0s autopkgtest [01:48:07]: starting date and time: 2024-03-19 01:48:07+0000 0s autopkgtest [01:48:07]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [01:48:07]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gipow9s9/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/3.0.13-0ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-3.secgroup --name adt-noble-ppc64el-htslib-20240319-014807-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 96s autopkgtest [01:49:43]: testbed dpkg architecture: ppc64el 96s autopkgtest [01:49:43]: testbed apt version: 2.7.12 96s autopkgtest [01:49:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 97s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 97s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [486 kB] 98s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 98s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 98s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3748 kB] 98s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [646 kB] 98s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 98s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 98s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 98s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4020 kB] 98s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 98s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.3 kB] 98s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 101s Fetched 9136 kB in 2s (3816 kB/s) 102s Reading package lists... 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 105s The following packages will be REMOVED: 105s libssl3 105s The following NEW packages will be installed: 105s libssl3t64 105s The following packages will be upgraded: 105s openssl 105s 1 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 105s Need to get 3151 kB of archives. 105s After this operation, 73.7 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 106s Fetched 3151 kB in 1s (4067 kB/s) 106s (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 ... 70095 files and directories currently installed.) 106s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 106s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 106s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 106s wget depends on libssl3 (>= 3.0.0). 106s tnftp depends on libssl3 (>= 3.0.0). 106s tcpdump depends on libssl3 (>= 3.0.0). 106s systemd-resolved depends on libssl3 (>= 3.0.0). 106s systemd depends on libssl3 (>= 3.0.0). 106s sudo depends on libssl3 (>= 3.0.0). 106s rsync depends on libssl3 (>= 3.0.0). 106s python3-cryptography depends on libssl3 (>= 3.0.0). 106s openssh-server depends on libssl3 (>= 3.0.10). 106s openssh-client depends on libssl3 (>= 3.0.10). 106s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 106s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 106s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 106s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 106s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 106s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 106s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 106s libnvme1 depends on libssl3 (>= 3.0.0). 106s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 106s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 106s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 106s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 106s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 106s kmod depends on libssl3 (>= 3.0.0). 106s dhcpcd-base depends on libssl3 (>= 3.0.0). 106s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 106s 106s (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 ... 70095 files and directories currently installed.) 106s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 106s Selecting previously unselected package libssl3t64:ppc64el. 106s (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 ... 70084 files and directories currently installed.) 106s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 106s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 106s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 106s Setting up openssl (3.0.13-0ubuntu2) ... 106s Processing triggers for man-db (2.12.0-3) ... 107s Processing triggers for libc-bin (2.39-0ubuntu2) ... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 108s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 108s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 108s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 109s Reading package lists... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Calculating upgrade... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [01:50:00]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 113s autopkgtest [01:50:00]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 116s Get:1 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (dsc) [2437 B] 116s Get:2 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (tar) [1469 kB] 116s Get:3 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (diff) [20.1 kB] 116s gpgv: Signature made Tue Nov 7 20:35:25 2023 UTC 116s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 116s gpgv: issuer "emollier@debian.org" 116s gpgv: Can't check signature: No public key 116s dpkg-source: warning: cannot verify inline signature for ./htslib_1.18+ds-1.dsc: no acceptable signature found 116s autopkgtest [01:50:03]: testing package htslib version 1.18+ds-1 117s autopkgtest [01:50:04]: build not needed 117s autopkgtest [01:50:04]: test run-unit-test: preparing testbed 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Starting pkgProblemResolver with broken count: 0 122s Starting 2 pkgProblemResolver with broken count: 0 122s Done 122s The following additional packages will be installed: 122s autoconf automake autopoint autotools-dev build-essential cpp cpp-13 122s cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper debugedit 122s dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 122s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 122s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext htslib-test 122s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 122s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 122s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 122s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 122s libhtscodecs-dev libhtscodecs2 libisl23 libitm1 liblsan0 liblzma-dev libmpc3 122s libnsl-dev libquadmath0 libssl-dev libstdc++-13-dev libsub-override-perl 122s libtirpc-dev libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf 123s rpcsvc-proto tabix zlib1g-dev 123s Suggested packages: 123s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 123s cpp-13-doc dh-make gcc-13-doc gcc-multilib manpages-dev flex bison gdb 123s gcc-doc gdb-powerpc64le-linux-gnu gettext-doc libasprintf-dev 123s libgettextpo-dev glibc-doc libcurl4-doc libgnutls28-dev libidn-dev 123s libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc 123s libssl-doc libstdc++-13-doc libtool-doc gfortran | fortran95-compiler 123s gcj-jdk m4-doc libmail-box-perl 123s Recommended packages: 123s bzip2-doc manpages manpages-dev libc-devtools libarchive-cpio-perl 123s libltdl-dev libmail-sendmail-perl 123s The following NEW packages will be installed: 123s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 123s cpp cpp-13 cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper 123s debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 123s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 123s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext htslib-test 123s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 123s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 123s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 123s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 123s libhtscodecs-dev libhtscodecs2 libisl23 libitm1 liblsan0 liblzma-dev libmpc3 123s libnsl-dev libquadmath0 libssl-dev libstdc++-13-dev libsub-override-perl 123s libtirpc-dev libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf 123s rpcsvc-proto tabix zlib1g-dev 123s 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. 123s Need to get 82.8 MB/82.8 MB of archives. 123s After this operation, 306 MB of additional disk space will be used. 123s Get:1 /tmp/autopkgtest.kzTFrJ/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [812 B] 123s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el m4 ppc64el 1.4.19-4 [275 kB] 123s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el autoconf all 2.71-3 [339 kB] 123s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 123s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 123s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el autopoint all 0.21-14ubuntu1 [422 kB] 123s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu2 [21.3 kB] 123s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-11.11 [1585 kB] 123s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 123s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1build1 [262 kB] 123s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libnsl-dev ppc64el 1.3.0-3 [79.2 kB] 123s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 123s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu2 [2102 kB] 124s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libisl23 ppc64el 0.26-3 [864 kB] 124s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libmpc3 ppc64el 1.3.1-1 [61.2 kB] 124s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [10.7 MB] 124s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13 ppc64el 13.2.0-17ubuntu2 [1038 B] 124s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] 124s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] 124s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libcc1-0 ppc64el 14-20240303-1ubuntu1 [48.1 kB] 124s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 124s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libitm1 ppc64el 14-20240303-1ubuntu1 [32.4 kB] 124s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libatomic1 ppc64el 14-20240303-1ubuntu1 [10.7 kB] 124s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libasan8 ppc64el 14-20240303-1ubuntu1 [2973 kB] 125s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el liblsan0 ppc64el 14-20240303-1ubuntu1 [1325 kB] 125s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libtsan2 ppc64el 14-20240303-1ubuntu1 [2734 kB] 125s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libubsan1 ppc64el 14-20240303-1ubuntu1 [1194 kB] 125s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libquadmath0 ppc64el 14-20240303-1ubuntu1 [158 kB] 125s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcc-13-dev ppc64el 13.2.0-17ubuntu2 [1581 kB] 125s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [20.6 MB] 125s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13 ppc64el 13.2.0-17ubuntu2 [477 kB] 125s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] 125s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] 126s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libstdc++-13-dev ppc64el 13.2.0-17ubuntu2 [2445 kB] 126s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [12.2 MB] 126s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13 ppc64el 13.2.0-17ubuntu2 [14.5 kB] 126s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] 126s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] 126s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 126s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 126s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libtool all 2.4.7-7 [166 kB] 126s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-autoreconf all 20 [16.1 kB] 126s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 126s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libsub-override-perl all 0.10-1 [10.0 kB] 126s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 126s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] 126s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libdw1 ppc64el 0.190-1 [294 kB] 126s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el debugedit ppc64el 1:5.0-5 [51.1 kB] 126s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el dwz ppc64el 0.15-1 [139 kB] 126s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext ppc64el 0.21-14ubuntu1 [979 kB] 126s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 126s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 126s Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el debhelper all 13.14.1ubuntu1 [869 kB] 126s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el htslib-test all 1.18+ds-1 [1120 kB] 126s Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el libbz2-dev ppc64el 1.0.8-5ubuntu1 [51.2 kB] 126s Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el libcurl4-gnutls-dev ppc64el 8.5.0-2ubuntu2 [530 kB] 126s Get:57 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 126s Get:58 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate-dev ppc64el 1.19-1 [69.7 kB] 126s Get:59 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 126s Get:60 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 126s Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el liblzma-dev ppc64el 5.4.5-0.3 [243 kB] 126s Get:62 http://ftpmaster.internal/ubuntu noble/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3ubuntu1 [902 kB] 126s Get:63 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts-dev ppc64el 1.18+ds-1 [6252 kB] 127s Get:64 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs-dev ppc64el 1.6.0-1 [3007 kB] 127s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl-dev ppc64el 3.0.13-0ubuntu2 [2667 kB] 127s Get:66 http://ftpmaster.internal/ubuntu noble/universe ppc64el tabix ppc64el 1.18+ds-1 [692 kB] 127s Fetched 82.8 MB in 4s (18.8 MB/s) 127s Selecting previously unselected package m4. 127s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70097 files and directories currently installed.) 127s Preparing to unpack .../00-m4_1.4.19-4_ppc64el.deb ... 127s Unpacking m4 (1.4.19-4) ... 127s Selecting previously unselected package autoconf. 127s Preparing to unpack .../01-autoconf_2.71-3_all.deb ... 127s Unpacking autoconf (2.71-3) ... 127s Selecting previously unselected package autotools-dev. 127s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 127s Unpacking autotools-dev (20220109.1) ... 127s Selecting previously unselected package automake. 127s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 127s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 127s Selecting previously unselected package autopoint. 127s Preparing to unpack .../04-autopoint_0.21-14ubuntu1_all.deb ... 127s Unpacking autopoint (0.21-14ubuntu1) ... 127s Selecting previously unselected package libc-dev-bin. 127s Preparing to unpack .../05-libc-dev-bin_2.39-0ubuntu2_ppc64el.deb ... 127s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 127s Selecting previously unselected package linux-libc-dev:ppc64el. 127s Preparing to unpack .../06-linux-libc-dev_6.8.0-11.11_ppc64el.deb ... 127s Unpacking linux-libc-dev:ppc64el (6.8.0-11.11) ... 128s Selecting previously unselected package libcrypt-dev:ppc64el. 128s Preparing to unpack .../07-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 128s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 128s Selecting previously unselected package libtirpc-dev:ppc64el. 128s Preparing to unpack .../08-libtirpc-dev_1.3.4+ds-1build1_ppc64el.deb ... 128s Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 128s Selecting previously unselected package libnsl-dev:ppc64el. 128s Preparing to unpack .../09-libnsl-dev_1.3.0-3_ppc64el.deb ... 128s Unpacking libnsl-dev:ppc64el (1.3.0-3) ... 128s Selecting previously unselected package rpcsvc-proto. 128s Preparing to unpack .../10-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 128s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 128s Selecting previously unselected package libc6-dev:ppc64el. 128s Preparing to unpack .../11-libc6-dev_2.39-0ubuntu2_ppc64el.deb ... 