0s autopkgtest [06:37:12]: starting date and time: 2024-03-24 06:37:12+0000 0s autopkgtest [06:37:12]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [06:37:12]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jv4kol9m/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl,src:orthanc-python --apt-upgrade htslib --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2 orthanc-python/4.1+ds-2build3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-14.secgroup --name adt-noble-s390x-htslib-20240324-063712-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 146s autopkgtest [06:39:38]: testbed dpkg architecture: s390x 147s autopkgtest [06:39:39]: testbed apt version: 2.7.12 147s autopkgtest [06:39:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 147s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 148s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 148s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4009 kB] 148s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 148s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 148s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [691 kB] 148s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 148s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 148s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 148s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4191 kB] 148s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 148s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.8 kB] 148s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 151s Fetched 9625 kB in 2s (3918 kB/s) 151s Reading package lists... 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Calculating upgrade... 154s The following packages will be REMOVED: 154s libssl3 154s The following NEW packages will be installed: 154s libssl3t64 154s The following packages have been kept back: 154s curl 154s The following packages will be upgraded: 154s openssl 154s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 154s Need to get 2685 kB of archives. 154s After this operation, 239 kB of additional disk space will be used. 154s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 154s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 155s Fetched 2685 kB in 1s (3857 kB/s) 155s (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 ... 52170 files and directories currently installed.) 155s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 155s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 155s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 155s wget depends on libssl3 (>= 3.0.0). 155s tnftp depends on libssl3 (>= 3.0.0). 155s tcpdump depends on libssl3 (>= 3.0.0). 155s systemd-resolved depends on libssl3 (>= 3.0.0). 155s systemd depends on libssl3 (>= 3.0.0). 155s sudo depends on libssl3 (>= 3.0.0). 155s s390-tools depends on libssl3 (>= 3.0.0). 155s rsync depends on libssl3 (>= 3.0.0). 155s python3-cryptography depends on libssl3 (>= 3.0.0). 155s openssh-server depends on libssl3 (>= 3.0.10). 155s openssh-client depends on libssl3 (>= 3.0.10). 155s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 155s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 155s libssh-4:s390x depends on libssl3 (>= 3.0.0). 155s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 155s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 155s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 155s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 155s libnvme1 depends on libssl3 (>= 3.0.0). 155s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 155s libkmod2:s390x depends on libssl3 (>= 3.0.0). 155s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 155s libcurl4:s390x depends on libssl3 (>= 3.0.0). 155s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 155s kmod depends on libssl3 (>= 3.0.0). 155s dhcpcd-base depends on libssl3 (>= 3.0.0). 155s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 155s 155s (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 ... 52170 files and directories currently installed.) 155s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 155s Selecting previously unselected package libssl3t64:s390x. 155s (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 ... 52159 files and directories currently installed.) 155s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 155s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 155s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 155s Setting up openssl (3.0.13-0ubuntu2) ... 155s Processing triggers for man-db (2.12.0-3) ... 156s Processing triggers for libc-bin (2.39-0ubuntu6) ... 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 156s Unknown architecture, assuming PC-style ttyS0 156s sh: Attempting to set up Debian/Ubuntu apt sources automatically 156s sh: Distribution appears to be Ubuntu 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s eatmydata is already the newest version (131-1). 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s dbus is already the newest version (1.14.10-4ubuntu1). 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s rng-tools-debian is already the newest version (2.4). 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s The following packages will be REMOVED: 159s cloud-init* python3-configobj* python3-debconf* 159s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 159s After this operation, 3256 kB disk space will be freed. 159s (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 ... 52172 files and directories currently installed.) 159s Removing cloud-init (24.1.2-0ubuntu1) ... 159s Removing python3-configobj (5.0.8-3) ... 159s Removing python3-debconf (1.5.86) ... 159s Processing triggers for man-db (2.12.0-3) ... 160s (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 ... 51783 files and directories currently installed.) 160s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 160s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 160s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 160s invoke-rc.d: policy-rc.d denied execution of try-restart. 160s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s linux-generic is already the newest version (6.8.0-11.11+1). 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 161s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 161s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 163s Reading package lists... 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Calculating upgrade... 163s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s autopkgtest [06:39:56]: rebooting testbed after setup commands that affected boot 183s autopkgtest [06:40:15]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 187s autopkgtest [06:40:19]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 191s Get:1 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (dsc) [2437 B] 191s Get:2 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (tar) [1469 kB] 191s Get:3 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (diff) [20.1 kB] 191s gpgv: Signature made Tue Nov 7 20:35:25 2023 UTC 191s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 191s gpgv: issuer "emollier@debian.org" 191s gpgv: Can't check signature: No public key 191s dpkg-source: warning: cannot verify inline signature for ./htslib_1.18+ds-1.dsc: no acceptable signature found 191s autopkgtest [06:40:23]: testing package htslib version 1.18+ds-1 192s autopkgtest [06:40:24]: build not needed 196s autopkgtest [06:40:28]: test run-unit-test: preparing testbed 202s Reading package lists... 202s Building dependency tree... 202s Reading state information... 202s Starting pkgProblemResolver with broken count: 1 202s Starting 2 pkgProblemResolver with broken count: 1 202s Investigating (0) libssl3t64:s390x < 3.0.13-0ubuntu2 @ii mK Ib > 202s Broken libssl3t64:s390x Breaks on libssl3:s390x < none -> 3.0.10-1ubuntu4 @un pumN > (< 3.0.13-0ubuntu2) 202s Considering libssl3:s390x 150 as a solution to libssl3t64:s390x 146 202s Removing libssl3t64:s390x rather than change libssl3:s390x 202s Investigating (0) openssl:s390x < 3.0.13-0ubuntu2 @ii mK Ib > 202s Broken openssl:s390x Depends on libssl3t64:s390x < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 202s Considering libssl3t64:s390x 146 as a solution to openssl:s390x 13 202s Removing openssl:s390x rather than change libssl3t64:s390x 202s Investigating (1) ca-certificates:s390x < 20240203 @ii mK Ib > 202s Broken ca-certificates:s390x Depends on openssl:s390x < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 202s Considering openssl:s390x 13 as a solution to ca-certificates:s390x 143 202s Added openssl:s390x to the remove list 202s Fixing ca-certificates:s390x via keep of openssl:s390x 202s Investigating (1) openssl:s390x < 3.0.13-0ubuntu2 @ii mK Ib > 202s Broken openssl:s390x Depends on libssl3t64:s390x < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 202s Considering libssl3t64:s390x 146 as a solution to openssl:s390x 13 202s Removing openssl:s390x rather than change libssl3t64:s390x 202s Investigating (2) ca-certificates:s390x < 20240203 @ii mK Ib > 202s Broken ca-certificates:s390x Depends on openssl:s390x < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 202s Considering openssl:s390x 13 as a solution to ca-certificates:s390x 143 202s Added openssl:s390x to the remove list 202s Fixing ca-certificates:s390x via keep of openssl:s390x 202s Investigating (2) openssl:s390x < 3.0.13-0ubuntu2 @ii mK Ib > 202s Broken openssl:s390x Depends on libssl3t64:s390x < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 202s Considering libssl3t64:s390x 146 as a solution to openssl:s390x 143 202s Removing openssl:s390x rather than change libssl3t64:s390x 202s Investigating (3) ca-certificates:s390x < 20240203 @ii mK Ib > 202s Broken ca-certificates:s390x Depends on openssl:s390x < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 202s Considering openssl:s390x 146 as a solution to ca-certificates:s390x 143 202s Removing ca-certificates:s390x rather than change openssl:s390x 202s Investigating (3) python3-httplib2:s390x < 0.20.4-3 @ii mK Ib > 202s Broken python3-httplib2:s390x Depends on ca-certificates:s390x < 20240203 @ii mR > 202s Considering ca-certificates:s390x 146 as a solution to python3-httplib2:s390x 6 202s Removing python3-httplib2:s390x rather than change ca-certificates:s390x 202s Investigating (3) python3-apport:s390x < 2.28.0-0ubuntu1 @ii mK Ib > 202s Broken python3-apport:s390x Depends on python3-httplib2:s390x < 0.20.4-3 @ii mR > 202s Considering python3-httplib2:s390x 146 as a solution to python3-apport:s390x 4 202s Removing python3-apport:s390x rather than change python3-httplib2:s390x 202s Investigating (3) ssh-import-id:s390x < 5.11-0ubuntu2 @ii mK Ib > 202s Broken ssh-import-id:s390x Depends on ca-certificates:s390x < 20240203 @ii mR > 202s Considering ca-certificates:s390x 146 as a solution to ssh-import-id:s390x 3 202s Removing ssh-import-id:s390x rather than change ca-certificates:s390x 202s Investigating (3) python3-certifi:s390x < 2023.11.17-1 @ii mK Ib > 202s Broken python3-certifi:s390x Depends on ca-certificates:s390x < 20240203 @ii mR > 202s Considering ca-certificates:s390x 146 as a solution to python3-certifi:s390x 2 202s Removing python3-certifi:s390x rather than change ca-certificates:s390x 202s Investigating (3) python3-launchpadlib:s390x < 1.11.0-6 @ii mK Ib > 202s Broken python3-launchpadlib:s390x Depends on python3-httplib2:s390x < 0.20.4-3 @ii mR > 202s Considering python3-httplib2:s390x 146 as a solution to python3-launchpadlib:s390x 2 202s Removing python3-launchpadlib:s390x rather than change python3-httplib2:s390x 202s Investigating (3) python3-lazr.restfulclient:s390x < 0.14.6-1 @ii mK Ib > 202s Broken python3-lazr.restfulclient:s390x Depends on python3-httplib2:s390x < 0.20.4-3 @ii mR > (>= 0.7.7) 202s Considering python3-httplib2:s390x 146 as a solution to python3-lazr.restfulclient:s390x 2 202s Removing python3-lazr.restfulclient:s390x rather than change python3-httplib2:s390x 202s Investigating (3) python3-requests:s390x < 2.31.0+dfsg-1ubuntu1 @ii mK Ib > 202s Broken python3-requests:s390x Depends on python3-certifi:s390x < 2023.11.17-1 @ii mR > 202s Considering python3-certifi:s390x 146 as a solution to python3-requests:s390x 2 202s Removing python3-requests:s390x rather than change python3-certifi:s390x 202s Investigating (4) apport:s390x < 2.28.0-0ubuntu1 @ii mK Ib > 202s Broken apport:s390x Depends on python3-apport:s390x < 2.28.0-0ubuntu1 @ii mR > (>= 2.28.0-0ubuntu1) 202s Considering python3-apport:s390x 146 as a solution to apport:s390x 6 202s Removing apport:s390x rather than change python3-apport:s390x 202s Investigating (4) apport-core-dump-handler:s390x < 2.28.0-0ubuntu1 @ii mK Ib > 202s Broken apport-core-dump-handler:s390x Depends on apport:s390x < 2.28.0-0ubuntu1 @ii mR > (>= 2.27.0-0ubuntu7~) 202s Considering apport:s390x 146 as a solution to apport-core-dump-handler:s390x 4 202s Removing apport-core-dump-handler:s390x rather than change apport:s390x 202s Done 202s The following packages were automatically installed and are no longer required: 202s apport-symptoms python3-blinker python3-chardet python3-cryptography 202s python3-jwt python3-lazr.uri python3-oauthlib python3-openssl 202s python3-problem-report python3-pyparsing python3-six python3-systemd 202s python3-urllib3 python3-wadllib 202s Use 'sudo apt autoremove' to remove them. 202s The following additional packages will be installed: 202s autoconf automake autopoint autotools-dev build-essential cpp cpp-13 202s cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit dh-autoreconf 202s dh-strip-nondeterminism dwz g++ g++-13 g++-13-s390x-linux-gnu 202s g++-s390x-linux-gnu gcc gcc-13 gcc-13-s390x-linux-gnu gcc-s390x-linux-gnu 202s gettext htslib-test intltool-debian libarchive-zip-perl libasan8 libatomic1 202s libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 202s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 202s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 202s libhtscodecs-dev libhtscodecs2 libisl23 libitm1 liblzma-dev libmpc3 202s libssl-dev libssl3 libstdc++-13-dev libsub-override-perl libtool libubsan1 202s linux-libc-dev m4 po-debconf rpcsvc-proto tabix zlib1g-dev 202s Suggested packages: 202s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 202s cpp-13-doc dh-make g++-multilib g++-13-multilib gcc-13-doc gcc-multilib 202s manpages-dev flex bison gdb gcc-doc gcc-13-multilib gdb-s390x-linux-gnu 202s gettext-doc libasprintf-dev libgettextpo-dev glibc-doc libcurl4-doc 202s libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev 202s libssh2-1-dev pkg-config liblzma-doc libssl-doc libstdc++-13-doc libtool-doc 202s gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl 202s Recommended packages: 202s bzip2-doc manpages manpages-dev libc-devtools libarchive-cpio-perl 202s libltdl-dev libmail-sendmail-perl 202s The following packages will be REMOVED: 202s apport apport-core-dump-handler ca-certificates libssl3t64 openssl 202s python3-apport python3-certifi python3-httplib2 python3-launchpadlib 202s python3-lazr.restfulclient python3-requests ssh-import-id 202s The following NEW packages will be installed: 202s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 202s cpp cpp-13 cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit 202s dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 g++-13-s390x-linux-gnu 202s g++-s390x-linux-gnu gcc gcc-13 gcc-13-s390x-linux-gnu gcc-s390x-linux-gnu 202s gettext htslib-test intltool-debian libarchive-zip-perl libasan8 libatomic1 202s libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 202s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 202s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 202s libhtscodecs-dev libhtscodecs2 libisl23 libitm1 liblzma-dev libmpc3 202s libssl-dev libssl3 libstdc++-13-dev libsub-override-perl libtool libubsan1 202s linux-libc-dev m4 po-debconf rpcsvc-proto tabix zlib1g-dev 202s 0 upgraded, 62 newly installed, 12 to remove and 0 not upgraded. 202s Need to get 73.9 MB/73.9 MB of archives. 