0s autopkgtest [07:55:07]: starting date and time: 2024-03-25 07:55:07+0000 0s autopkgtest [07:55:07]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [07:55:07]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qn4exjv3/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-2@bos02-arm64-13.secgroup --name adt-noble-arm64-htslib-20240325-075507-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 128s autopkgtest [07:57:15]: testbed dpkg architecture: arm64 128s autopkgtest [07:57:15]: testbed apt version: 2.7.12 128s autopkgtest [07:57:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 130s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 131s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3987 kB] 132s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 132s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.8 kB] 132s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 132s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 132s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 132s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 132s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 132s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4365 kB] 133s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 133s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [71.0 kB] 133s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 145s Fetched 9853 kB in 7s (1427 kB/s) 146s Reading package lists... 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 156s Calculating upgrade... 157s The following packages will be REMOVED: 157s libssl3 157s The following NEW packages will be installed: 157s libssl3t64 157s The following packages have been kept back: 157s curl 157s The following packages will be upgraded: 157s openssl 157s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 157s Need to get 2777 kB of archives. 157s After this operation, 139 kB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 158s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 160s Fetched 2777 kB in 1s (3645 kB/s) 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 ... 75911 files and directories currently installed.) 160s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 160s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 161s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 161s wget depends on libssl3 (>= 3.0.0). 161s u-boot-tools depends on libssl3 (>= 3.0.0). 161s tnftp depends on libssl3 (>= 3.0.0). 161s tcpdump depends on libssl3 (>= 3.0.0). 161s systemd-resolved depends on libssl3 (>= 3.0.0). 161s systemd depends on libssl3 (>= 3.0.0). 161s sudo depends on libssl3 (>= 3.0.0). 161s sbsigntool depends on libssl3 (>= 3.0.0). 161s rsync depends on libssl3 (>= 3.0.0). 161s python3-cryptography depends on libssl3 (>= 3.0.0). 161s openssh-server depends on libssl3 (>= 3.0.10). 161s openssh-client depends on libssl3 (>= 3.0.10). 161s mtd-utils depends on libssl3 (>= 3.0.0). 161s mokutil depends on libssl3 (>= 3.0.0). 161s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 161s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 161s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 161s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 161s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 161s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 161s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 161s libnvme1 depends on libssl3 (>= 3.0.0). 161s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 161s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 161s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 161s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 161s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 161s kmod depends on libssl3 (>= 3.0.0). 161s dhcpcd-base depends on libssl3 (>= 3.0.0). 161s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 161s 161s (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 ... 75911 files and directories currently installed.) 161s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 161s Selecting previously unselected package libssl3t64:arm64. 161s (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 ... 75900 files and directories currently installed.) 161s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 161s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 162s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 162s Setting up openssl (3.0.13-0ubuntu2) ... 162s Processing triggers for man-db (2.12.0-3) ... 163s Processing triggers for libc-bin (2.39-0ubuntu6) ... 165s Reading package lists... 166s Building dependency tree... 166s Reading state information... 168s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 170s sh: Attempting to set up Debian/Ubuntu apt sources automatically 170s sh: Distribution appears to be Ubuntu 173s Reading package lists... 174s Building dependency tree... 174s Reading state information... 177s eatmydata is already the newest version (131-1). 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 180s dbus is already the newest version (1.14.10-4ubuntu1). 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 183s rng-tools-debian is already the newest version (2.4). 183s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 183s Reading package lists... 184s Building dependency tree... 184s Reading state information... 186s The following packages will be REMOVED: 186s cloud-init* python3-configobj* python3-debconf* 187s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 187s After this operation, 3256 kB disk space will be freed. 188s (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 ... 75913 files and directories currently installed.) 188s Removing cloud-init (24.1.2-0ubuntu1) ... 191s Removing python3-configobj (5.0.8-3) ... 192s Removing python3-debconf (1.5.86) ... 192s Processing triggers for man-db (2.12.0-3) ... 193s (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 ... 75524 files and directories currently installed.) 193s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 196s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 197s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 197s invoke-rc.d: policy-rc.d denied execution of try-restart. 197s Reading package lists... 198s Building dependency tree... 198s Reading state information... 200s linux-generic is already the newest version (6.8.0-11.11+1). 200s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 201s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 201s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 201s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 212s Reading package lists... 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 215s Calculating upgrade... 216s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 216s Reading package lists... 217s Building dependency tree... 217s Reading state information... 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 221s autopkgtest [07:58:47]: rebooting testbed after setup commands that affected boot 390s autopkgtest [08:01:37]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 394s autopkgtest [08:01:41]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 402s Get:1 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (dsc) [2437 B] 402s Get:2 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (tar) [1469 kB] 402s Get:3 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (diff) [20.1 kB] 403s gpgv: Signature made Tue Nov 7 20:35:25 2023 UTC 403s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 403s gpgv: issuer "emollier@debian.org" 403s gpgv: Can't check signature: No public key 403s dpkg-source: warning: cannot verify inline signature for ./htslib_1.18+ds-1.dsc: no acceptable signature found 404s autopkgtest [08:01:51]: testing package htslib version 1.18+ds-1 405s autopkgtest [08:01:52]: build not needed 406s autopkgtest [08:01:53]: test run-unit-test: preparing testbed 412s Reading package lists... 413s Building dependency tree... 413s Reading state information... 414s Starting pkgProblemResolver with broken count: 1 414s Starting 2 pkgProblemResolver with broken count: 1 414s Investigating (0) libssl3t64:arm64 < 3.0.13-0ubuntu2 @ii mK Ib > 414s Broken libssl3t64:arm64 Breaks on libssl3:arm64 < none -> 3.0.10-1ubuntu4 @un pumN > (< 3.0.13-0ubuntu2) 414s Considering libssl3:arm64 156 as a solution to libssl3t64:arm64 152 414s Removing libssl3t64:arm64 rather than change libssl3:arm64 414s Investigating (0) openssl:arm64 < 3.0.13-0ubuntu2 @ii mK Ib > 414s Broken openssl:arm64 Depends on libssl3t64:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 414s Considering libssl3t64:arm64 152 as a solution to openssl:arm64 13 414s Removing openssl:arm64 rather than change libssl3t64:arm64 414s Investigating (1) ca-certificates:arm64 < 20240203 @ii mK Ib > 414s Broken ca-certificates:arm64 Depends on openssl:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 414s Considering openssl:arm64 13 as a solution to ca-certificates:arm64 142 414s Added openssl:arm64 to the remove list 414s Fixing ca-certificates:arm64 via keep of openssl:arm64 414s Investigating (1) openssl:arm64 < 3.0.13-0ubuntu2 @ii mK Ib > 414s Broken openssl:arm64 Depends on libssl3t64:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 414s Considering libssl3t64:arm64 152 as a solution to openssl:arm64 13 414s Removing openssl:arm64 rather than change libssl3t64:arm64 414s Investigating (2) ca-certificates:arm64 < 20240203 @ii mK Ib > 414s Broken ca-certificates:arm64 Depends on openssl:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 414s Considering openssl:arm64 13 as a solution to ca-certificates:arm64 142 414s Added openssl:arm64 to the remove list 414s Fixing ca-certificates:arm64 via keep of openssl:arm64 414s Investigating (2) openssl:arm64 < 3.0.13-0ubuntu2 @ii mK Ib > 414s Broken openssl:arm64 Depends on libssl3t64:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 414s Considering libssl3t64:arm64 152 as a solution to openssl:arm64 142 414s Removing openssl:arm64 rather than change libssl3t64:arm64 414s Investigating (3) ca-certificates:arm64 < 20240203 @ii mK Ib > 414s Broken ca-certificates:arm64 Depends on openssl:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 414s Considering openssl:arm64 152 as a solution to ca-certificates:arm64 142 414s Removing ca-certificates:arm64 rather than change openssl:arm64 414s Investigating (3) python3-httplib2:arm64 < 0.20.4-3 @ii mK Ib > 414s Broken python3-httplib2:arm64 Depends on ca-certificates:arm64 < 20240203 @ii mR > 414s Considering ca-certificates:arm64 152 as a solution to python3-httplib2:arm64 6 414s Removing python3-httplib2:arm64 rather than change ca-certificates:arm64 414s Investigating (3) python3-apport:arm64 < 2.28.0-0ubuntu1 @ii mK Ib > 414s Broken python3-apport:arm64 Depends on python3-httplib2:arm64 < 0.20.4-3 @ii mR > 414s Considering python3-httplib2:arm64 152 as a solution to python3-apport:arm64 4 414s Removing python3-apport:arm64 rather than change python3-httplib2:arm64 414s Investigating (3) ssh-import-id:arm64 < 5.11-0ubuntu2 @ii mK Ib > 414s Broken ssh-import-id:arm64 Depends on ca-certificates:arm64 < 20240203 @ii mR > 414s Considering ca-certificates:arm64 152 as a solution to ssh-import-id:arm64 3 414s Removing ssh-import-id:arm64 rather than change ca-certificates:arm64 414s Investigating (3) python3-certifi:arm64 < 2023.11.17-1 @ii mK Ib > 414s Broken python3-certifi:arm64 Depends on ca-certificates:arm64 < 20240203 @ii mR > 414s Considering ca-certificates:arm64 152 as a solution to python3-certifi:arm64 2 414s Removing python3-certifi:arm64 rather than change ca-certificates:arm64 414s Investigating (3) python3-requests:arm64 < 2.31.0+dfsg-1ubuntu1 @ii mK Ib > 414s Broken python3-requests:arm64 Depends on python3-certifi:arm64 < 2023.11.17-1 @ii mR > 414s Considering python3-certifi:arm64 152 as a solution to python3-requests:arm64 2 414s Removing python3-requests:arm64 rather than change python3-certifi:arm64 414s Investigating (3) python3-lazr.restfulclient:arm64 < 0.14.6-1 @ii mK Ib > 414s Broken python3-lazr.restfulclient:arm64 Depends on python3-httplib2:arm64 < 0.20.4-3 @ii mR > (>= 0.7.7) 414s Considering python3-httplib2:arm64 152 as a solution to python3-lazr.restfulclient:arm64 2 414s Removing python3-lazr.restfulclient:arm64 rather than change python3-httplib2:arm64 414s Investigating (3) python3-launchpadlib:arm64 < 1.11.0-6 @ii mK Ib > 414s Broken python3-launchpadlib:arm64 Depends on python3-httplib2:arm64 < 0.20.4-3 @ii mR > 414s Considering python3-httplib2:arm64 152 as a solution to python3-launchpadlib:arm64 2 414s Removing python3-launchpadlib:arm64 rather than change python3-httplib2:arm64 414s Investigating (4) apport:arm64 < 2.28.0-0ubuntu1 @ii mK Ib > 414s Broken apport:arm64 Depends on python3-apport:arm64 < 2.28.0-0ubuntu1 @ii mR > (>= 2.28.0-0ubuntu1) 414s Considering python3-apport:arm64 152 as a solution to apport:arm64 6 414s Removing apport:arm64 rather than change python3-apport:arm64 414s Investigating (4) apport-core-dump-handler:arm64 < 2.28.0-0ubuntu1 @ii mK Ib > 414s Broken apport-core-dump-handler:arm64 Depends on apport:arm64 < 2.28.0-0ubuntu1 @ii mR > (>= 2.27.0-0ubuntu7~) 414s Considering apport:arm64 152 as a solution to apport-core-dump-handler:arm64 4 414s Removing apport-core-dump-handler:arm64 rather than change apport:arm64 414s Done 416s The following packages were automatically installed and are no longer required: 416s apport-symptoms python3-blinker python3-chardet python3-cryptography 416s python3-jwt python3-lazr.uri python3-oauthlib python3-openssl 416s python3-problem-report python3-pyparsing python3-six python3-systemd 416s python3-urllib3 python3-wadllib 416s Use 'sudo apt autoremove' to remove them. 416s The following additional packages will be installed: 416s autoconf automake autopoint autotools-dev build-essential cpp cpp-13 416s cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 416s dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 416s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 416s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext htslib-test 416s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 416s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 416s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 416s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 416s libhtscodecs-dev libhtscodecs2 libhwasan0 libisl23 libitm1 liblsan0 416s liblzma-dev libmpc3 libssl-dev libssl3 libstdc++-13-dev libsub-override-perl 416s libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf rpcsvc-proto tabix 416s zlib1g-dev 416s Suggested packages: 416s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 416s cpp-13-doc dh-make gcc-13-doc gcc-multilib manpages-dev flex bison gdb 416s gcc-doc gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 416s glibc-doc libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev 416s librtmp-dev libssh2-1-dev pkg-config liblzma-doc libssl-doc libstdc++-13-doc 416s libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl 416s Recommended packages: 416s bzip2-doc manpages manpages-dev libc-devtools libarchive-cpio-perl 416s libltdl-dev libmail-sendmail-perl 416s The following packages will be REMOVED: 416s apport apport-core-dump-handler ca-certificates libssl3t64 openssl 416s python3-apport python3-certifi python3-httplib2 python3-launchpadlib 417s python3-lazr.restfulclient python3-requests ssh-import-id 417s The following NEW packages will be installed: 417s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 417s cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 417s debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 417s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 417s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext htslib-test 417s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 417s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 417s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 417s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 417s libhtscodecs-dev libhtscodecs2 libhwasan0 libisl23 libitm1 liblsan0 417s liblzma-dev libmpc3 libssl-dev libssl3 libstdc++-13-dev libsub-override-perl 417s libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf rpcsvc-proto tabix 417s zlib1g-dev 417s 0 upgraded, 65 newly installed, 12 to remove and 0 not upgraded. 417s Need to get 82.5 MB/82.5 MB of archives. 