128s Unpacking libc6-dev:ppc64el (2.39-0ubuntu2) ... 128s Selecting previously unselected package libisl23:ppc64el. 128s Preparing to unpack .../12-libisl23_0.26-3_ppc64el.deb ... 128s Unpacking libisl23:ppc64el (0.26-3) ... 128s Selecting previously unselected package libmpc3:ppc64el. 128s Preparing to unpack .../13-libmpc3_1.3.1-1_ppc64el.deb ... 128s Unpacking libmpc3:ppc64el (1.3.1-1) ... 128s Selecting previously unselected package cpp-13-powerpc64le-linux-gnu. 128s Preparing to unpack .../14-cpp-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 128s Unpacking cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 128s Selecting previously unselected package cpp-13. 128s Preparing to unpack .../15-cpp-13_13.2.0-17ubuntu2_ppc64el.deb ... 128s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 128s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 128s Preparing to unpack .../16-cpp-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 128s Unpacking cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 128s Selecting previously unselected package cpp. 128s Preparing to unpack .../17-cpp_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 128s Unpacking cpp (4:13.2.0-7ubuntu1) ... 128s Selecting previously unselected package libcc1-0:ppc64el. 128s Preparing to unpack .../18-libcc1-0_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package libgomp1:ppc64el. 128s Preparing to unpack .../19-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package libitm1:ppc64el. 128s Preparing to unpack .../20-libitm1_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking libitm1:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package libatomic1:ppc64el. 128s Preparing to unpack .../21-libatomic1_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking libatomic1:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package libasan8:ppc64el. 128s Preparing to unpack .../22-libasan8_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking libasan8:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package liblsan0:ppc64el. 128s Preparing to unpack .../23-liblsan0_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking liblsan0:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package libtsan2:ppc64el. 128s Preparing to unpack .../24-libtsan2_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking libtsan2:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package libubsan1:ppc64el. 128s Preparing to unpack .../25-libubsan1_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking libubsan1:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package libquadmath0:ppc64el. 128s Preparing to unpack .../26-libquadmath0_14-20240303-1ubuntu1_ppc64el.deb ... 128s Unpacking libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 128s Selecting previously unselected package libgcc-13-dev:ppc64el. 128s Preparing to unpack .../27-libgcc-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 128s Unpacking libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 129s Selecting previously unselected package gcc-13-powerpc64le-linux-gnu. 129s Preparing to unpack .../28-gcc-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 129s Unpacking gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 129s Selecting previously unselected package gcc-13. 129s Preparing to unpack .../29-gcc-13_13.2.0-17ubuntu2_ppc64el.deb ... 129s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 129s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 129s Preparing to unpack .../30-gcc-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 129s Unpacking gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 129s Selecting previously unselected package gcc. 129s Preparing to unpack .../31-gcc_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 129s Unpacking gcc (4:13.2.0-7ubuntu1) ... 129s Selecting previously unselected package libstdc++-13-dev:ppc64el. 129s Preparing to unpack .../32-libstdc++-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 129s Unpacking libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 129s Selecting previously unselected package g++-13-powerpc64le-linux-gnu. 129s Preparing to unpack .../33-g++-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 129s Unpacking g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 130s Selecting previously unselected package g++-13. 130s Preparing to unpack .../34-g++-13_13.2.0-17ubuntu2_ppc64el.deb ... 130s Unpacking g++-13 (13.2.0-17ubuntu2) ... 130s Selecting previously unselected package g++-powerpc64le-linux-gnu. 130s Preparing to unpack .../35-g++-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 130s Unpacking g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 130s Selecting previously unselected package g++. 130s Preparing to unpack .../36-g++_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 130s Unpacking g++ (4:13.2.0-7ubuntu1) ... 130s Selecting previously unselected package build-essential. 130s Preparing to unpack .../37-build-essential_12.10ubuntu1_ppc64el.deb ... 130s Unpacking build-essential (12.10ubuntu1) ... 130s Selecting previously unselected package libdebhelper-perl. 130s Preparing to unpack .../38-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 130s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 130s Selecting previously unselected package libtool. 130s Preparing to unpack .../39-libtool_2.4.7-7_all.deb ... 130s Unpacking libtool (2.4.7-7) ... 130s Selecting previously unselected package dh-autoreconf. 130s Preparing to unpack .../40-dh-autoreconf_20_all.deb ... 130s Unpacking dh-autoreconf (20) ... 130s Selecting previously unselected package libarchive-zip-perl. 130s Preparing to unpack .../41-libarchive-zip-perl_1.68-1_all.deb ... 130s Unpacking libarchive-zip-perl (1.68-1) ... 130s Selecting previously unselected package libsub-override-perl. 130s Preparing to unpack .../42-libsub-override-perl_0.10-1_all.deb ... 130s Unpacking libsub-override-perl (0.10-1) ... 130s Selecting previously unselected package libfile-stripnondeterminism-perl. 130s Preparing to unpack .../43-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 130s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 130s Selecting previously unselected package dh-strip-nondeterminism. 130s Preparing to unpack .../44-dh-strip-nondeterminism_1.13.1-1_all.deb ... 130s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 130s Selecting previously unselected package libdw1:ppc64el. 130s Preparing to unpack .../45-libdw1_0.190-1_ppc64el.deb ... 130s Unpacking libdw1:ppc64el (0.190-1) ... 130s Selecting previously unselected package debugedit. 130s Preparing to unpack .../46-debugedit_1%3a5.0-5_ppc64el.deb ... 130s Unpacking debugedit (1:5.0-5) ... 130s Selecting previously unselected package dwz. 130s Preparing to unpack .../47-dwz_0.15-1_ppc64el.deb ... 130s Unpacking dwz (0.15-1) ... 130s Selecting previously unselected package gettext. 130s Preparing to unpack .../48-gettext_0.21-14ubuntu1_ppc64el.deb ... 130s Unpacking gettext (0.21-14ubuntu1) ... 130s Selecting previously unselected package intltool-debian. 130s Preparing to unpack .../49-intltool-debian_0.35.0+20060710.6_all.deb ... 130s Unpacking intltool-debian (0.35.0+20060710.6) ... 130s Selecting previously unselected package po-debconf. 130s Preparing to unpack .../50-po-debconf_1.0.21+nmu1_all.deb ... 130s Unpacking po-debconf (1.0.21+nmu1) ... 130s Selecting previously unselected package debhelper. 130s Preparing to unpack .../51-debhelper_13.14.1ubuntu1_all.deb ... 130s Unpacking debhelper (13.14.1ubuntu1) ... 130s Selecting previously unselected package htslib-test. 130s Preparing to unpack .../52-htslib-test_1.18+ds-1_all.deb ... 130s Unpacking htslib-test (1.18+ds-1) ... 130s Selecting previously unselected package libbz2-dev:ppc64el. 130s Preparing to unpack .../53-libbz2-dev_1.0.8-5ubuntu1_ppc64el.deb ... 130s Unpacking libbz2-dev:ppc64el (1.0.8-5ubuntu1) ... 130s Selecting previously unselected package libcurl4-gnutls-dev:ppc64el. 130s Preparing to unpack .../54-libcurl4-gnutls-dev_8.5.0-2ubuntu2_ppc64el.deb ... 130s Unpacking libcurl4-gnutls-dev:ppc64el (8.5.0-2ubuntu2) ... 130s Selecting previously unselected package libdeflate0:ppc64el. 130s Preparing to unpack .../55-libdeflate0_1.19-1_ppc64el.deb ... 130s Unpacking libdeflate0:ppc64el (1.19-1) ... 130s Selecting previously unselected package libdeflate-dev:ppc64el. 130s Preparing to unpack .../56-libdeflate-dev_1.19-1_ppc64el.deb ... 130s Unpacking libdeflate-dev:ppc64el (1.19-1) ... 130s Selecting previously unselected package libhtscodecs2:ppc64el. 130s Preparing to unpack .../57-libhtscodecs2_1.6.0-1_ppc64el.deb ... 130s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 130s Selecting previously unselected package libhts3:ppc64el. 130s Preparing to unpack .../58-libhts3_1.18+ds-1_ppc64el.deb ... 130s Unpacking libhts3:ppc64el (1.18+ds-1) ... 130s Selecting previously unselected package liblzma-dev:ppc64el. 130s Preparing to unpack .../59-liblzma-dev_5.4.5-0.3_ppc64el.deb ... 130s Unpacking liblzma-dev:ppc64el (5.4.5-0.3) ... 130s Selecting previously unselected package zlib1g-dev:ppc64el. 130s Preparing to unpack .../60-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_ppc64el.deb ... 130s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 130s Selecting previously unselected package libhts-dev:ppc64el. 130s Preparing to unpack .../61-libhts-dev_1.18+ds-1_ppc64el.deb ... 130s Unpacking libhts-dev:ppc64el (1.18+ds-1) ... 130s Selecting previously unselected package libhtscodecs-dev:ppc64el. 130s Preparing to unpack .../62-libhtscodecs-dev_1.6.0-1_ppc64el.deb ... 130s Unpacking libhtscodecs-dev:ppc64el (1.6.0-1) ... 130s Selecting previously unselected package libssl-dev:ppc64el. 130s Preparing to unpack .../63-libssl-dev_3.0.13-0ubuntu2_ppc64el.deb ... 130s Unpacking libssl-dev:ppc64el (3.0.13-0ubuntu2) ... 131s Selecting previously unselected package tabix. 131s Preparing to unpack .../64-tabix_1.18+ds-1_ppc64el.deb ... 131s Unpacking tabix (1.18+ds-1) ... 131s Selecting previously unselected package autopkgtest-satdep. 131s Preparing to unpack .../65-1-autopkgtest-satdep.deb ... 131s Unpacking autopkgtest-satdep (0) ... 131s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 131s Setting up libdw1:ppc64el (0.190-1) ... 131s Setting up libarchive-zip-perl (1.68-1) ... 131s Setting up htslib-test (1.18+ds-1) ... 131s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 131s Setting up libdeflate0:ppc64el (1.19-1) ... 131s Setting up linux-libc-dev:ppc64el (6.8.0-11.11) ... 131s Setting up m4 (1.4.19-4) ... 131s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up libcurl4-gnutls-dev:ppc64el (8.5.0-2ubuntu2) ... 131s Setting up libhtscodecs-dev:ppc64el (1.6.0-1) ... 131s Setting up autotools-dev (20220109.1) ... 131s Setting up libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 131s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 131s Setting up libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up libssl-dev:ppc64el (3.0.13-0ubuntu2) ... 131s Setting up libmpc3:ppc64el (1.3.1-1) ... 131s Setting up libatomic1:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up autopoint (0.21-14ubuntu1) ... 131s Setting up autoconf (2.71-3) ... 131s Setting up liblzma-dev:ppc64el (5.4.5-0.3) ... 131s Setting up libubsan1:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up dwz (0.15-1) ... 131s Setting up libnsl-dev:ppc64el (1.3.0-3) ... 131s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 131s Setting up libasan8:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up debugedit (1:5.0-5) ... 131s Setting up libsub-override-perl (0.10-1) ... 131s Setting up libtsan2:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up libisl23:ppc64el (0.26-3) ... 131s Setting up libc-dev-bin (2.39-0ubuntu2) ... 131s Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 131s Setting up libdeflate-dev:ppc64el (1.19-1) ... 131s Setting up tabix (1.18+ds-1) ... 131s Setting up libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up liblsan0:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up libitm1:ppc64el (14-20240303-1ubuntu1) ... 131s Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 131s Setting up automake (1:1.16.5-1.3ubuntu1) ... 131s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 131s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 131s Setting up libhts3:ppc64el (1.18+ds-1) ... 131s Setting up gettext (0.21-14ubuntu1) ... 131s Setting up cpp-13 (13.2.0-17ubuntu2) ... 131s Setting up intltool-debian (0.35.0+20060710.6) ... 131s Setting up dh-strip-nondeterminism (1.13.1-1) ... 131s Setting up libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 131s Setting up cpp (4:13.2.0-7ubuntu1) ... 131s Setting up libc6-dev:ppc64el (2.39-0ubuntu2) ... 131s Setting up libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 131s Setting up libbz2-dev:ppc64el (1.0.8-5ubuntu1) ... 131s Setting up po-debconf (1.0.21+nmu1) ... 131s Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 131s Setting up gcc-13 (13.2.0-17ubuntu2) ... 131s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 131s Setting up libtool (2.4.7-7) ... 131s Setting up libhts-dev:ppc64el (1.18+ds-1) ... 131s Setting up g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 131s Setting up dh-autoreconf (20) ... 131s Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 131s Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 131s Setting up g++-13 (13.2.0-17ubuntu2) ... 131s Setting up debhelper (13.14.1ubuntu1) ... 131s Setting up gcc (4:13.2.0-7ubuntu1) ... 131s Setting up g++ (4:13.2.0-7ubuntu1) ... 131s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 131s Setting up build-essential (12.10ubuntu1) ... 131s Setting up autopkgtest-satdep (0) ... 131s Processing triggers for man-db (2.12.0-3) ... 132s Processing triggers for install-info (7.1-3) ... 132s Processing triggers for libc-bin (2.39-0ubuntu2) ... 135s (Reading database ... 75069 files and directories currently installed.) 135s Removing autopkgtest-satdep (0) ... 