202s After this operation, 230 MB of additional disk space will be used. 202s Get:1 /tmp/autopkgtest.VumChj/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [812 B] 202s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libssl3 s390x 3.0.10-1ubuntu4 [1648 kB] 203s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x m4 s390x 1.4.19-4 [255 kB] 203s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x autoconf all 2.71-3 [339 kB] 203s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x autotools-dev all 20220109.1 [44.9 kB] 203s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x automake all 1:1.16.5-1.3ubuntu1 [558 kB] 204s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x autopoint all 0.21-14ubuntu1 [422 kB] 204s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.39-0ubuntu6 [20.2 kB] 204s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-11.11 [1590 kB] 204s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB] 204s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu6 [64.7 kB] 204s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.39-0ubuntu6 [1629 kB] 204s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libisl23 s390x 0.26-3 [722 kB] 204s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libmpc3 s390x 1.3.1-1 [54.9 kB] 204s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [9929 kB] 205s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-17ubuntu2 [1026 B] 205s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] 205s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] 205s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 14-20240303-1ubuntu1 [49.9 kB] 205s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 206s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 14-20240303-1ubuntu1 [31.1 kB] 206s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240303-1ubuntu1 [9392 B] 206s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 14-20240303-1ubuntu1 [2998 kB] 206s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 14-20240303-1ubuntu1 [1186 kB] 206s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-17ubuntu2 [1003 kB] 206s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [19.1 MB] 207s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-17ubuntu2 [467 kB] 207s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] 207s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] 207s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-17ubuntu2 [2430 kB] 207s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [11.3 MB] 207s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-17ubuntu2 [14.4 kB] 207s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] 207s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] 207s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 207s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 207s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libtool all 2.4.7-7 [166 kB] 207s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x dh-autoreconf all 20 [16.1 kB] 207s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 207s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libsub-override-perl all 0.10-1 [10.0 kB] 207s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 207s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x dh-strip-nondeterminism all 1.13.1-1 [5362 B] 207s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libdw1 s390x 0.190-1 [282 kB] 207s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x debugedit s390x 1:5.0-5 [47.5 kB] 207s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x dwz s390x 0.15-1 [108 kB] 207s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x gettext s390x 0.21-14ubuntu1 [917 kB] 207s Get:47 http://ftpmaster.internal/ubuntu noble/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] 207s Get:48 http://ftpmaster.internal/ubuntu noble/main s390x po-debconf all 1.0.21+nmu1 [233 kB] 207s Get:49 http://ftpmaster.internal/ubuntu noble/main s390x debhelper all 13.14.1ubuntu1 [869 kB] 207s Get:50 http://ftpmaster.internal/ubuntu noble/universe s390x htslib-test all 1.18+ds-1 [1120 kB] 207s Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libbz2-dev s390x 1.0.8-5ubuntu1 [39.4 kB] 207s Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libcurl4-gnutls-dev s390x 8.5.0-2ubuntu2 [466 kB] 207s Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 207s Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate-dev s390x 1.19-1 [52.4 kB] 207s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 207s Get:56 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 207s Get:57 http://ftpmaster.internal/ubuntu noble/main s390x liblzma-dev s390x 5.4.5-0.3 [215 kB] 207s Get:58 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g-dev s390x 1:1.3.dfsg-3ubuntu1 [905 kB] 207s Get:59 http://ftpmaster.internal/ubuntu noble/universe s390x libhts-dev s390x 1.18+ds-1 [5867 kB] 207s Get:60 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs-dev s390x 1.6.0-1 [2981 kB] 208s Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libssl-dev s390x 3.0.10-1ubuntu4 [2128 kB] 208s Get:62 http://ftpmaster.internal/ubuntu noble/universe s390x tabix s390x 1.18+ds-1 [527 kB] 208s Fetched 73.9 MB in 6s (13.3 MB/s) 208s (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 ... 51728 files and directories currently installed.) 208s Removing ssh-import-id (5.11-0ubuntu2) ... 208s Removing apport-core-dump-handler (2.28.0-0ubuntu1) ... 209s Removing apport (2.28.0-0ubuntu1) ... 209s Removing python3-apport (2.28.0-0ubuntu1) ... 209s Removing python3-requests (2.31.0+dfsg-1ubuntu1) ... 209s dpkg: ca-certificates: dependency problems, but removing anyway as you requested: 209s python3-httplib2 depends on ca-certificates. 209s python3-certifi depends on ca-certificates. 209s 209s Removing ca-certificates (20240203) ... 209s Removing dangling symlinks from /etc/ssl/certs... done. 209s Removing openssl (3.0.13-0ubuntu2) ... 209s dpkg: libssl3t64:s390x: dependency problems, but removing anyway as you requested: 209s wget depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s tnftp depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s tcpdump depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s systemd-resolved depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s systemd depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s sudo depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s s390-tools depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s rsync depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s python3-cryptography depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s openssh-server depends on libssl3 (>= 3.0.10); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s openssh-client depends on libssl3 (>= 3.0.10); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libssh-4:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libsasl2-2:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libnvme1 depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libkrb5-3:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libkmod2:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libfido2-1:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libcurl4:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s kmod depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s dhcpcd-base depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s bind9-libs:s390x depends on libssl3 (>= 3.0.0); however: 209s Package libssl3 is not installed. 209s Package libssl3t64:s390x which provides libssl3 is to be removed. 209s 209s Removing libssl3t64:s390x (3.0.13-0ubuntu2) ... 209s Selecting previously unselected package libssl3:s390x. 209s (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 ... 51067 files and directories currently installed.) 209s Preparing to unpack .../libssl3_3.0.10-1ubuntu4_s390x.deb ... 209s Unpacking libssl3:s390x (3.0.10-1ubuntu4) ... 209s (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 ... 51078 files and directories currently installed.) 209s Removing python3-certifi (2023.11.17-1) ... 209s Removing python3-launchpadlib (1.11.0-6) ... 209s Removing python3-lazr.restfulclient (0.14.6-1) ... 210s Removing python3-httplib2 (0.20.4-3) ... 210s Selecting previously unselected package m4. 210s (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 ... 50964 files and directories currently installed.) 210s Preparing to unpack .../00-m4_1.4.19-4_s390x.deb ... 210s Unpacking m4 (1.4.19-4) ... 210s Selecting previously unselected package autoconf. 210s Preparing to unpack .../01-autoconf_2.71-3_all.deb ... 210s Unpacking autoconf (2.71-3) ... 210s Selecting previously unselected package autotools-dev. 210s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 210s Unpacking autotools-dev (20220109.1) ... 210s Selecting previously unselected package automake. 210s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 210s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 210s Selecting previously unselected package autopoint. 210s Preparing to unpack .../04-autopoint_0.21-14ubuntu1_all.deb ... 210s Unpacking autopoint (0.21-14ubuntu1) ... 210s Selecting previously unselected package libc-dev-bin. 210s Preparing to unpack .../05-libc-dev-bin_2.39-0ubuntu6_s390x.deb ... 210s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 210s Selecting previously unselected package linux-libc-dev:s390x. 210s Preparing to unpack .../06-linux-libc-dev_6.8.0-11.11_s390x.deb ... 210s Unpacking linux-libc-dev:s390x (6.8.0-11.11) ... 210s Selecting previously unselected package libcrypt-dev:s390x. 210s Preparing to unpack .../07-libcrypt-dev_1%3a4.4.36-4_s390x.deb ... 210s Unpacking libcrypt-dev:s390x (1:4.4.36-4) ... 210s Selecting previously unselected package rpcsvc-proto. 210s Preparing to unpack .../08-rpcsvc-proto_1.4.2-0ubuntu6_s390x.deb ... 210s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 210s Selecting previously unselected package libc6-dev:s390x. 210s Preparing to unpack .../09-libc6-dev_2.39-0ubuntu6_s390x.deb ... 210s Unpacking libc6-dev:s390x (2.39-0ubuntu6) ... 210s Selecting previously unselected package libisl23:s390x. 210s Preparing to unpack .../10-libisl23_0.26-3_s390x.deb ... 210s Unpacking libisl23:s390x (0.26-3) ... 210s Selecting previously unselected package libmpc3:s390x. 210s Preparing to unpack .../11-libmpc3_1.3.1-1_s390x.deb ... 210s Unpacking libmpc3:s390x (1.3.1-1) ... 210s Selecting previously unselected package cpp-13-s390x-linux-gnu. 210s Preparing to unpack .../12-cpp-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 210s Unpacking cpp-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 210s Selecting previously unselected package cpp-13. 210s Preparing to unpack .../13-cpp-13_13.2.0-17ubuntu2_s390x.deb ... 210s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 210s Selecting previously unselected package cpp-s390x-linux-gnu. 210s Preparing to unpack .../14-cpp-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 210s Unpacking cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 210s Selecting previously unselected package cpp. 210s Preparing to unpack .../15-cpp_4%3a13.2.0-7ubuntu1_s390x.deb ... 210s Unpacking cpp (4:13.2.0-7ubuntu1) ... 210s Selecting previously unselected package libcc1-0:s390x. 210s Preparing to unpack .../16-libcc1-0_14-20240303-1ubuntu1_s390x.deb ... 210s Unpacking libcc1-0:s390x (14-20240303-1ubuntu1) ... 210s Selecting previously unselected package libgomp1:s390x. 210s Preparing to unpack .../17-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 210s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 210s Selecting previously unselected package libitm1:s390x. 210s Preparing to unpack .../18-libitm1_14-20240303-1ubuntu1_s390x.deb ... 210s Unpacking libitm1:s390x (14-20240303-1ubuntu1) ... 210s Selecting previously unselected package libatomic1:s390x. 210s Preparing to unpack .../19-libatomic1_14-20240303-1ubuntu1_s390x.deb ... 210s Unpacking libatomic1:s390x (14-20240303-1ubuntu1) ... 210s Selecting previously unselected package libasan8:s390x. 210s Preparing to unpack .../20-libasan8_14-20240303-1ubuntu1_s390x.deb ... 210s Unpacking libasan8:s390x (14-20240303-1ubuntu1) ... 211s Selecting previously unselected package libubsan1:s390x. 211s Preparing to unpack .../21-libubsan1_14-20240303-1ubuntu1_s390x.deb ... 211s Unpacking libubsan1:s390x (14-20240303-1ubuntu1) ... 211s Selecting previously unselected package libgcc-13-dev:s390x. 211s Preparing to unpack .../22-libgcc-13-dev_13.2.0-17ubuntu2_s390x.deb ... 211s Unpacking libgcc-13-dev:s390x (13.2.0-17ubuntu2) ... 211s Selecting previously unselected package gcc-13-s390x-linux-gnu. 211s Preparing to unpack .../23-gcc-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 211s Unpacking gcc-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 211s Selecting previously unselected package gcc-13. 211s Preparing to unpack .../24-gcc-13_13.2.0-17ubuntu2_s390x.deb ... 211s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 211s Selecting previously unselected package gcc-s390x-linux-gnu. 211s Preparing to unpack .../25-gcc-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 211s Unpacking gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 211s Selecting previously unselected package gcc. 211s Preparing to unpack .../26-gcc_4%3a13.2.0-7ubuntu1_s390x.deb ... 211s Unpacking gcc (4:13.2.0-7ubuntu1) ... 211s Selecting previously unselected package libstdc++-13-dev:s390x. 211s Preparing to unpack .../27-libstdc++-13-dev_13.2.0-17ubuntu2_s390x.deb ... 211s Unpacking libstdc++-13-dev:s390x (13.2.0-17ubuntu2) ... 211s Selecting previously unselected package g++-13-s390x-linux-gnu. 211s Preparing to unpack .../28-g++-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 211s Unpacking g++-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 212s Selecting previously unselected package g++-13. 212s Preparing to unpack .../29-g++-13_13.2.0-17ubuntu2_s390x.deb ... 212s Unpacking g++-13 (13.2.0-17ubuntu2) ... 212s Selecting previously unselected package g++-s390x-linux-gnu. 212s Preparing to unpack .../30-g++-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 212s Unpacking g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 212s Selecting previously unselected package g++. 212s Preparing to unpack .../31-g++_4%3a13.2.0-7ubuntu1_s390x.deb ... 212s Unpacking g++ (4:13.2.0-7ubuntu1) ... 212s Selecting previously unselected package build-essential. 212s Preparing to unpack .../32-build-essential_12.10ubuntu1_s390x.deb ... 212s Unpacking build-essential (12.10ubuntu1) ... 212s Selecting previously unselected package libdebhelper-perl. 212s Preparing to unpack .../33-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 212s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 212s Selecting previously unselected package libtool. 212s Preparing to unpack .../34-libtool_2.4.7-7_all.deb ... 212s Unpacking libtool (2.4.7-7) ... 212s Selecting previously unselected package dh-autoreconf. 212s Preparing to unpack .../35-dh-autoreconf_20_all.deb ... 212s Unpacking dh-autoreconf (20) ... 212s Selecting previously unselected package libarchive-zip-perl. 212s Preparing to unpack .../36-libarchive-zip-perl_1.68-1_all.deb ... 212s Unpacking libarchive-zip-perl (1.68-1) ... 212s Selecting previously unselected package libsub-override-perl. 212s Preparing to unpack .../37-libsub-override-perl_0.10-1_all.deb ... 212s Unpacking libsub-override-perl (0.10-1) ... 212s Selecting previously unselected package libfile-stripnondeterminism-perl. 212s Preparing to unpack .../38-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 212s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 212s Selecting previously unselected package dh-strip-nondeterminism. 212s Preparing to unpack .../39-dh-strip-nondeterminism_1.13.1-1_all.deb ... 212s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 212s Selecting previously unselected package libdw1:s390x. 212s Preparing to unpack .../40-libdw1_0.190-1_s390x.deb ... 212s Unpacking libdw1:s390x (0.190-1) ... 212s Selecting previously unselected package debugedit. 212s Preparing to unpack .../41-debugedit_1%3a5.0-5_s390x.deb ... 212s Unpacking debugedit (1:5.0-5) ... 212s Selecting previously unselected package dwz. 212s Preparing to unpack .../42-dwz_0.15-1_s390x.deb ... 212s Unpacking dwz (0.15-1) ... 212s Selecting previously unselected package gettext. 212s Preparing to unpack .../43-gettext_0.21-14ubuntu1_s390x.deb ... 212s Unpacking gettext (0.21-14ubuntu1) ... 212s Selecting previously unselected package intltool-debian. 212s Preparing to unpack .../44-intltool-debian_0.35.0+20060710.6_all.deb ... 212s Unpacking intltool-debian (0.35.0+20060710.6) ... 212s Selecting previously unselected package po-debconf. 212s Preparing to unpack .../45-po-debconf_1.0.21+nmu1_all.deb ... 212s Unpacking po-debconf (1.0.21+nmu1) ... 212s Selecting previously unselected package debhelper. 212s Preparing to unpack .../46-debhelper_13.14.1ubuntu1_all.deb ... 212s Unpacking debhelper (13.14.1ubuntu1) ... 212s Selecting previously unselected package htslib-test. 212s Preparing to unpack .../47-htslib-test_1.18+ds-1_all.deb ... 212s Unpacking htslib-test (1.18+ds-1) ... 212s Selecting previously unselected package libbz2-dev:s390x. 212s Preparing to unpack .../48-libbz2-dev_1.0.8-5ubuntu1_s390x.deb ... 212s Unpacking libbz2-dev:s390x (1.0.8-5ubuntu1) ... 