417s After this operation, 273 MB of additional disk space will be used. 417s Get:1 /tmp/autopkgtest.1VWTPy/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [816 B] 417s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libssl3 arm64 3.0.10-1ubuntu4 [1764 kB] 417s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4 [240 kB] 417s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB] 417s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB] 417s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 418s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 autopoint all 0.21-14ubuntu1 [422 kB] 418s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu6 [19.7 kB] 418s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 418s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 418s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 418s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu6 [1596 kB] 418s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 418s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 418s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 418s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 418s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 418s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 418s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 418s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 418s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 418s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 418s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 418s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 419s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 419s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 419s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 419s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 419s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 420s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 420s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 420s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 420s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 420s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 421s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 421s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 421s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 421s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 421s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 421s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7 [166 kB] 421s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB] 421s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 421s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB] 421s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 421s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] 421s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libdw1 arm64 0.190-1 [254 kB] 421s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] 421s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 dwz arm64 0.15-1 [110 kB] 421s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 gettext arm64 0.21-14ubuntu1 [846 kB] 421s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 421s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 421s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 debhelper all 13.14.1ubuntu1 [869 kB] 421s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 htslib-test all 1.18+ds-1 [1120 kB] 421s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 421s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libcurl4-gnutls-dev arm64 8.5.0-2ubuntu2 [448 kB] 421s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 421s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate-dev arm64 1.19-1 [51.2 kB] 421s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 421s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 421s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 421s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 421s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts-dev arm64 1.18+ds-1 [5806 kB] 421s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs-dev arm64 1.6.0-1 [2975 kB] 422s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libssl-dev arm64 3.0.10-1ubuntu4 [2330 kB] 422s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 tabix arm64 1.18+ds-1 [505 kB] 423s Fetched 82.5 MB in 5s (16.1 MB/s) 424s (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 ... 75469 files and directories currently installed.) 424s Removing ssh-import-id (5.11-0ubuntu2) ... 424s Removing apport-core-dump-handler (2.28.0-0ubuntu1) ... 426s Removing apport (2.28.0-0ubuntu1) ... 428s Removing python3-apport (2.28.0-0ubuntu1) ... 428s Removing python3-requests (2.31.0+dfsg-1ubuntu1) ... 429s dpkg: ca-certificates: dependency problems, but removing anyway as you requested: 429s python3-httplib2 depends on ca-certificates. 429s python3-certifi depends on ca-certificates. 429s 429s Removing ca-certificates (20240203) ... 430s Removing dangling symlinks from /etc/ssl/certs... done. 430s Removing openssl (3.0.13-0ubuntu2) ... 430s dpkg: libssl3t64:arm64: dependency problems, but removing anyway as you requested: 430s wget depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s u-boot-tools depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s tnftp depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s tcpdump depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s systemd-resolved depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s systemd depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s sudo depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s sbsigntool depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s rsync depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s python3-cryptography depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s openssh-server depends on libssl3 (>= 3.0.10); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s openssh-client depends on libssl3 (>= 3.0.10); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s mtd-utils depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s mokutil depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libssh-4:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libnvme1 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libkmod2:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libfido2-1:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libcurl4:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s kmod depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s dhcpcd-base depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s bind9-libs:arm64 depends on libssl3 (>= 3.0.0); however: 430s Package libssl3 is not installed. 430s Package libssl3t64:arm64 which provides libssl3 is to be removed. 430s 430s Removing libssl3t64:arm64 (3.0.13-0ubuntu2) ... 430s Selecting previously unselected package libssl3:arm64. 430s (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 ... 74808 files and directories currently installed.) 430s Preparing to unpack .../libssl3_3.0.10-1ubuntu4_arm64.deb ... 430s Unpacking libssl3:arm64 (3.0.10-1ubuntu4) ... 431s (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 ... 74819 files and directories currently installed.) 431s Removing python3-certifi (2023.11.17-1) ... 431s Removing python3-launchpadlib (1.11.0-6) ... 431s Removing python3-lazr.restfulclient (0.14.6-1) ... 432s Removing python3-httplib2 (0.20.4-3) ... 432s Selecting previously unselected package m4. 432s (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 ... 74705 files and directories currently installed.) 432s Preparing to unpack .../00-m4_1.4.19-4_arm64.deb ... 432s Unpacking m4 (1.4.19-4) ... 432s Selecting previously unselected package autoconf. 432s Preparing to unpack .../01-autoconf_2.71-3_all.deb ... 432s Unpacking autoconf (2.71-3) ... 432s Selecting previously unselected package autotools-dev. 433s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 433s Unpacking autotools-dev (20220109.1) ... 433s Selecting previously unselected package automake. 433s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 433s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 433s Selecting previously unselected package autopoint. 433s Preparing to unpack .../04-autopoint_0.21-14ubuntu1_all.deb ... 433s Unpacking autopoint (0.21-14ubuntu1) ... 433s Selecting previously unselected package libc-dev-bin. 433s Preparing to unpack .../05-libc-dev-bin_2.39-0ubuntu6_arm64.deb ... 433s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 433s Selecting previously unselected package linux-libc-dev:arm64. 433s Preparing to unpack .../06-linux-libc-dev_6.8.0-11.11_arm64.deb ... 433s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 434s Selecting previously unselected package libcrypt-dev:arm64. 434s Preparing to unpack .../07-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 434s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 434s Selecting previously unselected package rpcsvc-proto. 434s Preparing to unpack .../08-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 434s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 434s Selecting previously unselected package libc6-dev:arm64. 434s Preparing to unpack .../09-libc6-dev_2.39-0ubuntu6_arm64.deb ... 434s Unpacking libc6-dev:arm64 (2.39-0ubuntu6) ... 435s Selecting previously unselected package libisl23:arm64. 435s Preparing to unpack .../10-libisl23_0.26-3_arm64.deb ... 435s Unpacking libisl23:arm64 (0.26-3) ... 435s Selecting previously unselected package libmpc3:arm64. 435s Preparing to unpack .../11-libmpc3_1.3.1-1_arm64.deb ... 435s Unpacking libmpc3:arm64 (1.3.1-1) ... 435s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 435s Preparing to unpack .../12-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 435s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 436s Selecting previously unselected package cpp-13. 437s Preparing to unpack .../13-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 437s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 437s Selecting previously unselected package cpp-aarch64-linux-gnu. 437s Preparing to unpack .../14-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 437s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 437s Selecting previously unselected package cpp. 437s Preparing to unpack .../15-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 437s Unpacking cpp (4:13.2.0-7ubuntu1) ... 437s Selecting previously unselected package libcc1-0:arm64. 437s Preparing to unpack .../16-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 437s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 437s Selecting previously unselected package libgomp1:arm64. 437s Preparing to unpack .../17-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 437s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 437s Selecting previously unselected package libitm1:arm64. 437s Preparing to unpack .../18-libitm1_14-20240303-1ubuntu1_arm64.deb ... 437s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 437s Selecting previously unselected package libatomic1:arm64. 437s Preparing to unpack .../19-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 437s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 437s Selecting previously unselected package libasan8:arm64. 437s Preparing to unpack .../20-libasan8_14-20240303-1ubuntu1_arm64.deb ... 437s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 438s Selecting previously unselected package liblsan0:arm64. 438s Preparing to unpack .../21-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 438s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 438s Selecting previously unselected package libtsan2:arm64. 438s Preparing to unpack .../22-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 438s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 438s Selecting previously unselected package libubsan1:arm64. 438s Preparing to unpack .../23-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 438s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 438s Selecting previously unselected package libhwasan0:arm64. 438s Preparing to unpack .../24-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 438s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 439s Selecting previously unselected package libgcc-13-dev:arm64. 439s Preparing to unpack .../25-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 439s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 439s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 439s Preparing to unpack .../26-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 439s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 442s Selecting previously unselected package gcc-13. 442s Preparing to unpack .../27-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 442s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 442s Selecting previously unselected package gcc-aarch64-linux-gnu. 442s Preparing to unpack .../28-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 442s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 442s Selecting previously unselected package gcc. 442s Preparing to unpack .../29-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 442s Unpacking gcc (4:13.2.0-7ubuntu1) ... 442s Selecting previously unselected package libstdc++-13-dev:arm64. 442s Preparing to unpack .../30-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 442s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 443s Selecting previously unselected package g++-13-aarch64-linux-gnu. 443s Preparing to unpack .../31-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 443s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 444s Selecting previously unselected package g++-13. 445s Preparing to unpack .../32-g++-13_13.2.0-17ubuntu2_arm64.deb ... 445s Unpacking g++-13 (13.2.0-17ubuntu2) ... 445s Selecting previously unselected package g++-aarch64-linux-gnu. 445s Preparing to unpack .../33-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 445s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 445s Selecting previously unselected package g++. 445s Preparing to unpack .../34-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 445s Unpacking g++ (4:13.2.0-7ubuntu1) ... 445s Selecting previously unselected package build-essential. 445s Preparing to unpack .../35-build-essential_12.10ubuntu1_arm64.deb ... 445s Unpacking build-essential (12.10ubuntu1) ... 445s Selecting previously unselected package libdebhelper-perl. 445s Preparing to unpack .../36-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 445s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 445s Selecting previously unselected package libtool. 445s Preparing to unpack .../37-libtool_2.4.7-7_all.deb ... 445s Unpacking libtool (2.4.7-7) ... 445s Selecting previously unselected package dh-autoreconf. 445s Preparing to unpack .../38-dh-autoreconf_20_all.deb ... 445s Unpacking dh-autoreconf (20) ... 445s Selecting previously unselected package libarchive-zip-perl. 445s Preparing to unpack .../39-libarchive-zip-perl_1.68-1_all.deb ... 445s Unpacking libarchive-zip-perl (1.68-1) ... 445s Selecting previously unselected package libsub-override-perl. 445s Preparing to unpack .../40-libsub-override-perl_0.10-1_all.deb ... 445s Unpacking libsub-override-perl (0.10-1) ... 446s Selecting previously unselected package libfile-stripnondeterminism-perl. 446s Preparing to unpack .../41-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 446s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 446s Selecting previously unselected package dh-strip-nondeterminism. 446s Preparing to unpack .../42-dh-strip-nondeterminism_1.13.1-1_all.deb ... 446s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 446s Selecting previously unselected package libdw1:arm64. 446s Preparing to unpack .../43-libdw1_0.190-1_arm64.deb ... 446s Unpacking libdw1:arm64 (0.190-1) ... 446s Selecting previously unselected package debugedit. 446s Preparing to unpack .../44-debugedit_1%3a5.0-5_arm64.deb ... 446s Unpacking debugedit (1:5.0-5) ... 446s Selecting previously unselected package dwz. 446s Preparing to unpack .../45-dwz_0.15-1_arm64.deb ... 446s Unpacking dwz (0.15-1) ... 446s Selecting previously unselected package gettext. 446s Preparing to unpack .../46-gettext_0.21-14ubuntu1_arm64.deb ... 446s Unpacking gettext (0.21-14ubuntu1) ... 446s Selecting previously unselected package intltool-debian. 446s Preparing to unpack .../47-intltool-debian_0.35.0+20060710.6_all.deb ... 446s Unpacking intltool-debian (0.35.0+20060710.6) ... 446s Selecting previously unselected package po-debconf. 447s Preparing to unpack .../48-po-debconf_1.0.21+nmu1_all.deb ... 447s Unpacking po-debconf (1.0.21+nmu1) ... 447s Selecting previously unselected package debhelper. 447s Preparing to unpack .../49-debhelper_13.14.1ubuntu1_all.deb ... 447s Unpacking debhelper (13.14.1ubuntu1) ... 447s Selecting previously unselected package htslib-test. 447s Preparing to unpack .../50-htslib-test_1.18+ds-1_all.deb ... 447s Unpacking htslib-test (1.18+ds-1) ... 448s Selecting previously unselected package libbz2-dev:arm64. 448s Preparing to unpack .../51-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 448s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 448s Selecting previously unselected package libcurl4-gnutls-dev:arm64. 448s Preparing to unpack .../52-libcurl4-gnutls-dev_8.5.0-2ubuntu2_arm64.deb ... 448s Unpacking libcurl4-gnutls-dev:arm64 (8.5.0-2ubuntu2) ... 448s Selecting previously unselected package libdeflate0:arm64. 448s Preparing to unpack .../53-libdeflate0_1.19-1_arm64.deb ... 448s Unpacking libdeflate0:arm64 (1.19-1) ... 448s Selecting previously unselected package libdeflate-dev:arm64. 448s Preparing to unpack .../54-libdeflate-dev_1.19-1_arm64.deb ... 448s Unpacking libdeflate-dev:arm64 (1.19-1) ... 448s Selecting previously unselected package libhtscodecs2:arm64. 448s Preparing to unpack .../55-libhtscodecs2_1.6.0-1_arm64.deb ... 448s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 448s Selecting previously unselected package libhts3:arm64. 448s Preparing to unpack .../56-libhts3_1.18+ds-1_arm64.deb ... 448s Unpacking libhts3:arm64 (1.18+ds-1) ... 448s Selecting previously unselected package liblzma-dev:arm64. 448s Preparing to unpack .../57-liblzma-dev_5.4.5-0.3_arm64.deb ... 448s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 449s Selecting previously unselected package zlib1g-dev:arm64. 