136s autopkgtest [01:50:23]: test run-unit-test: [----------------------- 136s + pkg=htslib 136s + '[' /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp = '' ']' 136s + cp -aL /usr/share/htslib-test/Makefile /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/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.kzTFrJ/autopkgtest_tmp 136s + cp -aL htslib.pc.in /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp 136s + cp -aL htslib.map /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp 136s + cd /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp 136s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 136s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 136s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 136s + grep sse /proc/cpuinfo 136s + export CFLAGS 136s + make -e check 136s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c 136s : warning: "_FORTIFY_SOURCE" redefined 136s : note: this is the location of the previous definition 136s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c 136s : warning: "_FORTIFY_SOURCE" redefined 136s : note: this is the location of the previous definition 137s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c 137s : warning: "_FORTIFY_SOURCE" redefined 137s : note: this is the location of the previous definition 137s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c 137s : warning: "_FORTIFY_SOURCE" redefined 137s : note: this is the location of the previous definition 138s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c 138s : warning: "_FORTIFY_SOURCE" redefined 138s : note: this is the location of the previous definition 138s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c 139s : warning: "_FORTIFY_SOURCE" redefined 139s : note: this is the location of the previous definition 139s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c 139s : warning: "_FORTIFY_SOURCE" redefined 139s : note: this is the location of the previous definition 141s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c 141s : warning: "_FORTIFY_SOURCE" redefined 141s : note: this is the location of the previous definition 141s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c 141s : warning: "_FORTIFY_SOURCE" redefined 141s : note: this is the location of the previous definition 144s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c 144s : warning: "_FORTIFY_SOURCE" redefined 144s : note: this is the location of the previous definition 144s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c 144s : warning: "_FORTIFY_SOURCE" redefined 144s : note: this is the location of the previous definition 144s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c 144s : warning: "_FORTIFY_SOURCE" redefined 144s : note: this is the location of the previous definition 145s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c 145s : warning: "_FORTIFY_SOURCE" redefined 145s : note: this is the location of the previous definition 145s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c 145s : warning: "_FORTIFY_SOURCE" redefined 145s : note: this is the location of the previous definition 145s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c 145s : warning: "_FORTIFY_SOURCE" redefined 145s : note: this is the location of the previous definition 145s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c 145s : warning: "_FORTIFY_SOURCE" redefined 145s : note: this is the location of the previous definition 146s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c 146s : warning: "_FORTIFY_SOURCE" redefined 146s : note: this is the location of the previous definition 146s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c 146s : warning: "_FORTIFY_SOURCE" redefined 146s : note: this is the location of the previous definition 150s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c 150s : warning: "_FORTIFY_SOURCE" redefined 150s : note: this is the location of the previous definition 150s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c 150s : warning: "_FORTIFY_SOURCE" redefined 150s : note: this is the location of the previous definition 151s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c 151s : warning: "_FORTIFY_SOURCE" redefined 151s : note: this is the location of the previous definition 151s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c 151s : warning: "_FORTIFY_SOURCE" redefined 151s : note: this is the location of the previous definition 151s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c 151s : warning: "_FORTIFY_SOURCE" redefined 151s : note: this is the location of the previous definition 151s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c 151s : warning: "_FORTIFY_SOURCE" redefined 151s : note: this is the location of the previous definition 152s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c 152s : warning: "_FORTIFY_SOURCE" redefined 152s : note: this is the location of the previous definition 157s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c 157s : warning: "_FORTIFY_SOURCE" redefined 157s : note: this is the location of the previous definition 158s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c 158s : warning: "_FORTIFY_SOURCE" redefined 158s : note: this is the location of the previous definition 159s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c 159s : warning: "_FORTIFY_SOURCE" redefined 159s : note: this is the location of the previous definition 161s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c 161s : warning: "_FORTIFY_SOURCE" redefined 161s : note: this is the location of the previous definition 163s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c 163s : warning: "_FORTIFY_SOURCE" redefined 163s : note: this is the location of the previous definition 164s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c 164s : warning: "_FORTIFY_SOURCE" redefined 164s : note: this is the location of the previous definition 164s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c 164s : warning: "_FORTIFY_SOURCE" redefined 164s : note: this is the location of the previous definition 167s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c 167s : warning: "_FORTIFY_SOURCE" redefined 167s : note: this is the location of the previous definition 167s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c 167s : warning: "_FORTIFY_SOURCE" redefined 167s : note: this is the location of the previous definition 167s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c 167s : warning: "_FORTIFY_SOURCE" redefined 167s : note: this is the location of the previous definition 167s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c 167s : warning: "_FORTIFY_SOURCE" redefined 167s : note: this is the location of the previous definition 167s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c 167s : warning: "_FORTIFY_SOURCE" redefined 167s : note: this is the location of the previous definition 167s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c 167s : warning: "_FORTIFY_SOURCE" redefined 167s : note: this is the location of the previous definition 167s 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 167s ranlib libhts.a 167s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c 167s : warning: "_FORTIFY_SOURCE" redefined 167s : note: this is the location of the previous definition 168s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c 168s : warning: "_FORTIFY_SOURCE" redefined 168s : note: this is the location of the previous definition 168s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c 168s : warning: "_FORTIFY_SOURCE" redefined 168s : note: this is the location of the previous definition 169s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c 169s : warning: "_FORTIFY_SOURCE" redefined 169s : note: this is the location of the previous definition 170s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c 170s : warning: "_FORTIFY_SOURCE" redefined 170s : note: this is the location of the previous definition 170s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c 170s : warning: "_FORTIFY_SOURCE" redefined 170s : note: this is the location of the previous definition 170s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c 170s : warning: "_FORTIFY_SOURCE" redefined 170s : note: this is the location of the previous definition 172s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c 172s : warning: "_FORTIFY_SOURCE" redefined 172s : note: this is the location of the previous definition 172s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c 172s : warning: "_FORTIFY_SOURCE" redefined 172s : note: this is the location of the previous definition 175s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c 175s : warning: "_FORTIFY_SOURCE" redefined 175s : note: this is the location of the previous definition 176s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c 176s : warning: "_FORTIFY_SOURCE" redefined 176s : note: this is the location of the previous definition 176s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c 176s : warning: "_FORTIFY_SOURCE" redefined 176s : note: this is the location of the previous definition 176s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c 176s : warning: "_FORTIFY_SOURCE" redefined 176s : note: this is the location of the previous definition 176s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c 176s : warning: "_FORTIFY_SOURCE" redefined 176s : note: this is the location of the previous definition 176s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c 176s : warning: "_FORTIFY_SOURCE" redefined 176s : note: this is the location of the previous definition 176s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c 176s : warning: "_FORTIFY_SOURCE" redefined 176s : note: this is the location of the previous definition 177s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c 177s : warning: "_FORTIFY_SOURCE" redefined 177s : note: this is the location of the previous definition 177s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c 177s : warning: "_FORTIFY_SOURCE" redefined 177s : note: this is the location of the previous definition 181s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c 181s : warning: "_FORTIFY_SOURCE" redefined 181s : note: this is the location of the previous definition 181s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c 181s : warning: "_FORTIFY_SOURCE" redefined 181s : note: this is the location of the previous definition 182s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 182s : warning: "_FORTIFY_SOURCE" redefined 182s : note: this is the location of the previous definition 182s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c 182s : warning: "_FORTIFY_SOURCE" redefined 182s : note: this is the location of the previous definition 182s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c 182s : warning: "_FORTIFY_SOURCE" redefined 182s : note: this is the location of the previous definition 183s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c 183s : warning: "_FORTIFY_SOURCE" redefined 183s : note: this is the location of the previous definition 183s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c 183s : warning: "_FORTIFY_SOURCE" redefined 183s : note: this is the location of the previous definition 187s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c 187s : warning: "_FORTIFY_SOURCE" redefined 187s : note: this is the location of the previous definition 188s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c 188s : warning: "_FORTIFY_SOURCE" redefined 188s : note: this is the location of the previous definition 190s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c 190s : warning: "_FORTIFY_SOURCE" redefined 190s : note: this is the location of the previous definition 192s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c 192s : warning: "_FORTIFY_SOURCE" redefined 192s : note: this is the location of the previous definition 194s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c 194s : warning: "_FORTIFY_SOURCE" redefined 194s : note: this is the location of the previous definition 195s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c 195s : warning: "_FORTIFY_SOURCE" redefined 195s : note: this is the location of the previous definition 195s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c 195s : warning: "_FORTIFY_SOURCE" redefined 195s : note: this is the location of the previous definition 197s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c 197s : warning: "_FORTIFY_SOURCE" redefined 197s : note: this is the location of the previous definition 197s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c 197s : warning: "_FORTIFY_SOURCE" redefined 197s : note: this is the location of the previous definition 198s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c 198s : warning: "_FORTIFY_SOURCE" redefined 198s : note: this is the location of the previous definition 198s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c 198s : warning: "_FORTIFY_SOURCE" redefined 198s : note: this is the location of the previous definition 198s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c 198s : warning: "_FORTIFY_SOURCE" redefined 198s : note: this is the location of the previous definition 198s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c 198s : warning: "_FORTIFY_SOURCE" redefined 198s : note: this is the location of the previous definition 198s 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 198s ln -sf libhts.so libhts.so.3 198s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c 198s : warning: "_FORTIFY_SOURCE" redefined 198s : note: this is the location of the previous definition 198s 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 198s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c 198s : warning: "_FORTIFY_SOURCE" redefined 198s : note: this is the location of the previous definition 199s 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 199s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c 199s : warning: "_FORTIFY_SOURCE" redefined 199s : note: this is the location of the previous definition 199s 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 199s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 199s : warning: "_FORTIFY_SOURCE" redefined 199s : note: this is the location of the previous definition 200s 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 200s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 200s : warning: "_FORTIFY_SOURCE" redefined 200s : note: this is the location of the previous definition 200s 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 200s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c 200s : warning: "_FORTIFY_SOURCE" redefined 200s : note: this is the location of the previous definition 201s 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 201s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c 201s : warning: "_FORTIFY_SOURCE" redefined 201s : note: this is the location of the previous definition 201s 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 201s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c 201s : warning: "_FORTIFY_SOURCE" redefined 201s : note: this is the location of the previous definition 202s 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 202s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c 202s : warning: "_FORTIFY_SOURCE" redefined 202s : note: this is the location of the previous definition 202s 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 202s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c 202s : warning: "_FORTIFY_SOURCE" redefined 202s : note: this is the location of the previous definition 202s 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 202s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c 202s : warning: "_FORTIFY_SOURCE" redefined 202s : note: this is the location of the previous definition 202s 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 202s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup_mod.o test/pileup_mod.c 202s : warning: "_FORTIFY_SOURCE" redefined 202s : note: this is the location of the previous definition 202s 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 202s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c 202s : warning: "_FORTIFY_SOURCE" redefined 202s : note: this is the location of the previous definition 203s 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 203s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c 203s : warning: "_FORTIFY_SOURCE" redefined 203s : note: this is the location of the previous definition 203s 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 204s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c 204s : warning: "_FORTIFY_SOURCE" redefined 204s : note: this is the location of the previous definition 204s 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 204s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c 204s : warning: "_FORTIFY_SOURCE" redefined 204s : note: this is the location of the previous definition 204s 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 204s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_faidx.o test/test_faidx.c 204s : warning: "_FORTIFY_SOURCE" redefined 204s : note: this is the location of the previous definition 204s 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 204s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c 204s : warning: "_FORTIFY_SOURCE" redefined 204s : note: this is the location of the previous definition 205s 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 205s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c 205s : warning: "_FORTIFY_SOURCE" redefined 205s : note: this is the location of the previous definition 205s 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 205s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_mod.o test/test_mod.c 205s : warning: "_FORTIFY_SOURCE" redefined 205s : note: this is