212s Selecting previously unselected package libcurl4-gnutls-dev:s390x. 212s Preparing to unpack .../49-libcurl4-gnutls-dev_8.5.0-2ubuntu2_s390x.deb ... 212s Unpacking libcurl4-gnutls-dev:s390x (8.5.0-2ubuntu2) ... 212s Selecting previously unselected package libdeflate0:s390x. 212s Preparing to unpack .../50-libdeflate0_1.19-1_s390x.deb ... 212s Unpacking libdeflate0:s390x (1.19-1) ... 212s Selecting previously unselected package libdeflate-dev:s390x. 212s Preparing to unpack .../51-libdeflate-dev_1.19-1_s390x.deb ... 212s Unpacking libdeflate-dev:s390x (1.19-1) ... 212s Selecting previously unselected package libhtscodecs2:s390x. 212s Preparing to unpack .../52-libhtscodecs2_1.6.0-1_s390x.deb ... 212s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 212s Selecting previously unselected package libhts3:s390x. 212s Preparing to unpack .../53-libhts3_1.18+ds-1_s390x.deb ... 212s Unpacking libhts3:s390x (1.18+ds-1) ... 212s Selecting previously unselected package liblzma-dev:s390x. 212s Preparing to unpack .../54-liblzma-dev_5.4.5-0.3_s390x.deb ... 212s Unpacking liblzma-dev:s390x (5.4.5-0.3) ... 212s Selecting previously unselected package zlib1g-dev:s390x. 212s Preparing to unpack .../55-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_s390x.deb ... 212s Unpacking zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ... 212s Selecting previously unselected package libhts-dev:s390x. 212s Preparing to unpack .../56-libhts-dev_1.18+ds-1_s390x.deb ... 212s Unpacking libhts-dev:s390x (1.18+ds-1) ... 212s Selecting previously unselected package libhtscodecs-dev:s390x. 212s Preparing to unpack .../57-libhtscodecs-dev_1.6.0-1_s390x.deb ... 212s Unpacking libhtscodecs-dev:s390x (1.6.0-1) ... 212s Selecting previously unselected package libssl-dev:s390x. 212s Preparing to unpack .../58-libssl-dev_3.0.10-1ubuntu4_s390x.deb ... 212s Unpacking libssl-dev:s390x (3.0.10-1ubuntu4) ... 212s Selecting previously unselected package tabix. 212s Preparing to unpack .../59-tabix_1.18+ds-1_s390x.deb ... 212s Unpacking tabix (1.18+ds-1) ... 212s Selecting previously unselected package autopkgtest-satdep. 212s Preparing to unpack .../60-1-autopkgtest-satdep.deb ... 212s Unpacking autopkgtest-satdep (0) ... 212s Setting up libhtscodecs2:s390x (1.6.0-1) ... 212s Setting up libdw1:s390x (0.190-1) ... 212s Setting up libarchive-zip-perl (1.68-1) ... 212s Setting up htslib-test (1.18+ds-1) ... 212s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 212s Setting up libssl3:s390x (3.0.10-1ubuntu4) ... 212s Setting up libdeflate0:s390x (1.19-1) ... 212s Setting up linux-libc-dev:s390x (6.8.0-11.11) ... 212s Setting up m4 (1.4.19-4) ... 212s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 212s Setting up libcurl4-gnutls-dev:s390x (8.5.0-2ubuntu2) ... 212s Setting up libhtscodecs-dev:s390x (1.6.0-1) ... 212s Setting up autotools-dev (20220109.1) ... 212s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 212s Setting up libssl-dev:s390x (3.0.10-1ubuntu4) ... 212s Setting up libmpc3:s390x (1.3.1-1) ... 212s Setting up libatomic1:s390x (14-20240303-1ubuntu1) ... 212s Setting up autopoint (0.21-14ubuntu1) ... 212s Setting up autoconf (2.71-3) ... 212s Setting up liblzma-dev:s390x (5.4.5-0.3) ... 212s Setting up libubsan1:s390x (14-20240303-1ubuntu1) ... 212s Setting up dwz (0.15-1) ... 212s Setting up libcrypt-dev:s390x (1:4.4.36-4) ... 212s Setting up libasan8:s390x (14-20240303-1ubuntu1) ... 212s Setting up debugedit (1:5.0-5) ... 212s Setting up libsub-override-perl (0.10-1) ... 212s Setting up libisl23:s390x (0.26-3) ... 212s Setting up libc-dev-bin (2.39-0ubuntu6) ... 212s Setting up libdeflate-dev:s390x (1.19-1) ... 212s Setting up tabix (1.18+ds-1) ... 212s Setting up libcc1-0:s390x (14-20240303-1ubuntu1) ... 212s Setting up libitm1:s390x (14-20240303-1ubuntu1) ... 213s Setting up automake (1:1.16.5-1.3ubuntu1) ... 213s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 213s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 213s Setting up libhts3:s390x (1.18+ds-1) ... 213s Setting up gettext (0.21-14ubuntu1) ... 213s Setting up intltool-debian (0.35.0+20060710.6) ... 213s Setting up cpp-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 213s Setting up dh-strip-nondeterminism (1.13.1-1) ... 213s Setting up libgcc-13-dev:s390x (13.2.0-17ubuntu2) ... 213s Setting up libc6-dev:s390x (2.39-0ubuntu6) ... 213s Setting up libstdc++-13-dev:s390x (13.2.0-17ubuntu2) ... 213s Setting up libbz2-dev:s390x (1.0.8-5ubuntu1) ... 213s Setting up cpp-13 (13.2.0-17ubuntu2) ... 213s Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 213s Setting up po-debconf (1.0.21+nmu1) ... 213s Setting up gcc-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 213s Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 213s Setting up g++-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 213s Setting up gcc-13 (13.2.0-17ubuntu2) ... 213s Setting up zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ... 213s Setting up cpp (4:13.2.0-7ubuntu1) ... 213s Setting up g++-13 (13.2.0-17ubuntu2) ... 213s Setting up libtool (2.4.7-7) ... 213s Setting up libhts-dev:s390x (1.18+ds-1) ... 213s Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 213s Setting up gcc (4:13.2.0-7ubuntu1) ... 213s Setting up dh-autoreconf (20) ... 213s Setting up g++ (4:13.2.0-7ubuntu1) ... 213s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 213s Setting up build-essential (12.10ubuntu1) ... 213s Setting up debhelper (13.14.1ubuntu1) ... 213s Setting up autopkgtest-satdep (0) ... 213s Processing triggers for man-db (2.12.0-3) ... 213s Processing triggers for install-info (7.1-3) ... 213s Processing triggers for libc-bin (2.39-0ubuntu6) ... 216s (Reading database ... 55796 files and directories currently installed.) 216s Removing autopkgtest-satdep (0) ... 217s autopkgtest [06:40:49]: test run-unit-test: [----------------------- 217s + pkg=htslib 217s + '[' /tmp/autopkgtest.VumChj/autopkgtest_tmp = '' ']' 217s + 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.VumChj/autopkgtest_tmp 217s + cp -aL htslib.pc.in /tmp/autopkgtest.VumChj/autopkgtest_tmp 217s + cp -aL htslib.map /tmp/autopkgtest.VumChj/autopkgtest_tmp 217s + cd /tmp/autopkgtest.VumChj/autopkgtest_tmp 217s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 217s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 217s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 217s + grep sse /proc/cpuinfo 217s + export CFLAGS 217s + make -e check 217s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c 217s : warning: "_FORTIFY_SOURCE" redefined 217s : note: this is the location of the previous definition 217s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c 217s : warning: "_FORTIFY_SOURCE" redefined 217s : note: this is the location of the previous definition 218s 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 218s : warning: "_FORTIFY_SOURCE" redefined 218s : note: this is the location of the previous definition 218s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c 218s : warning: "_FORTIFY_SOURCE" redefined 218s : note: this is the location of the previous definition 219s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c 219s : warning: "_FORTIFY_SOURCE" redefined 219s : note: this is the location of the previous definition 219s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c 219s : warning: "_FORTIFY_SOURCE" redefined 219s : note: this is the location of the previous definition 220s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c 220s : warning: "_FORTIFY_SOURCE" redefined 220s : note: this is the location of the previous definition 221s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c 221s : warning: "_FORTIFY_SOURCE" redefined 221s : note: this is the location of the previous definition 222s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c 222s : warning: "_FORTIFY_SOURCE" redefined 222s : note: this is the location of the previous definition 224s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c 224s : warning: "_FORTIFY_SOURCE" redefined 224s : note: this is the location of the previous definition 225s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c 225s : warning: "_FORTIFY_SOURCE" redefined 225s : note: this is the location of the previous definition 225s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c 225s : warning: "_FORTIFY_SOURCE" redefined 225s : note: this is the location of the previous definition 225s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c 225s : warning: "_FORTIFY_SOURCE" redefined 225s : note: this is the location of the previous definition 225s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c 225s : warning: "_FORTIFY_SOURCE" redefined 225s : note: this is the location of the previous definition 225s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c 225s : warning: "_FORTIFY_SOURCE" redefined 225s : note: this is the location of the previous definition 225s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c 225s : warning: "_FORTIFY_SOURCE" redefined 225s : note: this is the location of the previous definition 226s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c 226s : warning: "_FORTIFY_SOURCE" redefined 226s : note: this is the location of the previous definition 226s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c 226s : warning: "_FORTIFY_SOURCE" redefined 226s : note: this is the location of the previous definition 229s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c 229s : warning: "_FORTIFY_SOURCE" redefined 229s : note: this is the location of the previous definition 230s 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 230s : warning: "_FORTIFY_SOURCE" redefined 230s : note: this is the location of the previous definition 230s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c 230s : warning: "_FORTIFY_SOURCE" redefined 230s : note: this is the location of the previous definition 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c 231s : warning: "_FORTIFY_SOURCE" redefined 231s : note: this is the location of the previous definition 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c 231s : warning: "_FORTIFY_SOURCE" redefined 231s : note: this is the location of the previous definition 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c 231s : warning: "_FORTIFY_SOURCE" redefined 231s : note: this is the location of the previous definition 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c 231s : warning: "_FORTIFY_SOURCE" redefined 231s : note: this is the location of the previous definition 236s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c 236s : warning: "_FORTIFY_SOURCE" redefined 236s : note: this is the location of the previous definition 236s 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 236s : warning: "_FORTIFY_SOURCE" redefined 236s : note: this is the location of the previous definition 238s 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 238s : warning: "_FORTIFY_SOURCE" redefined 238s : note: this is the location of the previous definition 240s 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 240s : warning: "_FORTIFY_SOURCE" redefined 240s : note: this is the location of the previous definition 242s 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 242s : warning: "_FORTIFY_SOURCE" redefined 242s : note: this is the location of the previous definition 242s 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 242s : warning: "_FORTIFY_SOURCE" redefined 242s : note: this is the location of the previous definition 242s 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 242s : warning: "_FORTIFY_SOURCE" redefined 242s : note: this is the location of the previous definition 245s 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 245s : warning: "_FORTIFY_SOURCE" redefined 245s : note: this is the location of the previous definition 245s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c 245s : warning: "_FORTIFY_SOURCE" redefined 245s : note: this is the location of the previous definition 245s 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 245s : warning: "_FORTIFY_SOURCE" redefined 245s : note: this is the location of the previous definition 245s 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 245s : warning: "_FORTIFY_SOURCE" redefined 245s : note: this is the location of the previous definition 245s 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 245s : warning: "_FORTIFY_SOURCE" redefined 245s : note: this is the location of the previous definition 245s 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 245s : warning: "_FORTIFY_SOURCE" redefined 245s : note: this is the location of the previous definition 245s 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 245s ranlib libhts.a 245s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c 245s : warning: "_FORTIFY_SOURCE" redefined 245s : note: this is the location of the previous definition 246s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c 246s : warning: "_FORTIFY_SOURCE" redefined 246s : note: this is the location of the previous definition 246s 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 246s : warning: "_FORTIFY_SOURCE" redefined 246s : note: this is the location of the previous definition 246s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c 246s : warning: "_FORTIFY_SOURCE" redefined 246s : note: this is the location of the previous definition 247s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c 247s : warning: "_FORTIFY_SOURCE" redefined 247s : note: this is the location of the previous definition 247s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c 247s : warning: "_FORTIFY_SOURCE" redefined 248s : note: this is the location of the previous definition 248s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c 248s : warning: "_FORTIFY_SOURCE" redefined 248s : note: this is the location of the previous definition 249s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c 249s : warning: "_FORTIFY_SOURCE" redefined 249s : note: this is the location of the previous definition 250s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c 250s : warning: "_FORTIFY_SOURCE" redefined 250s : note: this is the location of the previous definition 252s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c 252s : warning: "_FORTIFY_SOURCE" redefined 252s : note: this is the location of the previous definition 253s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c 253s : warning: "_FORTIFY_SOURCE" redefined 253s : note: this is the location of the previous definition 253s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c 253s : warning: "_FORTIFY_SOURCE" redefined 253s : note: this is the location of the previous definition 253s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c 253s : warning: "_FORTIFY_SOURCE" redefined 253s : note: this is the location of the previous definition 253s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c 253s : warning: "_FORTIFY_SOURCE" redefined 253s : note: this is the location of the previous definition 253s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c 253s : warning: "_FORTIFY_SOURCE" redefined 253s : note: this is the location of the previous definition 253s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c 253s : warning: "_FORTIFY_SOURCE" redefined 253s : note: this is the location of the previous definition 254s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c 254s : warning: "_FORTIFY_SOURCE" redefined 254s : note: this is the location of the previous definition 254s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c 254s : warning: "_FORTIFY_SOURCE" redefined 254s : note: this is the location of the previous definition 257s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c 257s : warning: "_FORTIFY_SOURCE" redefined 257s : note: this is the location of the previous definition 258s 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 258s : warning: "_FORTIFY_SOURCE" redefined 258s : note: this is the location of the previous definition 258s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 258s : warning: "_FORTIFY_SOURCE" redefined 258s : note: this is the location of the previous definition 259s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c 259s : warning: "_FORTIFY_SOURCE" redefined 259s : note: this is the location of the previous definition 259s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c 259s : warning: "_FORTIFY_SOURCE" redefined 259s : note: this is the location of the previous definition 259s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c 259s : warning: "_FORTIFY_SOURCE" redefined 259s : note: this is the location of the previous definition 259s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c 259s : warning: "_FORTIFY_SOURCE" redefined 259s : note: this is the location of the previous