449s Preparing to unpack .../58-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 449s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 449s Selecting previously unselected package libhts-dev:arm64. 449s Preparing to unpack .../59-libhts-dev_1.18+ds-1_arm64.deb ... 449s Unpacking libhts-dev:arm64 (1.18+ds-1) ... 449s Selecting previously unselected package libhtscodecs-dev:arm64. 449s Preparing to unpack .../60-libhtscodecs-dev_1.6.0-1_arm64.deb ... 449s Unpacking libhtscodecs-dev:arm64 (1.6.0-1) ... 450s Selecting previously unselected package libssl-dev:arm64. 450s Preparing to unpack .../61-libssl-dev_3.0.10-1ubuntu4_arm64.deb ... 450s Unpacking libssl-dev:arm64 (3.0.10-1ubuntu4) ... 450s Selecting previously unselected package tabix. 450s Preparing to unpack .../62-tabix_1.18+ds-1_arm64.deb ... 450s Unpacking tabix (1.18+ds-1) ... 451s Selecting previously unselected package autopkgtest-satdep. 451s Preparing to unpack .../63-1-autopkgtest-satdep.deb ... 451s Unpacking autopkgtest-satdep (0) ... 451s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 451s Setting up libdw1:arm64 (0.190-1) ... 451s Setting up libarchive-zip-perl (1.68-1) ... 451s Setting up htslib-test (1.18+ds-1) ... 451s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 451s Setting up libssl3:arm64 (3.0.10-1ubuntu4) ... 451s Setting up libdeflate0:arm64 (1.19-1) ... 451s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 451s Setting up m4 (1.4.19-4) ... 451s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 451s Setting up libcurl4-gnutls-dev:arm64 (8.5.0-2ubuntu2) ... 451s Setting up libhtscodecs-dev:arm64 (1.6.0-1) ... 451s Setting up autotools-dev (20220109.1) ... 451s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 451s Setting up libssl-dev:arm64 (3.0.10-1ubuntu4) ... 451s Setting up libmpc3:arm64 (1.3.1-1) ... 451s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 451s Setting up autopoint (0.21-14ubuntu1) ... 451s Setting up autoconf (2.71-3) ... 451s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 451s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 451s Setting up dwz (0.15-1) ... 451s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 451s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 451s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 451s Setting up debugedit (1:5.0-5) ... 451s Setting up libsub-override-perl (0.10-1) ... 451s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 451s Setting up libisl23:arm64 (0.26-3) ... 451s Setting up libc-dev-bin (2.39-0ubuntu6) ... 451s Setting up libdeflate-dev:arm64 (1.19-1) ... 451s Setting up tabix (1.18+ds-1) ... 451s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 451s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 451s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 451s Setting up automake (1:1.16.5-1.3ubuntu1) ... 451s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 451s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 451s Setting up libhts3:arm64 (1.18+ds-1) ... 451s Setting up gettext (0.21-14ubuntu1) ... 451s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 451s Setting up intltool-debian (0.35.0+20060710.6) ... 451s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 451s Setting up dh-strip-nondeterminism (1.13.1-1) ... 451s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 451s Setting up libc6-dev:arm64 (2.39-0ubuntu6) ... 451s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 451s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 451s Setting up cpp-13 (13.2.0-17ubuntu2) ... 451s Setting up po-debconf (1.0.21+nmu1) ... 451s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 451s Setting up gcc-13 (13.2.0-17ubuntu2) ... 451s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 451s Setting up cpp (4:13.2.0-7ubuntu1) ... 451s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 451s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 451s Setting up g++-13 (13.2.0-17ubuntu2) ... 451s Setting up libtool (2.4.7-7) ... 451s Setting up libhts-dev:arm64 (1.18+ds-1) ... 451s Setting up gcc (4:13.2.0-7ubuntu1) ... 451s Setting up dh-autoreconf (20) ... 451s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 451s Setting up debhelper (13.14.1ubuntu1) ... 451s Setting up g++ (4:13.2.0-7ubuntu1) ... 451s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 451s Setting up build-essential (12.10ubuntu1) ... 451s Setting up autopkgtest-satdep (0) ... 451s Processing triggers for man-db (2.12.0-3) ... 454s Processing triggers for install-info (7.1-3) ... 454s Processing triggers for libc-bin (2.39-0ubuntu6) ... 464s (Reading database ... 79541 files and directories currently installed.) 464s Removing autopkgtest-satdep (0) ... 465s autopkgtest [08:02:52]: test run-unit-test: [----------------------- 465s + pkg=htslib 465s + '[' /tmp/autopkgtest.1VWTPy/autopkgtest_tmp = '' ']' 465s + 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.1VWTPy/autopkgtest_tmp 466s + cp -aL htslib.pc.in /tmp/autopkgtest.1VWTPy/autopkgtest_tmp 466s + cp -aL htslib.map /tmp/autopkgtest.1VWTPy/autopkgtest_tmp 466s + cd /tmp/autopkgtest.1VWTPy/autopkgtest_tmp 466s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 466s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 466s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 466s + grep sse /proc/cpuinfo 466s + export CFLAGS 466s + make -e check 466s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c 466s : warning: "_FORTIFY_SOURCE" redefined 466s : note: this is the location of the previous definition 466s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c 466s : warning: "_FORTIFY_SOURCE" redefined 466s : note: this is the location of the previous definition 467s 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 467s : warning: "_FORTIFY_SOURCE" redefined 467s : note: this is the location of the previous definition 470s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c 470s : warning: "_FORTIFY_SOURCE" redefined 470s : note: this is the location of the previous definition 473s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c 473s : warning: "_FORTIFY_SOURCE" redefined 473s : note: this is the location of the previous definition 474s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c 474s : warning: "_FORTIFY_SOURCE" redefined 474s : note: this is the location of the previous definition 476s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c 476s : warning: "_FORTIFY_SOURCE" redefined 476s : note: this is the location of the previous definition 481s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c 481s : warning: "_FORTIFY_SOURCE" redefined 481s : note: this is the location of the previous definition 482s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c 483s : warning: "_FORTIFY_SOURCE" redefined 483s : note: this is the location of the previous definition 492s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c 492s : warning: "_FORTIFY_SOURCE" redefined 492s : note: this is the location of the previous definition 494s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c 494s : warning: "_FORTIFY_SOURCE" redefined 494s : note: this is the location of the previous definition 494s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c 494s : warning: "_FORTIFY_SOURCE" redefined 494s : note: this is the location of the previous definition 495s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c 495s : warning: "_FORTIFY_SOURCE" redefined 495s : note: this is the location of the previous definition 495s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c 495s : warning: "_FORTIFY_SOURCE" redefined 495s : note: this is the location of the previous definition 496s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c 496s : warning: "_FORTIFY_SOURCE" redefined 496s : note: this is the location of the previous definition 497s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c 497s : warning: "_FORTIFY_SOURCE" redefined 497s : note: this is the location of the previous definition 499s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c 499s : warning: "_FORTIFY_SOURCE" redefined 499s : note: this is the location of the previous definition 500s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c 500s : warning: "_FORTIFY_SOURCE" redefined 500s : note: this is the location of the previous definition 514s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c 514s : warning: "_FORTIFY_SOURCE" redefined 514s : note: this is the location of the previous definition 515s 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 515s : warning: "_FORTIFY_SOURCE" redefined 515s : note: this is the location of the previous definition 518s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c 518s : warning: "_FORTIFY_SOURCE" redefined 518s : note: this is the location of the previous definition 518s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c 518s : warning: "_FORTIFY_SOURCE" redefined 518s : note: this is the location of the previous definition 519s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c 519s : warning: "_FORTIFY_SOURCE" redefined 519s : note: this is the location of the previous definition 520s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c 520s : warning: "_FORTIFY_SOURCE" redefined 520s : note: this is the location of the previous definition 521s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c 521s : warning: "_FORTIFY_SOURCE" redefined 521s : note: this is the location of the previous definition 538s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c 538s : warning: "_FORTIFY_SOURCE" redefined 538s : note: this is the location of the previous definition 542s 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 542s : warning: "_FORTIFY_SOURCE" redefined 542s : note: this is the location of the previous definition 549s 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 549s : warning: "_FORTIFY_SOURCE" redefined 549s : note: this is the location of the previous definition 556s 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 556s : warning: "_FORTIFY_SOURCE" redefined 556s : note: this is the location of the previous definition 565s 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 565s : warning: "_FORTIFY_SOURCE" redefined 565s : note: this is the location of the previous definition 566s 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 566s : warning: "_FORTIFY_SOURCE" redefined 566s : note: this is the location of the previous definition 568s 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 568s : warning: "_FORTIFY_SOURCE" redefined 568s : note: this is the location of the previous definition 576s 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 576s : warning: "_FORTIFY_SOURCE" redefined 576s : note: this is the location of the previous definition 577s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c 577s : warning: "_FORTIFY_SOURCE" redefined 577s : note: this is the location of the previous definition 578s 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 578s : warning: "_FORTIFY_SOURCE" redefined 578s : note: this is the location of the previous definition 579s 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 579s : warning: "_FORTIFY_SOURCE" redefined 579s : note: this is the location of the previous definition 579s 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 579s : warning: "_FORTIFY_SOURCE" redefined 579s : note: this is the location of the previous definition 579s 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 579s : warning: "_FORTIFY_SOURCE" redefined 579s : note: this is the location of the previous definition 580s 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 580s ranlib libhts.a 580s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c 580s : warning: "_FORTIFY_SOURCE" redefined 580s : note: this is the location of the previous definition 581s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c 581s : warning: "_FORTIFY_SOURCE" redefined 581s : note: this is the location of the previous definition 582s 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 582s : warning: "_FORTIFY_SOURCE" redefined 582s : note: this is the location of the previous definition 585s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c 585s : warning: "_FORTIFY_SOURCE" redefined 585s : note: this is the location of the previous definition 588s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c 588s : warning: "_FORTIFY_SOURCE" redefined 588s : note: this is the location of the previous definition 589s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c 589s : warning: "_FORTIFY_SOURCE" redefined 589s : note: this is the location of the previous definition 591s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c 591s : warning: "_FORTIFY_SOURCE" redefined 591s : note: this is the location of the previous definition 596s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c 596s : warning: "_FORTIFY_SOURCE" redefined 596s : note: this is the location of the previous definition 598s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c 598s : warning: "_FORTIFY_SOURCE" redefined 598s : note: this is the location of the previous definition 608s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c 608s : warning: "_FORTIFY_SOURCE" redefined 608s : note: this is the location of the previous definition 610s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c 610s : warning: "_FORTIFY_SOURCE" redefined 610s : note: this is the location of the previous definition 610s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c 610s : warning: "_FORTIFY_SOURCE" redefined 610s : note: this is the location of the previous definition 611s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c 611s : warning: "_FORTIFY_SOURCE" redefined 611s : note: this is the location of the previous definition 612s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c 612s : warning: "_FORTIFY_SOURCE" redefined 612s : note: this is the location of the previous definition 613s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c 613s : warning: "_FORTIFY_SOURCE" redefined 613s : note: this is the location of the previous definition 614s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c 614s : warning: "_FORTIFY_SOURCE" redefined 614s : note: this is the location of the previous definition 615s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c 615s : warning: "_FORTIFY_SOURCE" redefined 615s : note: this is the location of the previous definition 616s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c 616s : warning: "_FORTIFY_SOURCE" redefined 616s : note: this is the location of the previous definition 630s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c 630s : warning: "_FORTIFY_SOURCE" redefined 630s : note: this is the location of the previous definition 631s 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 631s : warning: "_FORTIFY_SOURCE" redefined 631s : note: this is the location of the previous definition 634s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 635s : warning: "_FORTIFY_SOURCE" redefined 635s : note: this is the location of the previous definition 635s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c 635s : warning: "_FORTIFY_SOURCE" redefined 635s : note: this is the location of the previous definition 636s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c 636s : warning: "_FORTIFY_SOURCE" redefined 636s : note: this is the location of the previous definition 637s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c 637s : warning: "_FORTIFY_SOURCE" redefined 637s : note: this is the location of the previous definition 638s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c 638s : warning: "_FORTIFY_SOURCE" redefined 638s : note: this is the location of the previous definition 655s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c 656s : warning: "_FORTIFY_SOURCE" redefined 656s : note: this is the location of the previous definition 660s 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 660s : warning: "_FORTIFY_SOURCE" redefined 660s : note: this is the location of the previous definition 666s 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 667s : warning: "_FORTIFY_SOURCE" redefined 667s : note: this is the location of the previous definition 674s 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 674s : warning: "_FORTIFY_SOURCE" redefined 674s : note: this is the location of the previous definition 684s 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 684s : warning: "_FORTIFY_SOURCE" redefined 684s : note: this is the location of the previous definition 686s 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 686s : warning: "_FORTIFY_SOURCE" redefined 686s : note: this is the location of the previous definition 687s 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 687s : warning: "_FORTIFY_SOURCE" redefined 687s : note: this is the location of the previous definition 696s 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 696s : warning: "_FORTIFY_SOURCE" redefined 696s : note: this is the location of the previous definition 697s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c 697s : warning: "_FORTIFY_SOURCE" redefined 697s : note: this is the location of the previous definition 698s 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 698s : warning: "_FORTIFY_SOURCE" redefined 698s : note: this is the location of the previous definition 699s 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 699s : warning: "_FORTIFY_SOURCE" redefined 699s : note: this is the location of the previous definition 699s 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 699s : warning: "_FORTIFY_SOURCE" redefined 699s : note: this is the location of the previous definition 699s 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 699s : warning: "_FORTIFY_SOURCE" redefined 699s : note: this is the location of the previous definition 700s 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 700s ln -sf libhts.so libhts.so.3 700s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c 700s : warning: "_FORTIFY_SOURCE" redefined 700s : note: this is the location of the previous definition 701s 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 702s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c 702s : warning: "_FORTIFY_SOURCE" redefined 702s : note: this is the location of the previous definition 702s 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 703s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c 703s : warning: "_FORTIFY_SOURCE" redefined 703s : note: this is the location of the previous definition 704s 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 704s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 704s : warning: "_FORTIFY_SOURCE" redefined 704s : note: this is the location of the previous definition 708s 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 708s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 708s : warning: "_FORTIFY_SOURCE" redefined 708s : note: this is the location of the previous definition 708s 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 708s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c 708s : warning: "_FORTIFY_SOURCE" redefined 708s : note: this is the location of the previous definition 712s 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 712s 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 712s : warning: "_FORTIFY_SOURCE" redefined 712s : note: this is the location of the previous definition 714s 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 714s 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 714s : warning: "_FORTIFY_SOURCE" redefined 714s : note: this is the location of the previous definition 715s 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 716s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c 716s : warning: "_FORTIFY_SOURCE" redefined 716s : note: this is the location of the previous definition 716s 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 716s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c 716s : warning: "_FORTIFY_SOURCE" redefined 716s : note: this is the location of the previous definition 717s 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 717s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c 717s : warning: "_FORTIFY_SOURCE" redefined 717s : note: this is the location of the previous definition 718s 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 718s 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 718s : warning: "_FORTIFY_SOURCE" redefined 718s : note: this is the location of the previous definition 719s 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 719s 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 719s : warning: "_FORTIFY_SOURCE" redefined 719s : note: this is the location of the previous definition 719s 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 719s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c 719s : warning: "_FORTIFY_SOURCE" redefined 719s : note: this is the location of the previous definition 723s 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 723s 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 723s : warning: "_FORTIFY_SOURCE" redefined 723s : note: this is the location of the previous definition 725s 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 725s 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 725s : warning: "_FORTIFY_SOURCE" redefined 725s : note: this is the location of the previous definition 726s 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 726s 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 726s : warning: "_FORTIFY_SOURCE" redefined 726s : note: this is the location of the previous definition 727s 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 727s 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 727s : warning: "_FORTIFY_SOURCE" redefined 727s : note: this is the location of the previous definition 727s 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 727s 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 727s : warning: "_FORTIFY_SOURCE" redefined 727s : note: this is the location of the previous definition 728s 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 728s 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 728s : warning: "_FORTIFY_SOURCE" redefined 728s : note: this is the location of the previous definition 729s 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 729s 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 729s : warning: "_FORTIFY_SOURCE" redefined 729s : note: this is the location of the previous definition 729s 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 729s 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 729s : warning: "_FORTIFY_SOURCE" redefined 729s : note: this is the location of the previous definition 730s 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 730s 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 730s : warning: "_FORTIFY_SOURCE" redefined 730s : note: this is the location of the previous definition 731s 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 731s 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 731s : warning: "_FORTIFY_SOURCE" redefined 731s : note: this is the location of the previous definition 732s 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 732s 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 732s : warning: "_FORTIFY_SOURCE" redefined 732s : note: this is the location of the previous definition 733s 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 733s 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 733s : warning: "_FORTIFY_SOURCE" redefined 733s : note: this is the location of the previous definition 733s 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 734s 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 734s : warning: "_FORTIFY_SOURCE" redefined 734s : note: this is the location of the previous definition 735s 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 735s 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 735s : warning: "_FORTIFY_SOURCE" redefined 735s : note: this is the location of the previous definition 735s 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 736s 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 736s : warning: "_FORTIFY_SOURCE" redefined 736s : note: this is the location of the previous definition 736s 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 736s 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 737s : warning: "_FORTIFY_SOURCE" redefined 737s : note: this is the location of the previous definition 737s 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 737s : warning: "_FORTIFY_SOURCE" redefined 737s : note: this is the location of the previous definition 737s 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 737s 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 737s : warning: "_FORTIFY_SOURCE" redefined 737s : note: this is the location of the previous definition 738s 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 738s 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 738s : warning: "_FORTIFY_SOURCE" redefined 738s : note: this is the location of the previous definition 738s 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 739s 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 739s : warning: "_FORTIFY_SOURCE" redefined 739s : note: this is the location of the previous definition 755s 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 755s sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 755s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 755s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 755s test/hts_endian 755s test/test_expr 755s test/test_kfunc 755s test/test_kstring 755s test/test_str2int 755s test/test_time_funcs 756s test/fieldarith test/fieldarith.sam 756s test/hfile 756s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 756s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 756s fi 756s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 756s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 756s fi 756s test/test_bgzf test/bgziptest.txt 759s test/test-parse-reg -t test/colons.bam 759s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 759s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 759s Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" 759s Expected error: [E::hts_parse_region] Unexpected string "x" after region 759s Expected error: [E::hts_parse_region] Unexpected string "y" after region 759s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 759s cd test/faidx && ./test-faidx.sh faidx.tst 759s Testing faidx... 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 759s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 759s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 759s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 759s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 759s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 759s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 759s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 759s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 759s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 759s 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 759s 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 759s 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 759s 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 759s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 759s 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 759s 759s Expected passes: 25 759s Unexpected passes: 0 759s Expected failures: 0 759s Unexpected failures: 0 759s cd test/sam_filter && ./filter.sh filter.tst 759s Testing sam_filter... 759s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 759s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 759s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 759s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 759s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 759s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 759s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 759s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 759s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 759s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 760s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 760s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 760s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 760s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 760s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 760s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 760s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 760s 760s Expected passes: 17 760s Unexpected passes: 0 760s Expected failures: 0 760s Unexpected failures: 0 760s cd test/tabix && ./test-tabix.sh tabix.tst 760s Testing tabix... 760s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 760s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 760s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 760s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 760s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 760s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 760s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 760s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 760s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 760s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 760s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 760s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 760s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 760s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 760s 760s Expected passes: 14 760s Unexpected passes: 0 760s Expected failures: 0 760s Unexpected failures: 0 760s cd test/mpileup && ./test-pileup.sh mpileup.tst 760s Testing (m)pileup... 760s PASS : $pileup mp_D.sam 760s PASS : $pileup -m mp_D.sam 760s PASS : $pileup mp_DI.sam 760s PASS : $pileup -m mp_DI.sam 760s PASS : $pileup mp_I.sam 760s PASS : $pileup -m mp_I.sam 760s PASS : $pileup mp_P.sam 760s PASS : $pileup -m mp_P.sam 761s PASS : $pileup mp_ID.sam 761s PASS : $pileup -m mp_ID.sam 761s PASS : $pileup mp_N.sam 761s PASS : $pileup -m mp_N.sam 761s PASS : $pileup mp_N2.sam 761s PASS : $pileup -m mp_N2.sam 761s PASS : $pileup c1#pad1.sam 761s PASS : $pileup -m c1#pad1.sam 761s PASS : $pileup c1#pad2.sam 761s PASS : $pileup -m c1#pad2.sam 761s PASS : $pileup c1#pad3.sam 761s PASS : $pileup -m c1#pad3.sam 761s PASS : $pileup -m small.bam 761s 761s Expected passes: 21 761s Unexpected passes: 0 761s Expected failures: 0 761s Unexpected failures: 0 761s cd test/fastq && ./test-fastq.sh 761s Testing fastq support 761s PASS : $tview minimal.fq 761s PASS : $tview minimal.fa 761s PASS : $tview multiline.fq 761s PASS : $tview multiline.fa 761s PASS : $tview -i fastq_aux longline.fq 761s PASS : $tview single.fq 761s PASS : $tview single.fa 761s PASS : $tview -i fastq_aux single.fq 761s PASS : $tview -i fastq_aux single.fa 761s PASS : $tview interleaved.fq 761s PASS : $tview interleaved.fa 761s PASS : $tview -i fastq_aux interleaved.fq 761s PASS : $tview -i fastq_aux interleaved.fa 761s PASS : $tview -i fastq_casava interleaved_casava.fq 761s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 761s PASS : $tview -i fastq_casava interleaved_casava.fa 761s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 761s PASS : $tview -i fastq_casava filter_casava.fq 762s PASS : $tview -i fastq_casava filter_casava.fa 762s PASS : $tview -i fastq_aux r1.fq 762s PASS : $tview -i fastq_aux r2.fq 762s PASS : $tview -i fastq_aux r1.fa 762s PASS : $tview -i fastq_aux r2.fa 762s PASS : $tview -i fastq_name2 name2.fq 762s PASS : $tview -i fastq_name2 name2.fa 762s PASS : $tview -f minimal.sam 762s PASS : $tview -F minimal.sam 762s PASS : $tview -f -o fastq_aux single_aux.sam 762s PASS : $tview -F -o fastq_aux single_aux.sam 762s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 762s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 762s PASS : $tview -f -o fastq_casava inter_casava.sam 762s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 762s PASS : $tview -F -o fastq_casava inter_casava.sam 762s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 762s PASS : $tview -f -o fastq_casava filter_casava.sam 762s PASS : $tview -F -o fastq_casava filter_casava.sam 762s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 762s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 762s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 762s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 762s 762s Expected passes: 41 762s Unexpected passes: 0 762s Expected failures: 0 762s Unexpected failures: 0 762s cd test/base_mods && ./base-mods.sh base-mods.tst 762s Testing base-modifications... 762s PASS : $test_mod MM-chebi.sam 762s PASS : $test_mod MM-double.sam 762s PASS : $test_mod MM-multi.sam 762s PASS : $test_mod MM-explicit.sam 762s PASS : $test_mod -x MM-explicit.sam 762s PASS : $test_mod -f 1 MM-explicit.sam 762s PASS : $test_mod MM-not-all-modded.sam 762s PASS : $pileup_mod < MM-pileup.sam 763s PASS : $pileup_mod < MM-pileup2.sam 763s PASS : $pileup_mod < MM-MNp.sam 763s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 763s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 763s 763s Expected passes: 12 763s Unexpected passes: 0 763s Expected failures: 0 763s Unexpected failures: 0 763s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 763s (Expect trailing 'x' message for " -1,001x") 763s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 763s (Expect trailing 'k' message for "1.5e+3k") 763s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 763s (Expect dropped fraction message for "12.3456k") 763s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 763s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 763s (Expect invalid numeric message for "A") 763s [W::hts_parse_decimal] Invalid numeric value A[truncated] 763s (Expect invalid numeric message for "G") 763s [W::hts_parse_decimal] Invalid numeric value G[truncated] 763s (Expect invalid numeric message for " +/-") 763s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 763s (Expect invalid numeric message for " -.e+9999") 763s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 763s test/test-regidx 763s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 763s bgzip round-trip no threads: .. ok 763s 764s bgzip text mode round-trip no threads: .. ok 764s 764s bgzip -b no threads: .. ok 764s 764s bgzip -b -I no threads: .. ok 764s 764s bgzip round-trip 4 threads: .. ok 764s 765s bgzip text mode round-trip 4 threads: .. ok 765s 765s bgzip -b 4 threads: .. ok 765s 765s bgzip -b -I 4 threads: .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/RiQdrJOz8w/index.bam.