .. ok 149s 149s test_view testing c1#noseq.sam, ref c1.fa: 149s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 149s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 149s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 149s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 149s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 149s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 149s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 149s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 149s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 149s .. ok 149s 149s test_view testing c1#pad1.sam, ref c1.fa: 149s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 149s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 149s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 149s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 149s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 149s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 149s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 149s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 149s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 149s .. ok 149s 149s test_view testing c1#pad2.sam, ref c1.fa: 149s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 149s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 149s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 149s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 149s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 149s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 149s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 149s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 149s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 149s .. ok 149s 149s test_view testing c1#pad3.sam, ref c1.fa: 149s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 149s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 149s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 149s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 149s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 149s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 149s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 149s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 149s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 149s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 150s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 150s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 150s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 150s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 150s This is a technology demonstration that should not be used for archival data. 150s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 150s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 150s .. ok 150s 150s test_view testing c1#unknown.sam, ref c1.fa: 150s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 150s ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 150s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 150s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 150s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 150s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 150s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 150s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 150s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 150s .. ok 150s 150s test_view testing c2#pad.sam, ref c2.fa: 150s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 150s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 150s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 150s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 150s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 150s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 150s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 150s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 150s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 150s .. ok 150s 150s test_view testing ce#1.sam, ref ce.fa: 150s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 150s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 150s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 150s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 150s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 150s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 150s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 150s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 150s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 150s .. ok 150s 150s test_view testing ce#1000.sam, ref ce.fa: 150s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 150s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 150s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 150s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 150s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 150s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 150s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 150s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 151s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 151s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 151s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 151s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 151s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 151s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 151s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 151s ./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 151s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 151s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 151s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 151s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 151s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 151s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 151s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 151s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 151s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 151s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 151s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 151s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 151s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 151s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 151s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 151s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 151s This is a technology demonstration that should not be used for archival data. 151s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 152s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 152s .. ok 152s 152s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 152s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 152s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 152s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 152s ./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 152s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 152s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 152s ./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 152s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 152s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 152s .. ok 152s 152s test_view testing ce#2.sam, ref ce.fa: 152s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 152s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 152s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 152s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 152s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 152s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 152s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 152s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 152s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 152s .. ok 152s 152s test_view testing ce#5.sam, ref ce.fa: 152s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 152s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 152s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 152s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 152s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 152s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 152s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 152s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 152s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 152s ./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 152s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 152s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 152s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 152s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 152s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 152s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 152s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 152s This is a technology demonstration that should not be used for archival data. 152s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 152s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 152s .. ok 152s 152s test_view testing ce#5b.sam, ref ce.fa: 152s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 152s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 152s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 152s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 153s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 153s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 153s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 153s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 153s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 153s ./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 153s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 153s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 153s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 153s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 153s .. ok 153s 153s test_view testing ce#large_seq.sam, ref ce.fa: 153s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 153s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 153s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 153s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 153s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 153s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 