the location of the previous definition 205s 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 205s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c 205s : warning: "_FORTIFY_SOURCE" redefined 205s : note: this is the location of the previous definition 205s 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 205s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c 205s : warning: "_FORTIFY_SOURCE" redefined 205s : note: this is the location of the previous definition 205s 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 205s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c 205s : warning: "_FORTIFY_SOURCE" redefined 205s : note: this is the location of the previous definition 206s 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 206s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_time_funcs.o test/test_time_funcs.c 206s : warning: "_FORTIFY_SOURCE" redefined 206s : note: this is the location of the previous definition 206s 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 206s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c 206s : warning: "_FORTIFY_SOURCE" redefined 206s : note: this is the location of the previous definition 206s 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 206s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c 206s : warning: "_FORTIFY_SOURCE" redefined 206s : note: this is the location of the previous definition 206s 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 206s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c 206s : warning: "_FORTIFY_SOURCE" redefined 206s : note: this is the location of the previous definition 206s 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 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c 207s : warning: "_FORTIFY_SOURCE" redefined 207s : note: this is the location of the previous definition 207s 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 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c 207s : warning: "_FORTIFY_SOURCE" redefined 207s : note: this is the location of the previous definition 207s 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 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c 207s : warning: "_FORTIFY_SOURCE" redefined 207s : note: this is the location of the previous definition 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c 207s : warning: "_FORTIFY_SOURCE" redefined 207s : note: this is the location of the previous definition 207s 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 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c 207s : warning: "_FORTIFY_SOURCE" redefined 207s : note: this is the location of the previous definition 207s 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 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c 207s : warning: "_FORTIFY_SOURCE" redefined 207s : note: this is the location of the previous definition 207s 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 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c 207s : warning: "_FORTIFY_SOURCE" redefined 207s : note: this is the location of the previous definition 212s 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 212s sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 212s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 212s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 212s test/hts_endian 212s test/test_expr 212s test/test_kfunc 212s test/test_kstring 212s test/test_str2int 212s test/test_time_funcs 213s test/fieldarith test/fieldarith.sam 213s test/hfile 213s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 213s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 213s fi 213s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 213s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 213s fi 213s test/test_bgzf test/bgziptest.txt 214s test/test-parse-reg -t test/colons.bam 214s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 214s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 214s cd test/faidx && ./test-faidx.sh faidx.tst 214s Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" 214s Expected error: [E::hts_parse_region] Unexpected string "x" after region 214s Expected error: [E::hts_parse_region] Unexpected string "y" after region 214s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 214s Testing faidx... 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 214s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 214s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 214s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 214s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 214s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 214s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 214s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 214s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 214s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 214s 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 214s 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 214s 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 214s 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 214s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 214s 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 214s 214s Expected passes: 25 214s Unexpected passes: 0 214s Expected failures: 0 214s Unexpected failures: 0 214s cd test/sam_filter && ./filter.sh filter.tst 214s Testing sam_filter... 214s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 214s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 214s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 214s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 214s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 214s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 214s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 214s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 214s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 214s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 214s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 214s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 214s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 214s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 214s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 214s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 214s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 214s 214s Expected passes: 17 214s Unexpected passes: 0 214s Expected failures: 0 214s Unexpected failures: 0 214s cd test/tabix && ./test-tabix.sh tabix.tst 214s Testing tabix... 214s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 214s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 214s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 214s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 214s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 214s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 214s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 214s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 214s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 214s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 214s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 214s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 214s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 214s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 214s 214s Expected passes: 14 214s Unexpected passes: 0 214s Expected failures: 0 214s Unexpected failures: 0 214s cd test/mpileup && ./test-pileup.sh mpileup.tst 214s Testing (m)pileup... 214s PASS : $pileup mp_D.sam 214s PASS : $pileup -m mp_D.sam 214s PASS : $pileup mp_DI.sam 214s PASS : $pileup -m mp_DI.sam 214s PASS : $pileup mp_I.sam 214s PASS : $pileup -m mp_I.sam 214s PASS : $pileup mp_P.sam 214s PASS : $pileup -m mp_P.sam 214s PASS : $pileup mp_ID.sam 214s PASS : $pileup -m mp_ID.sam 214s PASS : $pileup mp_N.sam 214s PASS : $pileup -m mp_N.sam 214s PASS : $pileup mp_N2.sam 214s PASS : $pileup -m mp_N2.sam 214s PASS : $pileup c1#pad1.sam 214s PASS : $pileup -m c1#pad1.sam 214s PASS : $pileup c1#pad2.sam 214s PASS : $pileup -m c1#pad2.sam 214s PASS : $pileup c1#pad3.sam 214s PASS : $pileup -m c1#pad3.sam 214s PASS : $pileup -m small.bam 214s 214s Expected passes: 21 214s Unexpected passes: 0 214s Expected failures: 0 214s Unexpected failures: 0 214s cd test/fastq && ./test-fastq.sh 214s Testing fastq support 214s PASS : $tview minimal.fq 214s PASS : $tview minimal.fa 214s PASS : $tview multiline.fq 214s PASS : $tview multiline.fa 214s PASS : $tview -i fastq_aux longline.fq 214s PASS : $tview single.fq 214s PASS : $tview single.fa 214s PASS : $tview -i fastq_aux single.fq 214s PASS : $tview -i fastq_aux single.fa 214s PASS : $tview interleaved.fq 214s PASS : $tview interleaved.fa 214s PASS : $tview -i fastq_aux interleaved.fq 214s PASS : $tview -i fastq_aux interleaved.fa 214s PASS : $tview -i fastq_casava interleaved_casava.fq 214s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 214s PASS : $tview -i fastq_casava interleaved_casava.fa 214s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 214s PASS : $tview -i fastq_casava filter_casava.fq 214s PASS : $tview -i fastq_casava filter_casava.fa 214s PASS : $tview -i fastq_aux r1.fq 214s PASS : $tview -i fastq_aux r2.fq 214s PASS : $tview -i fastq_aux r1.fa 214s PASS : $tview -i fastq_aux r2.fa 214s PASS : $tview -i fastq_name2 name2.fq 214s PASS : $tview -i fastq_name2 name2.fa 214s PASS : $tview -f minimal.sam 214s PASS : $tview -F minimal.sam 214s PASS : $tview -f -o fastq_aux single_aux.sam 214s PASS : $tview -F -o fastq_aux single_aux.sam 214s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 214s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 214s PASS : $tview -f -o fastq_casava inter_casava.sam 214s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 214s PASS : $tview -F -o fastq_casava inter_casava.sam 214s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 214s PASS : $tview -f -o fastq_casava filter_casava.sam 214s PASS : $tview -F -o fastq_casava filter_casava.sam 214s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 214s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 214s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 214s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 214s 214s Expected passes: 41 214s Unexpected passes: 0 214s Expected failures: 0 214s Unexpected failures: 0 214s cd test/base_mods && ./base-mods.sh base-mods.tst 214s Testing base-modifications... 214s PASS : $test_mod MM-chebi.sam 214s PASS : $test_mod MM-double.sam 214s PASS : $test_mod MM-multi.sam 214s PASS : $test_mod MM-explicit.sam 214s PASS : $test_mod -x MM-explicit.sam 214s PASS : $test_mod -f 1 MM-explicit.sam 214s PASS : $test_mod MM-not-all-modded.sam 214s PASS : $pileup_mod < MM-pileup.sam 214s PASS : $pileup_mod < MM-pileup2.sam 214s PASS : $pileup_mod < MM-MNp.sam 214s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 214s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 214s 214s Expected passes: 12 214s Unexpected passes: 0 214s Expected failures: 0 214s Unexpected failures: 0 214s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 214s (Expect trailing 'x' message for " -1,001x") 214s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 214s (Expect trailing 'k' message for "1.5e+3k") 214s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 214s (Expect dropped fraction message for "12.3456k") 214s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 214s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 214s (Expect invalid numeric message for "A") 214s [W::hts_parse_decimal] Invalid numeric value A[truncated] 214s (Expect invalid numeric message for "G") 214s [W::hts_parse_decimal] Invalid numeric value G[truncated] 214s (Expect invalid numeric message for " +/-") 214s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 214s (Expect invalid numeric message for " -.e+9999") 214s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 214s test/test-regidx 214s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 215s bgzip round-trip no threads: .. ok 215s 215s bgzip text mode round-trip no threads: .. ok 215s 215s bgzip -b no threads: .. ok 215s 215s bgzip -b -I no threads: .. ok 215s 215s bgzip round-trip 4 threads: .. ok 215s 215s bgzip text mode round-trip 4 threads: .. ok 215s 215s bgzip -b 4 threads: .. ok 215s 215s bgzip -b -I 4 threads: .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/Mgs99Ylme7/index.bam.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.bam 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.bam 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/Mgs99Ylme7/index.bam.bai /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.bam 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -b /tmp/Mgs99Ylme7/index.bam 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/Mgs99Ylme7/index.sam.gz.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.sam.gz 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.sam.gz 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/Mgs99Ylme7/index.sam.gz.bai /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.sam.gz 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -b /tmp/Mgs99Ylme7/index.sam.gz 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/Mgs99Ylme7/index.sam.gz.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index_dos.sam > /tmp/Mgs99Ylme7/index.sam.gz 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.sam.gz 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/Mgs99Ylme7/index.sam.gz.bai /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index_dos.sam > /tmp/Mgs99Ylme7/index.sam.gz 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -b /tmp/Mgs99Ylme7/index.sam.gz 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/Mgs99Ylme7/index.cram.crai /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.cram 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index /tmp/Mgs99Ylme7/index.cram 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/Mgs99Ylme7/index.bcf.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.vcf > /tmp/Mgs99Ylme7/index.bcf 215s .. ok 215s 215s test_index: 215s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.bcf 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/Mgs99Ylme7/index.vcf.gz.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.vcf > /tmp/Mgs99Ylme7/index.vcf.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.vcf.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/Mgs99Ylme7/index.vcf.gz.tbi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.vcf > /tmp/Mgs99Ylme7/index.vcf.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -t /tmp/Mgs99Ylme7/index.vcf.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/tabix /tmp/Mgs99Ylme7/index.vcf.gz##idx##/tmp/Mgs99Ylme7/index.vcf.gz.tbi 1:10000060-10000060 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/Mgs99Ylme7/index2.bam 1:1000000-1000000 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/Mgs99Ylme7/index2.bam 1:2000000-2000000 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/Mgs99Ylme7/index2.bam 2:1000000-1000000 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/Mgs99Ylme7/index2.bam 2:2000000-2000000 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Mgs99Ylme7/index.bam.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.bam 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.bam 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/Mgs99Ylme7/index.bam.bai /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.bam 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -b /tmp/Mgs99Ylme7/index.bam 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Mgs99Ylme7/index.sam.gz.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.sam.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.sam.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Mgs99Ylme7/index.sam.gz.bai /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.sam.