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.bam 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.bam 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/RiQdrJOz8w/index.bam.bai /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.bam 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -b /tmp/RiQdrJOz8w/index.bam 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/RiQdrJOz8w/index.sam.gz.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.sam.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.sam.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/RiQdrJOz8w/index.sam.gz.bai /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.sam.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -b /tmp/RiQdrJOz8w/index.sam.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/RiQdrJOz8w/index.sam.gz.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index_dos.sam > /tmp/RiQdrJOz8w/index.sam.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.sam.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/RiQdrJOz8w/index.sam.gz.bai /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index_dos.sam > /tmp/RiQdrJOz8w/index.sam.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -b /tmp/RiQdrJOz8w/index.sam.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/RiQdrJOz8w/index.cram.crai /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.cram 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index /tmp/RiQdrJOz8w/index.cram 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/RiQdrJOz8w/index.bcf.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.vcf > /tmp/RiQdrJOz8w/index.bcf 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.bcf 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/RiQdrJOz8w/index.vcf.gz.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.vcf > /tmp/RiQdrJOz8w/index.vcf.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.vcf.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/RiQdrJOz8w/index.vcf.gz.tbi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.vcf > /tmp/RiQdrJOz8w/index.vcf.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -t /tmp/RiQdrJOz8w/index.vcf.gz 765s .. ok 765s 765s test_index: 765s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/tabix /tmp/RiQdrJOz8w/index.vcf.gz##idx##/tmp/RiQdrJOz8w/index.vcf.gz.tbi 1:10000060-10000060 765s .. ok 765s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/RiQdrJOz8w/index2.bam 1:1000000-1000000 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/RiQdrJOz8w/index2.bam 1:2000000-2000000 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/RiQdrJOz8w/index2.bam 2:1000000-1000000 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/RiQdrJOz8w/index2.bam 2:2000000-2000000 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/RiQdrJOz8w/index.bam.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.bam 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.bam 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/RiQdrJOz8w/index.bam.bai /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.bam 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -b /tmp/RiQdrJOz8w/index.bam 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/RiQdrJOz8w/index.sam.gz.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.sam.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.sam.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/RiQdrJOz8w/index.sam.gz.bai /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.sam.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -b /tmp/RiQdrJOz8w/index.sam.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/RiQdrJOz8w/index.sam.gz.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index_dos.sam > /tmp/RiQdrJOz8w/index.sam.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.sam.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/RiQdrJOz8w/index.sam.gz.bai /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index_dos.sam > /tmp/RiQdrJOz8w/index.sam.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -b /tmp/RiQdrJOz8w/index.sam.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/RiQdrJOz8w/index.cram.crai /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.sam > /tmp/RiQdrJOz8w/index.cram 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index /tmp/RiQdrJOz8w/index.cram 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/RiQdrJOz8w/index.bcf.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.vcf > /tmp/RiQdrJOz8w/index.bcf 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.bcf 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/RiQdrJOz8w/index.vcf.gz.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.vcf > /tmp/RiQdrJOz8w/index.vcf.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c /tmp/RiQdrJOz8w/index.vcf.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/RiQdrJOz8w/index.vcf.gz.tbi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/index.vcf > /tmp/RiQdrJOz8w/index.vcf.gz 766s .. ok 766s 766s test_index: 766s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -t /tmp/RiQdrJOz8w/index.vcf.gz 767s .. ok 767s 767s test_index: 767s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/tabix /tmp/RiQdrJOz8w/index.vcf.gz##idx##/tmp/RiQdrJOz8w/index.vcf.gz.tbi 1:10000060-10000060 767s .. ok 767s 767s test_index: 767s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/RiQdrJOz8w/index2.bam 1:1000000-1000000 767s .. ok 767s 767s test_index: 767s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/RiQdrJOz8w/index2.bam 1:2000000-2000000 767s .. ok 767s 767s test_index: 767s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/RiQdrJOz8w/index2.bam 2:1000000-1000000 767s .. ok 767s 767s test_index: 767s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/RiQdrJOz8w/index2.bam 2:2000000-2000000 767s .. ok 767s 767s test_view testing multi-ref CRAM modes: 767s ./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 767s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 767s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 767s ./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 767s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 767s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 767s ./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 767s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 767s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 768s .. ok 768s 768s test_view testing multi-ref CRAM modes: 768s ./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 768s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 768s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 768s ./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 768s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 768s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 768s ./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 768s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 768s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 769s .. ok 769s 769s test_view testing auxf#values.sam, ref auxf.fa: 769s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 769s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 769s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 769s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 769s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 769s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 769s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 769s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 769s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 769s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 769s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 769s .. ok 769s 769s test_view testing c1#bounds.sam, ref c1.fa: 769s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 769s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 769s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 769s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 769s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 769s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 769s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 769s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 769s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 769s .. ok 769s 769s test_view testing c1#clip.sam, ref c1.fa: 769s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 769s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 769s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 769s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 769s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 770s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 770s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 770s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 770s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 770s .. ok 770s 770s test_view testing c1#noseq.sam, ref c1.fa: 770s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 770s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 770s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 770s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 770s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 770s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 770s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 770s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 770s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 770s .. ok 770s 770s test_view testing c1#pad1.sam, ref c1.fa: 770s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 770s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 770s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 770s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 770s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 770s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 770s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 770s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 770s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 770s .. ok 770s 770s test_view testing c1#pad2.sam, ref c1.fa: 770s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 770s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 770s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 771s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 771s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 771s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 771s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 771s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 771s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 771s .. ok 771s 771s test_view testing c1#pad3.sam, ref c1.fa: 771s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 771s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 771s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 771s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 771s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 771s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 771s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 771s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 771s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 771s .. ok 771s 771s test_view testing c1#unknown.sam, ref c1.fa: 771s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 771s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 771s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 771s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 771s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 771s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 771s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 771s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 771s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 771s .. ok 771s 771s test_view testing c2#pad.sam, ref c2.fa: 771s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 771s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 771s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 772s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 772s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 772s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 772s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 772s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 772s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 772s .. ok 772s 772s test_view testing ce#1.sam, ref ce.fa: 772s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 772s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 772s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 772s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 772s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 772s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 772s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 772s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 772s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 772s .. ok 772s 772s test_view testing ce#1000.sam, ref ce.fa: 772s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 772s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 772s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 772s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 772s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 772s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 773s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 773s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 773s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 773s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 773s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 773s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 773s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 773s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 773s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 774s .. ok 774s 774s test_view testing ce#2.sam, ref ce.fa: 774s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 774s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 774s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 774s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 774s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 774s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 774s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 774s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 774s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 774s .. ok 774s 774s test_view testing ce#5.sam, ref ce.fa: 774s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 774s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 774s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 774s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 774s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 774s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 774s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 774s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 774s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 774s .. ok 774s 774s test_view testing ce#5b.sam, ref ce.fa: 774s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 774s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 774s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 774s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 774s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 774s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 774s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 774s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 774s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 774s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 774s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 774s .. ok 774s 774s test_view testing ce#large_seq.sam, ref ce.fa: 774s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 775s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 775s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 775s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 775s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 775s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 775s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 775s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 775s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 776s .. ok 776s 776s test_view testing ce#supp.sam, ref ce.fa: 776s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 776s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 776s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 776s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 776s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 776s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 776s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 776s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 776s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 776s .. ok 776s 776s test_view testing ce#tag_depadded.sam, ref ce.fa: 776s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 776s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 776s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 776s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 776s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 776s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 776s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 776s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 776s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 776s .. ok 776s 776s test_view testing ce#tag_padded.sam, ref ce.fa: 776s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 776s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 