153s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 153s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 153s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 153s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 153s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 154s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 154s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 154s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 154s This is a technology demonstration that should not be used for archival data. 154s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 154s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 154s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 154s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 154s This is a technology demonstration that should not be used for archival data. 154s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 154s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 154s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 154s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 154s This is a technology demonstration that should not be used for archival data. 154s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 154s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 154s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 154s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 154s This is a technology demonstration that should not be used for archival data. 155s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 155s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 155s .. ok 155s 155s test_view testing ce#supp.sam, ref ce.fa: 155s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 155s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 155s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 155s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 155s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 155s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 155s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 155s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 155s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 155s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 155s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 155s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 155s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 155s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 155s This is a technology demonstration that should not be used for archival data. 155s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 155s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 155s .. ok 155s 155s test_view testing ce#tag_depadded.sam, ref ce.fa: 155s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 155s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 155s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 155s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 155s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 155s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 155s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 155s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 155s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 155s .. ok 155s 155s test_view testing ce#tag_padded.sam, ref ce.fa: 155s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 155s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 155s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 155s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 155s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 155s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 155s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 155s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 155s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 156s .. ok 156s 156s test_view testing ce#unmap.sam, ref ce.fa: 156s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 156s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 156s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 156s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 156s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 156s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 156s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 156s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 156s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 156s ./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 156s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 156s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 156s .. ok 156s 156s test_view testing ce#unmap1.sam, ref ce.fa: 156s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 156s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 156s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 156s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 156s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 156s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 156s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 156s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 156s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 156s ./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 156s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 156s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 156s .. ok 156s 156s test_view testing ce#unmap2.sam, ref ce.fa: 156s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 156s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 156s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 156s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 156s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 156s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 156s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 156s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 156s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 156s ./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 156s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 156s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 156s .. ok 156s 156s test_view testing md#1.sam, ref md.fa: 156s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 156s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 156s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 156s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 156s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 156s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 156s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 156s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 156s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 156s .. ok 156s 156s test_view testing xx#blank.sam, ref xx.fa: 156s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 156s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 156s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 156s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 156s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 156s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 156s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 156s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 156s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 156s ./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 156s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 156s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 156s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 156s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 157s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 157s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 157s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 157s This is a technology demonstration that should not be used for archival data. 157s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 157s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 157s .. ok 157s 157s test_view testing xx#large_aux.sam, ref xx.fa: 157s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 157s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 157s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 157s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 157s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 157s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 157s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 157s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 157s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 157s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 157s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 157s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 157s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 157s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 157s This is a technology demonstration that should not be used for archival data. 157s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 157s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 157s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 157s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 157s This is a technology demonstration that should not be used for archival data. 157s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 157s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 157s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 157s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 157s This is a technology demonstration that should not be used for archival data. 157s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 158s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 158s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 158s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 158s This is a technology demonstration that should not be used for archival data. 158s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 158s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 158s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 158s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 158s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 158s .. ok 158s 158s test_view testing xx#large_aux2.sam, ref xx.fa: 158s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 158s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 158s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 158s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 