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -b /tmp/Mgs99Ylme7/index.sam.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Mgs99Ylme7/index.sam.gz.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index_dos.sam > /tmp/Mgs99Ylme7/index.sam.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.sam.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Mgs99Ylme7/index.sam.gz.bai /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index_dos.sam > /tmp/Mgs99Ylme7/index.sam.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -b /tmp/Mgs99Ylme7/index.sam.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/Mgs99Ylme7/index.cram.crai /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.sam > /tmp/Mgs99Ylme7/index.cram 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index /tmp/Mgs99Ylme7/index.cram 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Mgs99Ylme7/index.bcf.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.vcf > /tmp/Mgs99Ylme7/index.bcf 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.bcf 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Mgs99Ylme7/index.vcf.gz.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.vcf > /tmp/Mgs99Ylme7/index.vcf.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c /tmp/Mgs99Ylme7/index.vcf.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Mgs99Ylme7/index.vcf.gz.tbi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/index.vcf > /tmp/Mgs99Ylme7/index.vcf.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -t /tmp/Mgs99Ylme7/index.vcf.gz 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/tabix /tmp/Mgs99Ylme7/index.vcf.gz##idx##/tmp/Mgs99Ylme7/index.vcf.gz.tbi 1:10000060-10000060 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/Mgs99Ylme7/index2.bam 1:1000000-1000000 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/Mgs99Ylme7/index2.bam 1:2000000-2000000 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/Mgs99Ylme7/index2.bam 2:1000000-1000000 216s .. ok 216s 216s test_index: 216s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/Mgs99Ylme7/index2.bam 2:2000000-2000000 216s .. ok 216s 216s test_view testing multi-ref CRAM modes: 216s ./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 216s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 216s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 216s ./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 216s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 216s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 216s ./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 216s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 216s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 216s .. ok 216s 216s test_view testing multi-ref CRAM modes: 216s ./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 216s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 216s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 216s ./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 216s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 216s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 216s ./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 217s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 217s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 217s .. ok 217s 217s test_view testing auxf#values.sam, ref auxf.fa: 217s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 217s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 217s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 217s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 217s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 217s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 217s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 217s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 217s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 217s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 217s .. ok 217s 217s test_view testing c1#bounds.sam, ref c1.fa: 217s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 217s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 217s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 217s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 217s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 217s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 217s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 217s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing c1#clip.sam, ref c1.fa: 217s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 217s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 217s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 217s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 217s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 217s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 217s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 217s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing c1#noseq.sam, ref c1.fa: 217s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 217s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 217s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 217s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 217s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 217s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 217s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 217s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing c1#pad1.sam, ref c1.fa: 217s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 217s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 217s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 217s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 217s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 217s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 217s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 217s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing c1#pad2.sam, ref c1.fa: 217s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 217s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 217s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 217s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 217s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 217s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 217s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 217s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing c1#pad3.sam, ref c1.fa: 217s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 217s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 217s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 217s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 217s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 217s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 217s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 217s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing c1#unknown.sam, ref c1.fa: 217s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 217s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 217s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 217s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 217s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 217s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 217s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 217s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing c2#pad.sam, ref c2.fa: 217s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 217s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 217s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 217s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 217s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 217s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 217s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 217s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing ce#1.sam, ref ce.fa: 217s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 217s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 217s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 217s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 217s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 217s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 217s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 217s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 217s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 217s .. ok 217s 217s test_view testing ce#1000.sam, ref ce.fa: 217s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 217s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 217s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 217s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 217s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 217s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 218s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 218s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 218s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 218s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 218s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 218s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 218s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 218s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 218s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 218s .. ok 218s 218s test_view testing ce#2.sam, ref ce.fa: 218s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 218s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 218s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 218s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 218s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 218s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 218s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 218s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 218s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 218s .. ok 218s 218s test_view testing ce#5.sam, ref ce.fa: 218s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 218s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 218s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 218s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 218s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 218s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 218s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 218s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 218s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 218s .. ok 218s 218s test_view testing ce#5b.sam, ref ce.fa: 218s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 218s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 218s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 218s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 218s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 218s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 218s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 218s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 218s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 218s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 218s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 218s .. ok 218s 218s test_view testing ce#large_seq.sam, ref ce.fa: 218s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 218s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 218s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 218s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 218s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 218s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 218s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 218s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 218s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 218s .. ok 218s 218s test_view testing ce#supp.sam, ref ce.fa: 218s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 218s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 218s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 218s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 218s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 218s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 218s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 218s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 218s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 218s .. ok 218s 218s test_view testing ce#tag_depadded.sam, ref ce.fa: 218s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 218s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 218s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 218s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 218s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 218s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 218s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 218s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 218s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 218s .. ok 218s 218s test_view testing ce#tag_padded.sam, ref ce.fa: 218s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 219s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 219s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 219s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 219s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 219s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 219s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 219s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing ce#unmap.sam, ref ce.fa: 219s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 219s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 219s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 219s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 219s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 219s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 219s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 219s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing ce#unmap1.sam, ref ce.fa: 219s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 219s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 219s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 219s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 219s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 219s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 219s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 219s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing ce#unmap2.sam, ref ce.fa: 219s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 219s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 219s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 219s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 219s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 219s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 219s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 219s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing md#1.sam, ref md.fa: 219s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 219s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 219s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 219s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 219s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 219s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 219s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 219s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing xx#blank.sam, ref xx.fa: 219s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 219s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 219s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 219s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 219s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 219s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 219s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 219s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing xx#large_aux.sam, ref xx.fa: 219s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 219s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 219s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 219s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 219s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 219s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 219s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 219s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 219s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 219s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 219s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 219s .. ok 219s 219s test_view testing xx#large_aux2.sam, ref xx.fa: 219s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 219s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 219s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 219s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 219s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 219s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 219s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 219s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing xx#MD.sam, ref xx.fa: 219s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 219s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 219s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 219s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 219s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 219s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 219s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 219s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing xx#MD2.sam, ref xx.fa: 219s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 219s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 219s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 219s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 219s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 219s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 219s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 219s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 219s .. ok 219s 219s test_view testing xx#minimal.sam, ref xx.fa: 219s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 219s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 219s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 219s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 219s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 219s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 219s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 219s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 219s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 220s .. ok 220s 220s test_view testing xx#pair.sam, ref xx.fa: 220s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 220s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 220s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 220s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 220s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 220s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 220s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 220s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 220s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 220s .. ok 220s 220s test_view testing xx#repeated.sam, ref xx.fa: 220s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 220s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 220s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 220s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 220s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 220s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 220s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 220s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 220s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 220s .. ok 220s 220s test_view testing xx#rg.sam, ref xx.fa: 220s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 220s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 220s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 220s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 220s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 220s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 220s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 220s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 220s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 220s .. ok 220s 220s test_view testing xx#tlen.sam, ref xx.fa: 220s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 220s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 220s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 220s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 220s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 220s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 220s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 220s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 220s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 220s .. ok 220s 220s test_view testing xx#tlen2.sam, ref xx.fa: 220s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 220s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 220s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 220s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 220s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 220s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 220s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 220s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 220s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 220s .. ok 220s 220s test_view testing xx#triplet.sam, ref xx.fa: 220s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 220s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 220s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 220s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 220s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 220s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 220s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 220s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 220s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 220s .. ok 220s 220s test_view testing xx#unsorted.sam, ref xx.fa: 220s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 220s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 220s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 220s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 220s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 220s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 220s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 220s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 220s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 220s .. ok 220s 220s test_view testing embed_ref=2: 220s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 220s [W::cram_get_ref] Failed to populate reference for id 0 220s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 220s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 220s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 220s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 220s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 220s .. ok 220s 220s test_view testing region queries: 220s ./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 220s ./compare_sam.pl range.tmp range.out 220s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 220s ./compare_sam.pl range.tmp range.out 220s .. ok 220s 220s test_view testing BAM files with absent @SQ lines: 220s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 220s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 220s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 220s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 220s .. ok 220s 220s test_view testing large (> 2Gbases) positions: 220s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 220s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 220s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 220s test_view: 220s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 220s .. ok 220s 220s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 220s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 220s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 220s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 220s .. ok 220s 220s test_view testing auxf#values.sam, ref auxf.fa: 220s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 220s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 220s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 220s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 220s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 220s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 220s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 220s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 220s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 220s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 220s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 220s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 220s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 220s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 220s This is a technology demonstration that should not be used for archival data. 220s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 220s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 221s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 221s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 221s .. ok 221s 221s test_view testing c1#bounds.sam, ref c1.fa: 221s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 221s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 221s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 221s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 221s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 221s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 221s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 221s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 221s .. ok 221s 221s test_view testing c1#clip.sam, ref c1.fa: 221s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 221s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 221s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 221s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 221s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 221s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 221s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 221s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 221s .. ok 221s 221s test_view testing c1#noseq.sam, ref c1.fa: 221s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 221s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 221s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 221s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 221s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 221s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 221s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 221s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 221s .. ok 221s 221s test_view testing c1#pad1.sam, ref c1.fa: 221s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 221s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 221s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 221s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 221s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 221s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 221s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 221s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 221s .. ok 221s 221s test_view testing c1#pad2.sam, ref c1.fa: 221s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 221s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 221s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 221s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 221s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 221s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 221s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 221s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 221s .. ok 221s 221s test_view testing c1#pad3.sam, ref c1.fa: 221s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 221s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 221s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 221s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 221s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 221s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 221s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 221s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 221s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 221s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 221s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 221s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 221s This is a technology demonstration that should not be used for archival data. 221s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 221s .. ok 221s 221s test_view testing c1#unknown.sam, ref c1.fa: 221s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 221s ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 221s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 221s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 221s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 221s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 221s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 221s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 221s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 222s .. ok 222s 222s test_view testing c2#pad.sam, ref c2.fa: 222s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 222s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 222s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 222s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 222s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 222s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 222s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 222s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 222s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 222s .. ok 222s 222s test_view testing ce#1.sam, ref ce.fa: 222s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 222s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 222s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 222s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 222s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 222s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 222s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 222s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 222s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 222s .. ok 222s 222s test_view testing ce#1000.sam, ref ce.fa: 222s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 222s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 222s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 222s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 222s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 222s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 222s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 222s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 222s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 222s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 222s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 222s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 222s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 222s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 222s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 222s ./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 222s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 