definition 263s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c 263s : warning: "_FORTIFY_SOURCE" redefined 263s : note: this is the location of the previous definition 264s 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 264s : warning: "_FORTIFY_SOURCE" redefined 264s : note: this is the location of the previous definition 266s 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 266s : warning: "_FORTIFY_SOURCE" redefined 266s : note: this is the location of the previous definition 267s 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 267s : warning: "_FORTIFY_SOURCE" redefined 267s : note: this is the location of the previous definition 269s 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 269s : warning: "_FORTIFY_SOURCE" redefined 269s : note: this is the location of the previous definition 270s 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 270s : warning: "_FORTIFY_SOURCE" redefined 270s : note: this is the location of the previous definition 270s 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 270s : warning: "_FORTIFY_SOURCE" redefined 270s : note: this is the location of the previous definition 272s 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 272s : warning: "_FORTIFY_SOURCE" redefined 272s : note: this is the location of the previous definition 272s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c 272s : warning: "_FORTIFY_SOURCE" redefined 272s : note: this is the location of the previous definition 273s 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 273s : warning: "_FORTIFY_SOURCE" redefined 273s : note: this is the location of the previous definition 273s 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 273s : warning: "_FORTIFY_SOURCE" redefined 273s : note: this is the location of the previous definition 273s 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 273s : warning: "_FORTIFY_SOURCE" redefined 273s : note: this is the location of the previous definition 273s 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 273s : warning: "_FORTIFY_SOURCE" redefined 273s : note: this is the location of the previous definition 273s 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 273s ln -sf libhts.so libhts.so.3 273s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c 273s : warning: "_FORTIFY_SOURCE" redefined 273s : note: this is the location of the previous definition 273s 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 273s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c 273s : warning: "_FORTIFY_SOURCE" redefined 273s : note: this is the location of the previous definition 273s 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 274s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c 274s : warning: "_FORTIFY_SOURCE" redefined 274s : note: this is the location of the previous definition 274s 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 274s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 274s : warning: "_FORTIFY_SOURCE" redefined 274s : note: this is the location of the previous definition 275s 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 275s : warning: "_FORTIFY_SOURCE" redefined 275s : note: this is the location of the previous definition 275s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 275s 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 275s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c 275s : warning: "_FORTIFY_SOURCE" redefined 275s : note: this is the location of the previous definition 276s 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 276s 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 276s : warning: "_FORTIFY_SOURCE" redefined 276s : note: this is the location of the previous definition 276s 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 276s 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 276s : warning: "_FORTIFY_SOURCE" redefined 276s : note: this is the location of the previous definition 277s 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 277s : warning: "_FORTIFY_SOURCE" redefined 277s : note: this is the location of the previous definition 277s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c 277s 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 277s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c 277s 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 277s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c 277s 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 277s 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 277s 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 277s 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 277s : warning: "_FORTIFY_SOURCE" redefined 277s : note: this is the location of the previous definition 277s : warning: "_FORTIFY_SOURCE" redefined 277s : note: this is the location of the previous definition 277s : warning: "_FORTIFY_SOURCE" redefined 277s : note: this is the location of the previous definition 277s : warning: "_FORTIFY_SOURCE" redefined 277s : note: this is the location of the previous definition 277s 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 277s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c 277s : warning: "_FORTIFY_SOURCE" redefined 277s : note: this is the location of the previous definition 278s 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 278s 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 278s : warning: "_FORTIFY_SOURCE" redefined 278s : note: this is the location of the previous definition 278s 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 278s 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 278s : warning: "_FORTIFY_SOURCE" redefined 278s : note: this is the location of the previous definition 278s 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 279s 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 279s : warning: "_FORTIFY_SOURCE" redefined 279s : note: this is the location of the previous definition 279s 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 279s 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 279s : warning: "_FORTIFY_SOURCE" redefined 279s : note: this is the location of the previous definition 279s 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 279s 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 279s : warning: "_FORTIFY_SOURCE" redefined 279s : note: this is the location of the previous definition 279s 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 279s 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 279s : warning: "_FORTIFY_SOURCE" redefined 279s : note: this is the location of the previous definition 279s 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 279s 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 279s : warning: "_FORTIFY_SOURCE" redefined 279s : note: this is the location of the previous definition 279s 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 279s 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 279s : warning: "_FORTIFY_SOURCE" redefined 279s : note: this is the location of the previous definition 280s 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 280s 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 280s : warning: "_FORTIFY_SOURCE" redefined 280s : note: this is the location of the previous definition 280s 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 280s 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 280s : warning: "_FORTIFY_SOURCE" redefined 280s : note: this is the location of the previous definition 280s 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 280s 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 280s : warning: "_FORTIFY_SOURCE" redefined 280s : note: this is the location of the previous definition 280s 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 280s 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 280s : warning: "_FORTIFY_SOURCE" redefined 280s : note: this is the location of the previous definition 280s 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 280s 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 280s : warning: "_FORTIFY_SOURCE" redefined 280s : note: this is the location of the previous definition 281s 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 281s 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 281s : warning: "_FORTIFY_SOURCE" redefined 281s : note: this is the location of the previous definition 281s 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 281s 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 281s : warning: "_FORTIFY_SOURCE" redefined 281s : note: this is the location of the previous definition 281s 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 281s 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 281s : warning: "_FORTIFY_SOURCE" redefined 281s : note: this is the location of the previous definition 281s 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 281s : warning: "_FORTIFY_SOURCE" redefined 281s : note: this is the location of the previous definition 281s 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 281s 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 281s : warning: "_FORTIFY_SOURCE" redefined 281s : note: this is the location of the previous definition 281s 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 281s 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 281s : warning: "_FORTIFY_SOURCE" redefined 281s : note: this is the location of the previous definition 281s 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 281s 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 281s : warning: "_FORTIFY_SOURCE" redefined 281s : note: this is the location of the previous definition 288s 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 288s Expected error: [E::hts_parse_region] sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 288s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 288s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 288s test/hts_endian 288s test/test_expr 288s test/test_kfunc 288s test/test_kstring 288s test/test_str2int 288s test/test_time_funcs 288s test/fieldarith test/fieldarith.sam 288s test/hfile 288s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 288s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 288s fi 288s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 288s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 288s fi 288s test/test_bgzf test/bgziptest.txt 288s test/test-parse-reg -t test/colons.bam 288s cd test/faidx && ./test-faidx.sh faidx.tst 288s Testing faidx... 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 288s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 288s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 288s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 288s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 288s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 288s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 288s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 288s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 288s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 288s 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 288s 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 288s 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 288s 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 288s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 288s 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 288s 288s Expected passes: 25 288s Unexpected passes: 0 288s Expected failures: 0 288s Unexpected failures: 0 288s cd test/sam_filter && ./filter.sh filter.tst 288s Testing sam_filter... 288s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 288s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 288s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 288s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 288s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 288s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 288s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 288s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 288s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 288s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 288s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 288s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 288s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 288s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 288s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 288s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 288s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 288s 288s Expected passes: 17 288s Unexpected passes: 0 288s Expected failures: 0 288s Unexpected failures: 0 288s cd test/tabix && ./test-tabix.sh tabix.tst 288s Testing tabix... 288s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 288s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 288s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 288s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 288s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 288s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 288s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 288s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 288s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 288s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 288s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 288s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 288s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 288s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 288s 288s Expected passes: 14 288s Unexpected passes: 0 288s Expected failures: 0 288s Unexpected failures: 0 288s cd test/mpileup && ./test-pileup.sh mpileup.tst 288s Testing (m)pileup... 288s PASS : $pileup mp_D.sam 288s PASS : $pileup -m mp_D.sam 288s PASS : $pileup mp_DI.sam 288s PASS : $pileup -m mp_DI.sam 288s PASS : $pileup mp_I.sam 288s PASS : $pileup -m mp_I.sam 288s PASS : $pileup mp_P.sam 288s PASS : $pileup -m mp_P.sam 288s PASS : $pileup mp_ID.sam 288s PASS : $pileup -m mp_ID.sam 288s PASS : $pileup mp_N.sam 288s PASS : $pileup -m mp_N.sam 288s PASS : $pileup mp_N2.sam 288s PASS : $pileup -m mp_N2.sam 288s PASS : $pileup c1#pad1.sam 288s PASS : $pileup -m c1#pad1.sam 288s PASS : $pileup c1#pad2.sam 288s PASS : $pileup -m c1#pad2.sam 288s PASS : $pileup c1#pad3.sam 288s PASS : $pileup -m c1#pad3.sam 288s PASS : $pileup -m small.bam 288s 288s Expected passes: 21 288s Unexpected passes: 0 288s Expected failures: 0 288s Unexpected failures: 0 288s cd test/fastq && ./test-fastq.sh 288s Testing fastq support 288s PASS : $tview minimal.fq 288s PASS : $tview minimal.fa 288s PASS : $tview multiline.fq 288s PASS : $tview multiline.fa 288s PASS : $tview -i fastq_aux longline.fq 288s PASS : $tview single.fq 288s PASS : $tview single.fa 288s PASS : $tview -i fastq_aux single.fq 288s PASS : $tview -i fastq_aux single.fa 288s Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 288s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 288s Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" 288s Expected error: [E::hts_parse_region] Unexpected string "x" after region 288s Expected error: [E::hts_parse_region] Unexpected string "y" after region 288s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 288s PASS : $tview interleaved.fq 288s PASS : $tview interleaved.fa 288s PASS : $tview -i fastq_aux interleaved.fq 288s PASS : $tview -i fastq_aux interleaved.fa 288s PASS : $tview -i fastq_casava interleaved_casava.fq 288s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 288s PASS : $tview -i fastq_casava interleaved_casava.fa 288s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 288s PASS : $tview -i fastq_casava filter_casava.fq 288s PASS : $tview -i fastq_casava filter_casava.fa 288s PASS : $tview -i fastq_aux r1.fq 288s PASS : $tview -i fastq_aux r2.fq 288s PASS : $tview -i fastq_aux r1.fa 288s PASS : $tview -i fastq_aux r2.fa 288s PASS : $tview -i fastq_name2 name2.fq 288s PASS : $tview -i fastq_name2 name2.fa 288s PASS : $tview -f minimal.sam 288s PASS : $tview -F minimal.sam 288s PASS : $tview -f -o fastq_aux single_aux.sam 288s PASS : $tview -F -o fastq_aux single_aux.sam 288s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 288s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 288s PASS : $tview -f -o fastq_casava inter_casava.sam 288s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 288s PASS : $tview -F -o fastq_casava inter_casava.sam 288s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 288s PASS : $tview -f -o fastq_casava filter_casava.sam 288s PASS : $tview -F -o fastq_casava filter_casava.sam 288s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 288s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 288s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 288s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 288s 288s Expected passes: 41 288s Unexpected passes: 0 288s Expected failures: 0 288s Unexpected failures: 0 288s cd test/base_mods && ./base-mods.sh base-mods.tst 288s Testing base-modifications... 