158s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 158s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 158s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 158s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 158s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 158s .. ok 158s 158s test_view testing xx#MD.sam, ref xx.fa: 158s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 158s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 158s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 158s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 158s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 158s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 158s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 158s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 158s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 158s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 158s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 158s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 158s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 158s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 158s This is a technology demonstration that should not be used for archival data. 158s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 158s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 158s .. ok 158s 158s test_view testing xx#MD2.sam, ref xx.fa: 158s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 159s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 159s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 159s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 159s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 159s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 159s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 159s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 159s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 159s .. ok 159s 159s test_view testing xx#minimal.sam, ref xx.fa: 159s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 159s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 159s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 159s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 159s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 159s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 159s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 159s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 159s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 159s ./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 159s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 159s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 159s .. ok 159s 159s test_view testing xx#pair.sam, ref xx.fa: 159s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 159s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 159s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 159s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 159s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 159s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 159s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 159s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 159s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 159s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 159s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 159s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 159s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 159s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 159s This is a technology demonstration that should not be used for archival data. 159s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 159s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 159s .. ok 159s 159s test_view testing xx#repeated.sam, ref xx.fa: 159s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 159s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 159s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 159s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 159s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 159s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 159s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 159s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 159s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 159s .. ok 159s 159s test_view testing xx#rg.sam, ref xx.fa: 159s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 159s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 159s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 159s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 159s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 160s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 160s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 160s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 160s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 160s .. ok 160s 160s test_view testing xx#tlen.sam, ref xx.fa: 160s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 160s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 160s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 160s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 160s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 160s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 160s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 160s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 160s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 160s ./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 160s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 160s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 160s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 160s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 160s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 160s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 160s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 160s This is a technology demonstration that should not be used for archival data. 160s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 160s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 160s .. ok 160s 160s test_view testing xx#tlen2.sam, ref xx.fa: 160s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 160s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 160s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 160s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 160s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 160s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 160s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 160s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 160s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 160s ./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 160s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 160s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 160s .. ok 160s 160s test_view testing xx#triplet.sam, ref xx.fa: 160s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 160s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 160s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 160s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 160s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 160s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 160s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 160s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 160s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 160s ./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 160s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 160s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 160s .. ok 160s 160s test_view testing xx#unsorted.sam, ref xx.fa: 160s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 160s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 160s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 160s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 161s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 161s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 161s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 161s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 161s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 161s .. ok 161s 161s test_view testing embed_ref=2: 161s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 161s [W::cram_get_ref] Failed to populate reference for id 0 161s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 161s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 161s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 161s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 161s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 161s .. ok 161s 161s test_view testing region queries: 161s ./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 161s ./compare_sam.pl range.tmp range.out 161s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 161s ./compare_sam.pl range.tmp range.out 161s .. ok 161s 161s test_view testing BAM files with absent @SQ lines: 161s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 161s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 161s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 161s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 161s .. ok 161s 161s test_view testing large (> 2Gbases) positions: 161s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 161s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 161s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 161s test_view: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 161s .. ok 161s 161s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 161s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 161s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 161s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 161s .. ok 161s 161s 161s test_MD testing xx#MD.sam, ref xx.fa: 161s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 161s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 161s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 161s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 161s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 161s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 161s Checking for MD/NM in xx#MD.sam 161s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 