222s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 222s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 222s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 222s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 222s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 222s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 222s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 222s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 223s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 223s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 223s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 223s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 223s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 223s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 223s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 223s This is a technology demonstration that should not be used for archival data. 223s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 223s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 223s .. ok 223s 223s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 223s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 223s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 223s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 223s ./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 223s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 223s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 223s ./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 223s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 223s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 223s .. ok 223s 223s test_view testing ce#2.sam, ref ce.fa: 223s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 223s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 223s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 223s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 223s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 223s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 223s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 223s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 223s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 223s .. ok 223s 223s test_view testing ce#5.sam, ref ce.fa: 223s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 223s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 223s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 223s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 223s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 223s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 223s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 223s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 223s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 223s ./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 223s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 223s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 224s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 224s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 224s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 224s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 224s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 224s This is a technology demonstration that should not be used for archival data. 224s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 224s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 224s .. ok 224s 224s test_view testing ce#5b.sam, ref ce.fa: 224s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 224s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 224s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 224s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 224s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 224s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 224s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 224s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 224s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 224s ./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 224s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 224s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 224s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 224s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 224s .. ok 224s 224s test_view testing ce#large_seq.sam, ref ce.fa: 224s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 224s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 224s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 224s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 224s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 224s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 224s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 224s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 224s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 224s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 225s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 225s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 225s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 225s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 225s This is a technology demonstration that should not be used for archival data. 225s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 225s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 225s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 225s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 225s This is a technology demonstration that should not be used for archival data. 225s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 225s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 225s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 225s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 225s This is a technology demonstration that should not be used for archival data. 226s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 226s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 226s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 226s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 226s This is a technology demonstration that should not be used for archival data. 226s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 226s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 226s .. ok 226s 226s test_view testing ce#supp.sam, ref ce.fa: 226s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 226s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 226s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 226s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 226s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 226s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 226s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 226s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 226s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 226s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 226s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 226s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 226s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 226s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 226s This is a technology demonstration that should not be used for archival data. 226s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 226s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 226s .. ok 226s 226s test_view testing ce#tag_depadded.sam, ref ce.fa: 226s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 226s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 226s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 226s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 226s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 226s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 226s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 226s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 226s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 226s .. ok 226s 226s test_view testing ce#tag_padded.sam, ref ce.fa: 226s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 227s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 227s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 227s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 227s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 227s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 227s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 227s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 227s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 227s .. ok 227s 227s test_view testing ce#unmap.sam, ref ce.fa: 227s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 227s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 227s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 227s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 227s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 227s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 227s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 227s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 227s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 227s ./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 227s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 227s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 227s .. ok 227s 227s test_view testing ce#unmap1.sam, ref ce.fa: 227s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 227s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 227s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 227s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 227s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 227s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 227s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 227s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 227s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 227s ./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 227s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 227s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 227s .. ok 227s 227s test_view testing ce#unmap2.sam, ref ce.fa: 227s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 227s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 227s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 227s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 227s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 227s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 227s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 227s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 227s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 227s ./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 227s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 227s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 227s .. ok 227s 227s test_view testing md#1.sam, ref md.fa: 227s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 227s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 227s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 227s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 227s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 227s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 227s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 227s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 227s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 227s .. ok 227s 227s test_view testing xx#blank.sam, ref xx.fa: 227s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 227s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 227s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 227s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 227s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 227s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 227s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 227s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 227s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 227s ./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 227s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 227s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 227s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 227s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 227s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 227s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 227s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 227s This is a technology demonstration that should not be used for archival data. 227s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 227s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 227s .. ok 227s 227s test_view testing xx#large_aux.sam, ref xx.fa: 227s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 227s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 228s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 228s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 228s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 228s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 228s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 228s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 228s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 228s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 228s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 228s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 228s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 228s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 228s This is a technology demonstration that should not be used for archival data. 228s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 228s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 228s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 228s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 228s This is a technology demonstration that should not be used for archival data. 228s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 228s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 228s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 228s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 228s This is a technology demonstration that should not be used for archival data. 228s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 228s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 228s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 228s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 228s This is a technology demonstration that should not be used for archival data. 229s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 229s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 229s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 229s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 229s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 229s .. ok 229s 229s test_view testing xx#large_aux2.sam, ref xx.fa: 229s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 229s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 229s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 229s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 229s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 229s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 229s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 229s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 229s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 229s .. ok 229s 229s test_view testing xx#MD.sam, ref xx.fa: 229s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 229s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 229s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 229s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 229s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 229s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 