288s PASS : $test_mod MM-chebi.sam 288s PASS : $test_mod MM-double.sam 288s PASS : $test_mod MM-multi.sam 288s PASS : $test_mod MM-explicit.sam 288s PASS : $test_mod -x MM-explicit.sam 288s PASS : $test_mod -f 1 MM-explicit.sam 288s PASS : $test_mod MM-not-all-modded.sam 288s PASS : $pileup_mod < MM-pileup.sam 288s PASS : $pileup_mod < MM-pileup2.sam 288s PASS : $pileup_mod < MM-MNp.sam 288s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 288s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 288s 288s Expected passes: 12 288s Unexpected passes: 0 288s Expected failures: 0 288s Unexpected failures: 0 288s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 288s (Expect trailing 'x' message for " -1,001x") 288s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 288s (Expect trailing 'k' message for "1.5e+3k") 288s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 288s (Expect dropped fraction message for "12.3456k") 288s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 288s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 288s (Expect invalid numeric message for "A") 288s [W::hts_parse_decimal] Invalid numeric value A[truncated] 288s (Expect invalid numeric message for "G") 288s [W::hts_parse_decimal] Invalid numeric value G[truncated] 288s (Expect invalid numeric message for " +/-") 288s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 288s (Expect invalid numeric message for " -.e+9999") 288s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 288s test/test-regidx 288s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 288s bgzip round-trip no threads: .. ok 288s 289s bgzip text mode round-trip no threads: .. ok 289s 289s bgzip -b no threads: .. ok 289s 289s bgzip -b -I no threads: .. ok 289s 289s bgzip round-trip 4 threads: .. ok 289s 289s bgzip text mode round-trip 4 threads: .. ok 289s 289s bgzip -b 4 threads: .. ok 289s 289s bgzip -b -I 4 threads: .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/67i98fdpo3/index.bam.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.bam 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.bam 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/67i98fdpo3/index.bam.bai /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.bam 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -b /tmp/67i98fdpo3/index.bam 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/67i98fdpo3/index.sam.gz.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/67i98fdpo3/index.sam.gz.bai /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -b /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/67i98fdpo3/index.sam.gz.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index_dos.sam > /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/67i98fdpo3/index.sam.gz.bai /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index_dos.sam > /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -b /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/67i98fdpo3/index.cram.crai /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.cram 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index /tmp/67i98fdpo3/index.cram 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/67i98fdpo3/index.bcf.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.vcf > /tmp/67i98fdpo3/index.bcf 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.bcf 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/67i98fdpo3/index.vcf.gz.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.vcf > /tmp/67i98fdpo3/index.vcf.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.vcf.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/67i98fdpo3/index.vcf.gz.tbi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.vcf > /tmp/67i98fdpo3/index.vcf.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -t /tmp/67i98fdpo3/index.vcf.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/tabix /tmp/67i98fdpo3/index.vcf.gz##idx##/tmp/67i98fdpo3/index.vcf.gz.tbi 1:10000060-10000060 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/67i98fdpo3/index2.bam 1:1000000-1000000 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/67i98fdpo3/index2.bam 1:2000000-2000000 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/67i98fdpo3/index2.bam 2:1000000-1000000 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/67i98fdpo3/index2.bam 2:2000000-2000000 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/67i98fdpo3/index.bam.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.bam 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.bam 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/67i98fdpo3/index.bam.bai /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.bam 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -b /tmp/67i98fdpo3/index.bam 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/67i98fdpo3/index.sam.gz.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/67i98fdpo3/index.sam.gz.bai /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -b /tmp/67i98fdpo3/index.sam.gz 289s .. ok 289s 289s test_index: 289s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/67i98fdpo3/index.sam.gz.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index_dos.sam > /tmp/67i98fdpo3/index.sam.gz 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.sam.gz 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/67i98fdpo3/index.sam.gz.bai /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index_dos.sam > /tmp/67i98fdpo3/index.sam.gz 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -b /tmp/67i98fdpo3/index.sam.gz 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/67i98fdpo3/index.cram.crai /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.sam > /tmp/67i98fdpo3/index.cram 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index /tmp/67i98fdpo3/index.cram 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/67i98fdpo3/index.bcf.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.vcf > /tmp/67i98fdpo3/index.bcf 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.bcf 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/67i98fdpo3/index.vcf.gz.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.vcf > /tmp/67i98fdpo3/index.vcf.gz 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c /tmp/67i98fdpo3/index.vcf.gz 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/67i98fdpo3/index.vcf.gz.tbi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/index.vcf > /tmp/67i98fdpo3/index.vcf.gz 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -t /tmp/67i98fdpo3/index.vcf.gz 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/tabix /tmp/67i98fdpo3/index.vcf.gz##idx##/tmp/67i98fdpo3/index.vcf.gz.tbi 1:10000060-10000060 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/67i98fdpo3/index2.bam 1:1000000-1000000 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/67i98fdpo3/index2.bam 1:2000000-2000000 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/67i98fdpo3/index2.bam 2:1000000-1000000 290s .. ok 290s 290s test_index: 290s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/67i98fdpo3/index2.bam 2:2000000-2000000 290s .. ok 290s 290s test_view testing multi-ref CRAM modes: 290s ./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 290s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 290s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 290s ./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 290s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 290s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 290s ./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 290s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 290s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 290s .. ok 290s 290s test_view testing multi-ref CRAM modes: 290s ./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 290s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 290s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 290s ./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 290s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 290s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 290s ./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 290s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 290s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 290s .. ok 290s 290s test_view testing auxf#values.sam, ref auxf.fa: 290s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 290s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 290s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 290s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 290s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 290s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 290s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 290s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 290s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 290s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 290s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 290s .. ok 290s 290s test_view testing c1#bounds.sam, ref c1.fa: 290s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 290s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 290s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 290s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 290s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 290s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 290s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 290s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 290s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 290s .. ok 290s 290s test_view testing c1#clip.sam, ref c1.fa: 290s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 290s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 290s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 290s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 290s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 290s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 290s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 290s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 290s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing c1#noseq.sam, ref c1.fa: 291s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 291s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 291s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 291s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 291s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 291s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 291s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 291s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing c1#pad1.sam, ref c1.fa: 291s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 291s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 291s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 291s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 291s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 291s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 291s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 291s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing c1#pad2.sam, ref c1.fa: 291s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 291s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 291s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 291s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 291s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 291s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 291s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 291s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing c1#pad3.sam, ref c1.fa: 291s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 291s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 291s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 291s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 291s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 291s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 291s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 291s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing c1#unknown.sam, ref c1.fa: 291s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 291s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 291s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 291s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 291s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 291s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 291s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 291s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing c2#pad.sam, ref c2.fa: 291s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 291s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 291s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 291s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 291s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 291s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 291s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 291s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing ce#1.sam, ref ce.fa: 291s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 291s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 291s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 291s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 291s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 291s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 291s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 291s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing ce#1000.sam, ref ce.fa: 291s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 291s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 291s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 291s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 291s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 291s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 291s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 291s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 291s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 291s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 291s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 291s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 291s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 291s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing ce#2.sam, ref ce.fa: 291s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 291s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 291s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 291s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 291s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 291s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 291s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 291s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing ce#5.sam, ref ce.fa: 291s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 291s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 291s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 291s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 291s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 291s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 291s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 291s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 291s .. ok 291s 291s test_view testing ce#5b.sam, ref ce.fa: 291s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 291s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 291s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 291s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 291s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 291s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 291s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 291s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 291s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 291s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 291s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 291s .. ok 291s 291s test_view testing ce#large_seq.sam, ref ce.fa: 291s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 292s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 292s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 292s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 