776s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 777s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 777s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 777s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 777s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 777s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 777s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 777s .. ok 777s 777s test_view testing ce#unmap.sam, ref ce.fa: 777s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 777s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 777s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 777s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 777s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 777s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 777s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 777s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 777s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 777s .. ok 777s 777s test_view testing ce#unmap1.sam, ref ce.fa: 777s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 777s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 777s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 777s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 777s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 777s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 777s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 777s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 777s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 777s .. ok 777s 777s test_view testing ce#unmap2.sam, ref ce.fa: 777s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 777s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 777s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 778s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 778s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 778s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 778s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 778s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 778s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 778s .. ok 778s 778s test_view testing md#1.sam, ref md.fa: 778s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 778s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 778s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 778s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 778s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 778s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 778s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 778s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 778s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 778s .. ok 778s 778s test_view testing xx#blank.sam, ref xx.fa: 778s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 778s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 778s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 778s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 778s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 778s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 778s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 778s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 778s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 779s .. ok 779s 779s test_view testing xx#large_aux.sam, ref xx.fa: 779s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 779s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 779s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 779s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 779s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 779s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 779s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 779s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 779s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 779s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 779s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 779s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 779s .. ok 779s 779s test_view testing xx#large_aux2.sam, ref xx.fa: 779s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 779s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 779s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 780s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 780s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 780s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 780s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 780s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 780s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 780s .. ok 780s 780s test_view testing xx#MD.sam, ref xx.fa: 780s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 780s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 780s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 780s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 780s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 780s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 780s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 780s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 780s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 780s .. ok 780s 780s test_view testing xx#MD2.sam, ref xx.fa: 780s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 780s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 780s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 780s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 780s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 780s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 780s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 780s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 780s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 781s .. ok 781s 781s test_view testing xx#minimal.sam, ref xx.fa: 781s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 781s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 781s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 781s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 781s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 781s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 781s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 781s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 781s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 781s .. ok 781s 781s test_view testing xx#pair.sam, ref xx.fa: 781s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 781s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 781s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 781s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 781s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 781s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 781s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 781s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 781s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 781s .. ok 781s 781s test_view testing xx#repeated.sam, ref xx.fa: 781s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 781s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 781s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 781s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 781s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 781s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 782s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 782s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 782s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 782s .. ok 782s 782s test_view testing xx#rg.sam, ref xx.fa: 782s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 782s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 782s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 782s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 782s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 782s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 782s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 782s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 782s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 782s .. ok 782s 782s test_view testing xx#tlen.sam, ref xx.fa: 782s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 782s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 782s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 782s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 782s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 782s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 782s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 782s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 782s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 782s .. ok 782s 782s test_view testing xx#tlen2.sam, ref xx.fa: 782s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 782s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 782s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 782s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 782s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 782s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 783s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 783s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 783s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 783s .. ok 783s 783s test_view testing xx#triplet.sam, ref xx.fa: 783s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 783s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 783s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 783s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 783s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 783s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 783s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 783s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 783s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 783s .. ok 783s 783s test_view testing xx#unsorted.sam, ref xx.fa: 783s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 783s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 783s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 783s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 783s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 783s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 783s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 783s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 783s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 783s .. ok 783s 783s test_view testing embed_ref=2: 783s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 783s [W::cram_get_ref] Failed to populate reference for id 0 783s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 783s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 783s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 783s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 783s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 784s .. ok 784s 784s test_view testing region queries: 784s ./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 784s ./compare_sam.pl range.tmp range.out 784s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 784s ./compare_sam.pl range.tmp range.out 784s .. ok 784s 784s test_view testing BAM files with absent @SQ lines: 784s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 784s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 784s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 784s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 784s .. ok 784s 784s test_view testing large (> 2Gbases) positions: 784s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 784s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 784s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 784s test_view: 784s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 784s .. ok 784s 784s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 784s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 784s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 784s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 784s .. ok 784s 784s test_view testing auxf#values.sam, ref auxf.fa: 784s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 784s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 784s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 784s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 785s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 785s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 785s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 785s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 785s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 785s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 785s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 785s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 785s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 785s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 785s This is a technology demonstration that should not be used for archival data. 785s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 785s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 785s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 785s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 786s .. ok 786s 786s test_view testing c1#bounds.sam, ref c1.fa: 786s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 786s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 786s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 786s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 786s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 786s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 786s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 786s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 786s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 786s .. ok 786s 786s test_view testing c1#clip.sam, ref c1.fa: 786s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 786s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 786s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 786s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 786s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 786s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 786s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 786s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 786s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 786s .. ok 786s 786s test_view testing c1#noseq.sam, ref c1.fa: 786s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 786s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 786s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 786s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 786s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 787s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 787s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 787s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 787s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 787s .. ok 787s 787s test_view testing c1#pad1.sam, ref c1.fa: 787s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 787s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 787s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 787s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 787s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 787s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 787s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 787s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 787s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 787s .. ok 787s 787s test_view testing c1#pad2.sam, ref c1.fa: 787s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 787s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 787s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 787s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 787s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 787s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 787s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 787s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 787s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 788s .. ok 788s 788s test_view testing c1#pad3.sam, ref c1.fa: 788s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 788s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 788s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 788s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 788s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 788s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 788s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 788s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 788s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 788s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 788s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 788s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 788s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 788s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 788s This is a technology demonstration that should not be used for archival data. 788s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 788s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 789s .. ok 789s 789s test_view testing c1#unknown.sam, ref c1.fa: 789s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 789s ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 