229s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 229s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 229s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 229s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 229s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 229s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 229s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 229s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 229s This is a technology demonstration that should not be used for archival data. 229s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 229s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 229s .. ok 229s 229s test_view testing xx#MD2.sam, ref xx.fa: 229s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 229s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 229s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 229s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 229s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 229s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 229s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 229s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 229s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 229s .. ok 229s 229s test_view testing xx#minimal.sam, ref xx.fa: 229s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 229s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 229s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 229s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 229s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 229s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 229s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 229s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 229s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 229s ./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 229s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 229s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 229s .. ok 229s 229s test_view testing xx#pair.sam, ref xx.fa: 229s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 229s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 230s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 230s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 230s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 230s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 230s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 230s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 230s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 230s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 230s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 230s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 230s This is a technology demonstration that should not be used for archival data. 230s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 230s .. ok 230s 230s test_view testing xx#repeated.sam, ref xx.fa: 230s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 230s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 230s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 230s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 230s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 230s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 230s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 230s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 230s .. ok 230s 230s test_view testing xx#rg.sam, ref xx.fa: 230s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 230s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 230s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 230s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 230s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 230s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 230s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 230s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 230s .. ok 230s 230s test_view testing xx#tlen.sam, ref xx.fa: 230s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 230s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 230s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 230s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 230s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 230s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 230s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 230s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 230s ./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 230s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 230s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 230s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 230s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 230s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 230s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 230s This is a technology demonstration that should not be used for archival data. 230s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 230s .. ok 230s 230s test_view testing xx#tlen2.sam, ref xx.fa: 230s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 230s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 230s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 230s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 230s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 230s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 230s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 230s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 230s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 230s ./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 230s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 230s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 230s .. ok 230s 230s test_view testing xx#triplet.sam, ref xx.fa: 230s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 231s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 231s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 231s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 231s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 231s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 231s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 231s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 231s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 231s ./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 231s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 231s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 231s .. ok 231s 231s test_view testing xx#unsorted.sam, ref xx.fa: 231s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 231s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 231s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 231s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 231s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 231s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 231s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 231s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 231s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 231s .. ok 231s 231s test_view testing embed_ref=2: 231s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 231s [W::cram_get_ref] Failed to populate reference for id 0 231s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 231s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 231s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 231s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 231s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 231s .. ok 231s 231s test_view testing region queries: 231s ./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 231s ./compare_sam.pl range.tmp range.out 231s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 231s ./compare_sam.pl range.tmp range.out 231s .. ok 231s 231s test_view testing BAM files with absent @SQ lines: 231s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 231s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 231s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 231s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 231s .. ok 231s 231s test_view testing large (> 2Gbases) positions: 231s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 231s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 231s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 231s test_view: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 231s .. ok 231s 231s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 231s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 231s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 231s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 231s .. ok 231s 231s 231s test_MD testing xx#MD.sam, ref xx.fa: 231s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 231s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 231s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 231s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 231s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 231s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 231s Checking for MD/NM in xx#MD.sam 231s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 231s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 231s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 231s .. ok 231s 231s 231s test_MD testing xx#MD2.sam, ref xx.fa: 231s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 231s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 231s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 231s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 231s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 231s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 231s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 231s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 231s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 231s .. ok 231s 231s test_vcf_api: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-vcf-api /tmp/Mgs99Ylme7/test-vcf-api.bcf 231s [W::bcf_record_check] Bad BCF record at 1:1: No REF allele 231s [E::bcf_index_build3] TBI indices for BCF files are not supported 231s [E::idx_find_and_load] Could not retrieve index file for '/tmp/Mgs99Ylme7/test-vcf-api.bcf' 231s .. ok 231s 231s test_bcf2vcf: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/tabix/vcf_file.bcf 231s .. ok 231s 231s test_vcf_sweep: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-vcf-sweep /tmp/Mgs99Ylme7/test-vcf-api.bcf 231s .. ok 231s 231s test_vcf_various: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 231s .. ok 231s 231s test_vcf_various: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/formatcols.vcf 231s .. ok 231s 231s test_vcf_various: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/noroundtrip.vcf 231s .. ok 231s 231s test_vcf_various: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/formatmissing.vcf 231s .. ok 231s 231s test_vcf_various: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/vcf_meta_meta.vcf 231s .. ok 231s 231s test_vcf_various: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 231s .. ok 231s 231s test-bcf-sr: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 74452500 231s .. ok 231s 231s test-bcf-sr: 231s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 34270147 232s .. ok 232s 232s test-bcf-sr: 232s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 11108528 232s .. ok 232s 232s test-bcf-sr: 232s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 42233895 232s .. ok 232s 232s test-bcf-sr: 232s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 8111117 232s .. ok 232s 232s test-bcf-sr: 232s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 85644070 232s .. ok 232s 232s test-bcf-sr: 232s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 49879942 232s .. ok 232s 232s test-bcf-sr: 232s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 47881429 233s .. ok 233s 233s test-bcf-sr: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 69081244 233s .. ok 233s 233s test-bcf-sr: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/Mgs99Ylme7 -s 83459376 233s .. ok 233s 233s test_bcf_sr_no_index: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/Mgs99Ylme7/no_index_1.err 233s .. ok 233s 233s test_bcf_sr_no_index: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/Mgs99Ylme7/no_index_2.out 2> /tmp/Mgs99Ylme7/no_index_2.err (expected fail) 233s .. ok 233s 233s test_bcf_sr_no_index: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/Mgs99Ylme7/no_index_3.out 2> /tmp/Mgs99Ylme7/no_index_3.err (expected fail) 233s .. ok 233s 233s test_bcf_sr_no_index: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/Mgs99Ylme7/no_index_4.out 2> /tmp/Mgs99Ylme7/no_index_4.err (expected fail) 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -b -p /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf -x /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_1.out.vcf -r '1' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_2.out.vcf -r '1:1-2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_4.out.vcf -r '1:1-1' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_5.out.vcf -r '{1:1}' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf (expected fail) 233s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 233s Failed to set regions 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_14.out.vcf -t '1' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_15.out.vcf -t '1:1-2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_17.out.vcf -t '1:1-1' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_18.out.vcf -t '{1:1}' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf 233s .. ok 233s 233s test_bcf_sr_range: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/Mgs99Ylme7/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/Mgs99Ylme7/weird-chr-names.vcf.bcf (expected fail) 233s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 233s Failed to set targets 233s .. ok 233s 233s test_command: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf-translate - 233s .. ok 233s 233s test_convert_padded_header: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/Mgs99Ylme7/headernul0.bam 233s .. ok 233s 233s test_convert_padded_header: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/Mgs99Ylme7/headernul1.bam 233s .. ok 233s 233s test_convert_padded_header: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/Mgs99Ylme7/headernul678.bam 233s .. ok 233s 233s test_rebgzip: Alternate zlib/deflate library detected 233s test_rebgzip: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/bgziptest.txt 233s .. ok 233s 233s test-logging: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-logging.pl 233s .. ok 233s 233s test_plugin_loading: 233s HTS_PATH=/tmp/autopkgtest.kzTFrJ/autopkgtest_tmp /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn01.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn01.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn01.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02-r.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02_exp.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn02_exp-a.sam -o - 233s .. ok 233s 233s test_realn: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/realn03.sam -o - 233s .. ok 233s 233s test-bcf_set_variant_type: 233s /tmp/autopkgtest.kzTFrJ/autopkgtest_tmp/test/test-bcf_set_variant_type 233s .. ok 233s 233s 233s Number of tests: 233s total .. 211 233s passed .. 211 233s failed .. 0 233s 233s + echo PASS 233s PASS 233s autopkgtest [01:52:00]: test run-unit-test: -----------------------] 234s autopkgtest [01:52:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 234s run-unit-test PASS 234s autopkgtest [01:52:01]: @@@@@@@@@@@@@@@@@@@@ summary 234s run-unit-test PASS 259s Creating nova instance adt-noble-ppc64el-htslib-20240319-014807-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240319.img (UUID 6e7a6c13-d651-45a1-a24f-48d9d59effd9)...