292s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 292s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 292s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 292s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing ce#supp.sam, ref ce.fa: 292s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 292s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 292s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 292s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 292s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 292s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 292s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 292s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing ce#tag_depadded.sam, ref ce.fa: 292s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 292s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 292s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 292s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 292s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 292s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 292s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 292s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing ce#tag_padded.sam, ref ce.fa: 292s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 292s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 292s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 292s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 292s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 292s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 292s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 292s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing ce#unmap.sam, ref ce.fa: 292s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 292s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 292s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 292s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 292s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 292s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 292s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 292s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing ce#unmap1.sam, ref ce.fa: 292s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 292s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 292s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 292s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 292s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 292s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 292s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 292s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing ce#unmap2.sam, ref ce.fa: 292s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 292s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 292s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 292s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 292s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 292s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 292s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 292s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing md#1.sam, ref md.fa: 292s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 292s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 292s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 292s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 292s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 292s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 292s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 292s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing xx#blank.sam, ref xx.fa: 292s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 292s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 292s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 292s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 292s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 292s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 292s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 292s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 292s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 292s .. ok 292s 292s test_view testing xx#large_aux.sam, ref xx.fa: 292s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 293s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 293s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 293s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 293s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 293s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 293s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 293s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 293s .. ok 293s 293s test_view testing xx#large_aux2.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 293s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 293s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 293s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 293s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#MD.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 293s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 293s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 293s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 293s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#MD2.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 293s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 293s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 293s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 293s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#minimal.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 293s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 293s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 293s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 293s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#pair.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 293s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 293s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 293s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 293s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#repeated.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 293s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 293s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 293s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 293s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#rg.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 293s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 293s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 293s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 293s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#tlen.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 293s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 293s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 293s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 293s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#tlen2.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 293s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 293s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 293s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 293s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#triplet.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 293s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 293s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 293s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 293s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing xx#unsorted.sam, ref xx.fa: 293s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 293s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 293s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 293s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 293s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 293s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 293s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 293s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 293s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 293s .. ok 293s 293s test_view testing embed_ref=2: 293s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 293s [W::cram_get_ref] Failed to populate reference for id 0 293s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 293s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 293s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 293s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 293s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 294s .. ok 294s 294s test_view testing region queries: 294s ./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 294s ./compare_sam.pl range.tmp range.out 294s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 294s ./compare_sam.pl range.tmp range.out 294s .. ok 294s 294s test_view testing BAM files with absent @SQ lines: 294s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 294s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 294s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 294s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 294s .. ok 294s 294s test_view testing large (> 2Gbases) positions: 294s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 294s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 294s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 294s test_view: 294s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 294s .. ok 294s 294s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 294s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 294s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 294s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 294s .. ok 294s 294s test_view testing auxf#values.sam, ref auxf.fa: 294s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 294s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 294s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 294s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 294s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 294s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 294s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 294s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 294s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 294s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 294s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 294s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 294s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 294s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 294s This is a technology demonstration that should not be used for archival data. 295s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 295s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 295s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 295s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 295s .. ok 295s 295s test_view testing c1#bounds.sam, ref c1.fa: 295s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 295s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 295s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 295s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 295s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 295s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 295s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 295s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 295s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 295s .. ok 295s 295s test_view testing c1#clip.sam, ref c1.fa: 295s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 295s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 295s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 295s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 295s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 295s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 295s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 295s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 295s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 295s .. ok 295s 295s test_view testing c1#noseq.sam, ref c1.fa: 295s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 295s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 295s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 295s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 295s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 295s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 295s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 295s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 295s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 295s .. ok 295s 295s test_view testing c1#pad1.sam, ref c1.fa: 295s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 295s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 295s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 295s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 295s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 295s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 295s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 295s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 295s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 295s .. ok 295s 295s test_view testing c1#pad2.sam, ref c1.fa: 295s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 295s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 295s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 295s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 295s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 295s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 295s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 295s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 295s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 295s .. ok 295s 295s test_view testing c1#pad3.sam, ref c1.fa: 295s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 295s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 295s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 295s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 295s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 295s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 295s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 295s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 295s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 295s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 296s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 296s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 296s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 296s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 296s This is a technology demonstration that should not be used for archival data. 296s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 296s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 296s .. ok 296s 296s test_view testing c1#unknown.sam, ref c1.fa: 296s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 296s ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 296s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 296s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 296s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 296s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 296s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 296s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 296s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 296s .. ok 296s 296s test_view testing c2#pad.sam, ref c2.fa: 296s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 296s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 296s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 296s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 296s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 296s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 296s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 296s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 296s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 296s .. ok 296s 296s test_view testing ce#1.sam, ref ce.fa: 296s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 296s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 296s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 296s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 296s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 296s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 296s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 296s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 296s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 