161s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 161s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 161s .. ok 161s 161s 161s test_MD testing xx#MD2.sam, ref xx.fa: 161s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 161s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 161s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 161s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 161s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 161s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 161s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 161s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 161s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 161s .. ok 161s 161s test_vcf_api: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-vcf-api /tmp/UH836QVcau/test-vcf-api.bcf 161s .. ok 161s 161s test_bcf2vcf: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/tabix/vcf_file.bcf 161s .. ok 161s 161s test_vcf_sweep: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-vcf-sweep /tmp/UH836QVcau/test-vcf-api.bcf 161s .. ok 161s 161s test_vcf_various: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 161s .. ok 161s 161s test_vcf_various: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/formatcols.vcf 161s .. ok 161s 161s test_vcf_various: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/noroundtrip.vcf 161s .. ok 161s 161s test_vcf_various: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/formatmissing.vcf 161s .. ok 161s 161s test_vcf_various: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/vcf_meta_meta.vcf 161s .. ok 161s 161s test_vcf_various: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 161s .. ok 161s 161s test-bcf-sr: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 74452500 161s .. ok 161s 161s test-bcf-sr: 161s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 34270147 162s .. ok 162s 162s test-bcf-sr: 162s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 11108528 162s .. ok 162s 162s test-bcf-sr: 162s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 42233895 162s .. ok 162s 162s test-bcf-sr: 162s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 8111117 162s .. ok 162s 162s test-bcf-sr: 162s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 85644070 163s .. ok 163s 163s test-bcf-sr: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 49879942 163s .. ok 163s 163s test-bcf-sr: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 47881429 163s .. ok 163s 163s test-bcf-sr: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 69081244 163s .. ok 163s 163s test-bcf-sr: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/UH836QVcau -s 83459376 163s .. ok 163s 163s test_bcf_sr_no_index: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/UH836QVcau/no_index_1.err 163s .. ok 163s 163s test_bcf_sr_no_index: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/UH836QVcau/no_index_2.out 2> /tmp/UH836QVcau/no_index_2.err (expected fail) 163s .. ok 163s 163s test_bcf_sr_no_index: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/UH836QVcau/no_index_3.out 2> /tmp/UH836QVcau/no_index_3.err (expected fail) 163s .. ok 163s 163s test_bcf_sr_no_index: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/UH836QVcau/no_index_4.out 2> /tmp/UH836QVcau/no_index_4.err (expected fail) 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -b -p /tmp/UH836QVcau/weird-chr-names.vcf.bcf -x /tmp/UH836QVcau/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_1.out.vcf -r '1' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_2.out.vcf -r '1:1-2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_4.out.vcf -r '1:1-1' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_5.out.vcf -r '{1:1}' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf (expected fail) 163s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 163s Failed to set regions 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_14.out.vcf -t '1' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_15.out.vcf -t '1:1-2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_17.out.vcf -t '1:1-1' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_18.out.vcf -t '{1:1}' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf 163s .. ok 163s 163s test_bcf_sr_range: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/UH836QVcau/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/UH836QVcau/weird-chr-names.vcf.bcf (expected fail) 163s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 163s Failed to set targets 163s .. ok 163s 163s test_command: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf-translate - 163s .. ok 163s 163s test_convert_padded_header: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/UH836QVcau/headernul0.bam 163s .. ok 163s 163s test_convert_padded_header: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/UH836QVcau/headernul1.bam 163s .. ok 163s 163s test_convert_padded_header: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/UH836QVcau/headernul678.bam 163s .. ok 163s 163s test_rebgzip: Alternate zlib/deflate library detected 163s test_rebgzip: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/bgziptest.txt 163s .. ok 163s 163s test-logging: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-logging.pl 163s .. ok 163s 163s test_plugin_loading: 163s HTS_PATH=/tmp/autopkgtest.NWxfCW/autopkgtest_tmp /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 163s .. ok 163s 163s test_realn: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn01.sam -o - 163s .. ok 163s 163s test_realn: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.sam -o - 163s .. ok 163s 163s test_realn: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn01.sam -o - 163s .. ok 163s 163s test_realn: 163s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.sam -o - 164s .. ok 164s 164s test_realn: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn01.sam -o - 164s .. ok 164s 164s test_realn: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.sam -o - 164s .. ok 164s 164s test_realn: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02-r.sam -o - 164s .. ok 164s 164s test_realn: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02_exp.sam -o - 164s .. ok 164s 164s test_realn: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn02_exp-a.sam -o - 164s .. ok 164s 164s test_realn: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/realn03.sam -o - 164s .. ok 164s 164s test-bcf_set_variant_type: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/test-bcf_set_variant_type 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.1.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.2.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.3.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.3.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.3.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.3.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.3.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.3.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.4.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.4.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.4.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.4.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.4.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.4.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.5.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.5.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.5.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.5.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.5.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.5.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.6.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.6.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.6.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.6.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.6.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.6.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.7.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.7.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.7.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.7.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.7.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.7.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.8.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.8.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.8.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.8.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.8.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.8.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.9.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.9.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.9.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.9.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.9.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.9.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -f smpl -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -x -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -x -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -x -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -f smpl -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -f smpl -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -f smpl -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -x -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -x -s /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt 164s .. ok 164s 164s run_annot_tsv: 164s cat /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/annot-tsv -m smpl -x -t /tmp/autopkgtest.NWxfCW/autopkgtest_tmp/test/annot-tsv/dst.10.txt 164s .. ok 164s 164s 164s Number of tests: 164s total .. 293 164s passed .. 293 164s failed .. 0 164s 164s PASS 164s + echo PASS 164s autopkgtest [20:03:20]: test run-unit-test: -----------------------] 165s run-unit-test PASS 165s autopkgtest [20:03:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 165s autopkgtest [20:03:21]: @@@@@@@@@@@@@@@@@@@@ summary 165s run-unit-test PASS 177s nova [W] Skipping flock for amd64 177s Creating nova instance adt-plucky-amd64-htslib-20241129-200036-juju-7f2275-prod-proposed-migration-environment-20-4ea8cef6-5839-4420-9de3-dce6d7b6b2de from image adt/ubuntu-plucky-amd64-server-20241129.img (UUID c95ff410-802a-49bb-8eba-55253ddf6f2e)...