789s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 789s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 789s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 789s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 789s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 789s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 789s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 789s .. ok 789s 789s test_view testing c2#pad.sam, ref c2.fa: 789s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 789s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 789s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 789s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 789s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 789s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 789s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 789s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 789s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 789s .. ok 789s 789s test_view testing ce#1.sam, ref ce.fa: 789s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 789s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 789s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 790s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 790s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 790s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 790s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 790s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 790s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 790s .. ok 790s 790s test_view testing ce#1000.sam, ref ce.fa: 790s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 790s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 790s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 790s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 790s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 790s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 790s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 790s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 790s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 791s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 791s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 791s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 791s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 791s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 791s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 791s ./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 791s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 791s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 792s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 792s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 792s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 792s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 792s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 792s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 792s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 792s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 793s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 793s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 793s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 793s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 793s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 794s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 794s This is a technology demonstration that should not be used for archival data. 794s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 794s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 794s .. ok 794s 794s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 794s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 794s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 794s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 794s ./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 794s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 795s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 795s ./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 795s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 795s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 795s .. ok 795s 795s test_view testing ce#2.sam, ref ce.fa: 795s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 795s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 795s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 795s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 795s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 795s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 795s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 795s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 795s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 795s .. ok 795s 795s test_view testing ce#5.sam, ref ce.fa: 795s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 795s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 795s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 796s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 796s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 796s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 796s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 796s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 796s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 796s ./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 796s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 796s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 796s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 796s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 796s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 796s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 796s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 796s This is a technology demonstration that should not be used for archival data. 797s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 797s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 797s .. ok 797s 797s test_view testing ce#5b.sam, ref ce.fa: 797s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 797s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 797s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 797s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 797s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 797s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 797s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 797s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 797s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 797s ./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 797s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 797s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 798s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 798s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 798s .. ok 798s 798s test_view testing ce#large_seq.sam, ref ce.fa: 798s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 798s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 798s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 798s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 798s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 798s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 799s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 799s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 799s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 799s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 800s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 800s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 800s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 800s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 800s This is a technology demonstration that should not be used for archival data. 801s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 801s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 801s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 801s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 801s This is a technology demonstration that should not be used for archival data. 801s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 802s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 802s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 802s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 802s This is a technology demonstration that should not be used for archival data. 803s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 803s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 803s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 803s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 803s This is a technology demonstration that should not be used for archival data. 804s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 804s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 804s .. ok 804s 804s test_view testing ce#supp.sam, ref ce.fa: 804s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 804s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 804s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 804s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 805s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 805s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 805s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 805s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 805s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 805s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 805s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 805s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 805s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 805s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 805s This is a technology demonstration that should not be used for archival data. 805s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 805s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 805s .. ok 805s 805s test_view testing ce#tag_depadded.sam, ref ce.fa: 805s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 806s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 806s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 806s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 806s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 806s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 806s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 806s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 806s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 806s .. ok 806s 806s test_view testing ce#tag_padded.sam, ref ce.fa: 806s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 806s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 806s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 806s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 806s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 806s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 806s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 806s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 806s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 806s .. ok 806s 806s test_view testing ce#unmap.sam, ref ce.fa: 806s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 806s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 807s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 807s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 807s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 807s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 807s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 807s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 807s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 807s ./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 807s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 807s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 807s .. ok 807s 807s test_view testing ce#unmap1.sam, ref ce.fa: 807s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 807s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 807s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 807s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 807s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 807s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 807s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 807s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 807s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 807s ./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 807s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 807s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 808s .. ok 808s 808s test_view testing ce#unmap2.sam, ref ce.fa: 808s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 808s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 808s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 808s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 808s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 808s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 808s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 808s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 808s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 808s ./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 808s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 808s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 808s .. ok 808s 808s test_view testing md#1.sam, ref md.fa: 808s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 808s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 808s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 808s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 808s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 808s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 809s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 809s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 809s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 809s .. ok 809s 809s test_view testing xx#blank.sam, ref xx.fa: 809s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 809s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 809s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 809s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 809s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 809s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 809s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 809s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 809s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 809s ./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 809s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 809s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 809s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 809s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 809s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 809s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 809s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 809s This is a technology demonstration that should not be used for archival data. 809s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 809s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 809s .. ok 809s 809s test_view testing xx#large_aux.sam, ref xx.fa: 809s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 810s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 810s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 810s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 810s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 810s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 810s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 810s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 810s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 810s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 811s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 811s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 811s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 811s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 811s This is a technology demonstration that should not be used for archival data. 812s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 812s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 812s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 812s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 812s This is a technology demonstration that should not be used for archival data. 812s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 812s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 812s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 812s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 812s This is a technology demonstration that should not be used for archival data. 812s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 813s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 813s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 813s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 813s This is a technology demonstration that should not be used for archival data. 814s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 814s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 814s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 814s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 