296s .. ok 296s 296s test_view testing ce#1000.sam, ref ce.fa: 296s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 296s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 296s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 296s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 296s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 296s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 296s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 296s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 296s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 297s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 297s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 297s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 297s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 297s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 297s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 297s ./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 297s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 297s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 297s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 297s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 297s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 297s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 297s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 297s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 297s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 297s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 297s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 297s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 298s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 298s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 298s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 298s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 298s This is a technology demonstration that should not be used for archival data. 299s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 299s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 299s .. ok 299s 299s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 299s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 299s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 299s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 299s ./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 299s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 299s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 299s ./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 299s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 299s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 299s .. ok 299s 299s test_view testing ce#2.sam, ref ce.fa: 299s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 299s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 299s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 299s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 299s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 299s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 299s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 299s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 299s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 299s .. ok 299s 299s test_view testing ce#5.sam, ref ce.fa: 299s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 299s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 299s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 299s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 299s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 299s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 299s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 299s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 299s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 299s ./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 299s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 299s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 299s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 300s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 300s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 300s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 300s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 300s This is a technology demonstration that should not be used for archival data. 300s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 300s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 300s .. ok 300s 300s test_view testing ce#5b.sam, ref ce.fa: 300s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 300s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 300s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 300s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 300s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 300s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 300s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 300s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 300s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 300s ./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 300s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 300s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 300s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 300s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 300s .. ok 300s 300s test_view testing ce#large_seq.sam, ref ce.fa: 300s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 300s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 300s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 300s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 300s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 301s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 301s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 301s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 301s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 301s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 302s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 302s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 302s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 302s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 302s This is a technology demonstration that should not be used for archival data. 302s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 302s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 302s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 302s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 302s This is a technology demonstration that should not be used for archival data. 302s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 302s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 302s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 302s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 302s This is a technology demonstration that should not be used for archival data. 303s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 303s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 303s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 303s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 303s This is a technology demonstration that should not be used for archival data. 304s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 304s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 304s .. ok 304s 304s test_view testing ce#supp.sam, ref ce.fa: 304s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 304s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 304s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 304s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 304s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 304s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 304s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 304s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 304s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 304s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 304s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 304s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 304s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 304s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 304s This is a technology demonstration that should not be used for archival data. 305s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 305s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 305s .. ok 305s 305s test_view testing ce#tag_depadded.sam, ref ce.fa: 305s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 305s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 305s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 305s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 305s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 305s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 305s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 305s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 305s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 305s .. ok 305s 305s test_view testing ce#tag_padded.sam, ref ce.fa: 305s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 305s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 305s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 305s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 305s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 305s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 305s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 305s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 305s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 305s .. ok 305s 305s test_view testing ce#unmap.sam, ref ce.fa: 305s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 305s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 305s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 305s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 305s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 305s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 305s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 305s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 305s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 305s ./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 305s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 305s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 305s .. ok 305s 305s test_view testing ce#unmap1.sam, ref ce.fa: 305s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 305s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 305s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 305s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 305s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 305s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 305s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 305s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 305s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 305s ./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 305s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 305s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 305s .. ok 305s 305s test_view testing ce#unmap2.sam, ref ce.fa: 305s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 305s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 305s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 305s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 305s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 305s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 305s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 305s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 305s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 305s ./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 305s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 305s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 305s .. ok 305s 305s test_view testing md#1.sam, ref md.fa: 305s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 305s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 305s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 305s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 306s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 306s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 306s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 306s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 306s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 306s .. ok 306s 306s test_view testing xx#blank.sam, ref xx.fa: 306s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 306s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 306s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 306s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 306s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 306s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 306s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 306s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 306s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 306s ./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 306s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 306s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 306s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 306s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 306s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 306s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 306s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 306s This is a technology demonstration that should not be used for archival data. 306s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 306s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 306s .. ok 306s 306s test_view testing xx#large_aux.sam, ref xx.fa: 306s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 306s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 306s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 306s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 306s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 306s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 306s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 306s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 306s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 306s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 307s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 307s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 307s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 307s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 307s This is a technology demonstration that should not be used for archival data. 307s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 307s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 307s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 307s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 307s This is a technology demonstration that should not be used for archival data. 307s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 307s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 307s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 307s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 307s This is a technology demonstration that should not be used for archival data. 308s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 308s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 308s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 308s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 308s This is a technology demonstration that should not be used for archival data. 309s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 309s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 309s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 309s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 309s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 309s .. ok 309s 309s test_view testing xx#large_aux2.sam, ref xx.fa: 309s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 309s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 309s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 309s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 309s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 309s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 309s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 309s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 309s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 309s .. ok 309s 309s test_view testing xx#MD.sam, ref xx.fa: 309s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 309s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 