814s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 814s .. ok 814s 814s test_view testing xx#large_aux2.sam, ref xx.fa: 814s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 814s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 814s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 814s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 814s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 814s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 814s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 814s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 814s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 814s .. ok 814s 814s test_view testing xx#MD.sam, ref xx.fa: 814s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 814s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 814s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 815s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 815s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 815s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 815s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 815s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 815s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 815s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 815s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 815s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 815s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 815s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 815s This is a technology demonstration that should not be used for archival data. 815s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 815s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 815s .. ok 815s 815s test_view testing xx#MD2.sam, ref xx.fa: 815s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 815s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 816s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 816s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 816s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 816s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 816s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 816s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 816s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 816s .. ok 816s 816s test_view testing xx#minimal.sam, ref xx.fa: 816s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 816s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 816s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 816s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 816s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 816s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 816s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 816s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 816s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 816s ./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 816s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 816s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 816s .. ok 816s 816s test_view testing xx#pair.sam, ref xx.fa: 816s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 816s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 816s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 817s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 817s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 817s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 817s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 817s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 817s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 817s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 817s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 817s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 817s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 817s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 817s This is a technology demonstration that should not be used for archival data. 817s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 817s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 817s .. ok 817s 817s test_view testing xx#repeated.sam, ref xx.fa: 817s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 818s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 818s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 818s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 818s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 818s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 818s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 818s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 818s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 818s .. ok 818s 818s test_view testing xx#rg.sam, ref xx.fa: 818s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 818s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 818s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 818s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 818s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 818s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 818s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 818s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 818s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 818s .. ok 818s 818s test_view testing xx#tlen.sam, ref xx.fa: 818s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 818s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 818s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 818s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 818s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 819s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 819s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 819s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 819s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 819s ./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 819s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 819s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 819s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 819s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 819s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 819s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 819s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 819s This is a technology demonstration that should not be used for archival data. 820s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 820s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 820s .. ok 820s 820s test_view testing xx#tlen2.sam, ref xx.fa: 820s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 820s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 820s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 820s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 820s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 820s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 820s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 820s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 820s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 820s ./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 820s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 820s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 820s .. ok 820s 820s test_view testing xx#triplet.sam, ref xx.fa: 820s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 820s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 820s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 820s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 820s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 820s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 821s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 821s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 821s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 821s ./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 821s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 821s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 821s .. ok 821s 821s test_view testing xx#unsorted.sam, ref xx.fa: 821s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 821s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 821s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 821s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 821s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 821s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 821s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 821s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 821s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 821s .. ok 821s 821s test_view testing embed_ref=2: 821s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 821s [W::cram_get_ref] Failed to populate reference for id 0 821s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 821s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 821s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 821s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 821s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 822s .. ok 822s 822s test_view testing region queries: 822s ./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 822s ./compare_sam.pl range.tmp range.out 822s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 822s ./compare_sam.pl range.tmp range.out 822s .. ok 822s 822s test_view testing BAM files with absent @SQ lines: 822s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 822s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 822s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 822s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 822s .. ok 822s 822s test_view testing large (> 2Gbases) positions: 822s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 822s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 822s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 822s test_view: 822s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 822s .. ok 822s 822s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 822s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 822s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 822s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 822s .. ok 822s 822s 822s test_MD testing xx#MD.sam, ref xx.fa: 822s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 822s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 822s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 822s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 822s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 822s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 823s Checking for MD/NM in xx#MD.sam 823s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 823s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 823s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 823s .. ok 823s 823s 823s test_MD testing xx#MD2.sam, ref xx.fa: 823s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 823s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 823s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 823s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 823s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 823s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 823s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 823s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 823s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 823s .. ok 823s 823s test_vcf_api: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-vcf-api /tmp/RiQdrJOz8w/test-vcf-api.bcf 823s [W::bcf_record_check] Bad BCF record at 1:1: No REF allele 823s [E::bcf_index_build3] TBI indices for BCF files are not supported 823s [E::idx_find_and_load] Could not retrieve index file for '/tmp/RiQdrJOz8w/test-vcf-api.bcf' 823s .. ok 823s 823s test_bcf2vcf: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/tabix/vcf_file.bcf 823s .. ok 823s 823s test_vcf_sweep: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-vcf-sweep /tmp/RiQdrJOz8w/test-vcf-api.bcf 823s .. ok 823s 823s test_vcf_various: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 823s .. ok 823s 823s test_vcf_various: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/formatcols.vcf 823s .. ok 823s 823s test_vcf_various: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/noroundtrip.vcf 823s .. ok 823s 823s test_vcf_various: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/formatmissing.vcf 823s .. ok 823s 823s test_vcf_various: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/vcf_meta_meta.vcf 823s .. ok 823s 823s test_vcf_various: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 823s .. ok 823s 823s test-bcf-sr: 823s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 74452500 824s .. ok 824s 824s test-bcf-sr: 824s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 34270147 825s .. ok 825s 825s test-bcf-sr: 825s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 11108528 826s .. ok 826s 826s test-bcf-sr: 826s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 42233895 826s .. ok 826s 826s test-bcf-sr: 826s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 8111117 827s .. ok 827s 827s test-bcf-sr: 827s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 85644070 828s .. ok 828s 828s test-bcf-sr: 828s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 49879942 829s .. ok 829s 829s test-bcf-sr: 829s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 47881429 829s .. ok 829s 829s test-bcf-sr: 829s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 69081244 830s .. ok 830s 830s test-bcf-sr: 830s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/RiQdrJOz8w -s 83459376 831s .. ok 831s 831s test_bcf_sr_no_index: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/RiQdrJOz8w/no_index_1.err 831s .. ok 831s 831s test_bcf_sr_no_index: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/RiQdrJOz8w/no_index_2.out 2> /tmp/RiQdrJOz8w/no_index_2.err (expected fail) 831s .. ok 831s 831s test_bcf_sr_no_index: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/RiQdrJOz8w/no_index_3.out 2> /tmp/RiQdrJOz8w/no_index_3.err (expected fail) 831s .. ok 831s 831s test_bcf_sr_no_index: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/RiQdrJOz8w/no_index_4.out 2> /tmp/RiQdrJOz8w/no_index_4.err (expected fail) 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -b -p /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf -x /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_1.out.vcf -r '1' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_2.out.vcf -r '1:1-2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_4.out.vcf -r '1:1-1' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_5.out.vcf -r '{1:1}' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf (expected fail) 831s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 831s Failed to set regions 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_14.out.vcf -t '1' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_15.out.vcf -t '1:1-2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_17.out.vcf -t '1:1-1' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_18.out.vcf -t '{1:1}' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf 831s .. ok 831s 831s test_bcf_sr_range: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/RiQdrJOz8w/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/RiQdrJOz8w/weird-chr-names.vcf.bcf (expected fail) 831s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 831s Failed to set targets 831s .. ok 831s 831s test_command: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf-translate - 831s .. ok 831s 831s test_convert_padded_header: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/RiQdrJOz8w/headernul0.bam 831s .. ok 831s 831s test_convert_padded_header: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/RiQdrJOz8w/headernul1.bam 831s .. ok 831s 831s test_convert_padded_header: 831s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/RiQdrJOz8w/headernul678.bam 831s .. ok 831s 831s test_rebgzip: Alternate zlib/deflate library detected 832s test_rebgzip: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/bgziptest.txt 832s .. ok 832s 832s test-logging: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-logging.pl 832s .. ok 832s 832s test_plugin_loading: 832s HTS_PATH=/tmp/autopkgtest.1VWTPy/autopkgtest_tmp /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn01.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn01.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn01.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02-r.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02_exp.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn02_exp-a.sam -o - 832s .. ok 832s 832s test_realn: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/realn03.sam -o - 832s .. ok 832s 832s test-bcf_set_variant_type: 832s /tmp/autopkgtest.1VWTPy/autopkgtest_tmp/test/test-bcf_set_variant_type 832s .. ok 832s 832s 832s Number of tests: 832s total .. 211 832s passed .. 211 832s failed .. 0 832s 832s PASS 832s + echo PASS 832s autopkgtest [08:08:59]: test run-unit-test: -----------------------] 833s autopkgtest [08:09:00]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 833s run-unit-test PASS 834s autopkgtest [08:09:01]: @@@@@@@@@@@@@@@@@@@@ summary 834s run-unit-test PASS 845s Creating nova instance adt-noble-arm64-htslib-20240325-075507-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...