309s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 309s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 309s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 309s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 309s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 309s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 309s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 309s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 309s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 309s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 310s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 310s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 310s This is a technology demonstration that should not be used for archival data. 310s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 310s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 310s .. ok 310s 310s test_view testing xx#MD2.sam, ref xx.fa: 310s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 310s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 310s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 310s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 310s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 310s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 310s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 310s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 310s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 310s .. ok 310s 310s test_view testing xx#minimal.sam, ref xx.fa: 310s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 310s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 310s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 310s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 310s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 310s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 310s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 310s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 310s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 310s ./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 310s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 310s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 310s .. ok 310s 310s test_view testing xx#pair.sam, ref xx.fa: 310s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 310s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 310s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 310s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 310s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 310s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 310s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 310s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 310s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 310s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 311s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 311s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 311s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 311s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 311s This is a technology demonstration that should not be used for archival data. 311s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 311s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 311s .. ok 311s 311s test_view testing xx#repeated.sam, ref xx.fa: 311s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 311s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 311s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 311s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 311s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 311s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 311s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 311s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 311s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 311s .. ok 311s 311s test_view testing xx#rg.sam, ref xx.fa: 311s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 311s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 311s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 311s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 311s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 311s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 311s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 311s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 311s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 311s .. ok 311s 311s test_view testing xx#tlen.sam, ref xx.fa: 311s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 311s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 311s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 311s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 311s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 311s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 311s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 311s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 311s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 311s ./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 311s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 311s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 311s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 312s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 312s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 312s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 312s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 312s This is a technology demonstration that should not be used for archival data. 312s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 313s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 313s .. ok 313s 313s test_view testing xx#tlen2.sam, ref xx.fa: 313s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 313s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 313s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 313s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 313s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 313s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 313s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 313s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 313s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 313s ./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 313s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 313s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 313s .. ok 313s 313s test_view testing xx#triplet.sam, ref xx.fa: 313s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 313s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 313s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 313s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 313s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 313s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 313s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 313s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 313s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 313s ./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 313s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 313s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 313s .. ok 313s 313s test_view testing xx#unsorted.sam, ref xx.fa: 313s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 313s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 313s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 313s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 313s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 313s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 313s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 313s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 313s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 313s .. ok 313s 313s test_view testing embed_ref=2: 313s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 313s [W::cram_get_ref] Failed to populate reference for id 0 313s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 313s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 313s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 313s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 313s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 313s .. ok 313s 313s test_view testing region queries: 313s ./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 313s ./compare_sam.pl range.tmp range.out 313s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 313s ./compare_sam.pl range.tmp range.out 313s .. ok 313s 313s test_view testing BAM files with absent @SQ lines: 313s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 313s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 313s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 313s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 313s .. ok 313s 313s test_view testing large (> 2Gbases) positions: 313s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 313s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 313s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 313s test_view: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 313s .. ok 313s 313s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 313s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 313s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 313s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 313s .. ok 313s 313s 313s test_MD testing xx#MD.sam, ref xx.fa: 313s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 313s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 313s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 313s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 313s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 313s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 313s Checking for MD/NM in xx#MD.sam 313s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 313s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 313s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 313s .. ok 313s 313s 313s test_MD testing xx#MD2.sam, ref xx.fa: 313s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 313s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 313s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 313s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 313s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 313s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 313s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 313s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 313s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 313s .. ok 313s 313s test_vcf_api: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-vcf-api /tmp/67i98fdpo3/test-vcf-api.bcf 313s [W::bcf_record_check] Bad BCF record at 1:1: No REF allele 313s [E::bcf_index_build3] TBI indices for BCF files are not supported 313s [E::idx_find_and_load] Could not retrieve index file for '/tmp/67i98fdpo3/test-vcf-api.bcf' 313s .. ok 313s 313s test_bcf2vcf: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/tabix/vcf_file.bcf 313s .. ok 313s 313s test_vcf_sweep: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-vcf-sweep /tmp/67i98fdpo3/test-vcf-api.bcf 313s .. ok 313s 313s test_vcf_various: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 313s .. ok 313s 313s test_vcf_various: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/formatcols.vcf 313s .. ok 313s 313s test_vcf_various: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/noroundtrip.vcf 313s .. ok 313s 313s test_vcf_various: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/formatmissing.vcf 313s .. ok 313s 313s test_vcf_various: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/vcf_meta_meta.vcf 313s .. ok 313s 313s test_vcf_various: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 313s .. ok 313s 313s test-bcf-sr: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 74452500 313s .. ok 313s 313s test-bcf-sr: 313s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 34270147 314s .. ok 314s 314s test-bcf-sr: 314s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 11108528 314s .. ok 314s 314s test-bcf-sr: 314s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 42233895 314s .. ok 314s 314s test-bcf-sr: 314s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 8111117 314s .. ok 314s 314s test-bcf-sr: 314s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 85644070 314s .. ok 314s 314s test-bcf-sr: 314s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 49879942 314s .. ok 314s 314s test-bcf-sr: 314s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 47881429 314s .. ok 314s 314s test-bcf-sr: 314s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 69081244 315s .. ok 315s 315s test-bcf-sr: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/67i98fdpo3 -s 83459376 315s .. ok 315s 315s test_bcf_sr_no_index: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/67i98fdpo3/no_index_1.err 315s .. ok 315s 315s test_bcf_sr_no_index: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/67i98fdpo3/no_index_2.out 2> /tmp/67i98fdpo3/no_index_2.err (expected fail) 315s .. ok 315s 315s test_bcf_sr_no_index: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/67i98fdpo3/no_index_3.out 2> /tmp/67i98fdpo3/no_index_3.err (expected fail) 315s .. ok 315s 315s test_bcf_sr_no_index: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/67i98fdpo3/no_index_4.out 2> /tmp/67i98fdpo3/no_index_4.err (expected fail) 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -b -p /tmp/67i98fdpo3/weird-chr-names.vcf.bcf -x /tmp/67i98fdpo3/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_1.out.vcf -r '1' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_2.out.vcf -r '1:1-2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_4.out.vcf -r '1:1-1' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_5.out.vcf -r '{1:1}' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf (expected fail) 315s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 315s Failed to set regions 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_14.out.vcf -t '1' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_15.out.vcf -t '1:1-2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_17.out.vcf -t '1:1-1' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_18.out.vcf -t '{1:1}' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf 315s .. ok 315s 315s test_bcf_sr_range: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/67i98fdpo3/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/67i98fdpo3/weird-chr-names.vcf.bcf (expected fail) 315s .. ok 315s 315s test_command: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf-translate - 315s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 315s Failed to set targets 315s .. ok 315s 315s test_convert_padded_header: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/67i98fdpo3/headernul0.bam 315s .. ok 315s 315s test_convert_padded_header: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/67i98fdpo3/headernul1.bam 315s .. ok 315s 315s test_convert_padded_header: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/67i98fdpo3/headernul678.bam 315s .. ok 315s 315s test_rebgzip: Alternate zlib/deflate library detected 315s test_rebgzip: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/bgziptest.txt 315s .. ok 315s 315s test-logging: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-logging.pl 315s .. ok 315s 315s test_plugin_loading: 315s HTS_PATH=/tmp/autopkgtest.VumChj/autopkgtest_tmp /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.VumChj/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn01.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn01.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn01.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02-r.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02_exp.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn02_exp-a.sam -o - 315s .. ok 315s 315s test_realn: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/realn03.sam -o - 315s .. ok 315s 315s test-bcf_set_variant_type: 315s /tmp/autopkgtest.VumChj/autopkgtest_tmp/test/test-bcf_set_variant_type 315s .. ok 315s 315s 315s Number of tests: 315s total .. 211 315s passed .. 211 315s failed .. 0 315s 315s PASS 315s + echo PASS 315s autopkgtest [06:42:27]: test run-unit-test: -----------------------] 316s autopkgtest [06:42:28]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 316s run-unit-test PASS 316s autopkgtest [06:42:28]: @@@@@@@@@@@@@@@@@@@@ summary 316s run-unit-test PASS 327s Creating nova instance adt-noble-s390x-htslib-20240324-063712-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240324.img (UUID e13d5247-1289-46d4-b3a9-3aa9fa45fdc9)...