0s autopkgtest [14:51:19]: starting date and time: 2024-03-18 14:51:19+0000 0s autopkgtest [14:51:19]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [14:51:19]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.e2p6blly/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:openssl --apt-upgrade htslib --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=openssl/3.0.13-0ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-10.secgroup --name adt-noble-arm64-htslib-20240318-145118-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 149s autopkgtest [14:53:48]: testbed dpkg architecture: arm64 154s autopkgtest [14:53:48]: testbed apt version: 2.7.12 154s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 154s autopkgtest [14:53:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 154s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 154s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 154s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3728 kB] 154s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 154s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 154s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 154s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 154s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 154s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4103 kB] 154s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 154s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 154s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 154s Fetched 9246 kB in 2s (5212 kB/s) 154s Reading package lists... 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Calculating upgrade... 161s The following packages will be REMOVED: 161s libssl3 161s The following NEW packages will be installed: 161s libssl3t64 161s The following packages will be upgraded: 161s openssl 161s 1 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 161s Need to get 2777 kB of archives. 161s After this operation, 139 kB of additional disk space will be used. 161s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 161s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 162s Fetched 2777 kB in 1s (3948 kB/s) 164s (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 ... 74758 files and directories currently installed.) 164s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 164s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 164s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 164s wget depends on libssl3 (>= 3.0.0). 164s u-boot-tools depends on libssl3 (>= 3.0.0). 164s tnftp depends on libssl3 (>= 3.0.0). 164s tcpdump depends on libssl3 (>= 3.0.0). 164s systemd-resolved depends on libssl3 (>= 3.0.0). 164s systemd depends on libssl3 (>= 3.0.0). 164s sudo depends on libssl3 (>= 3.0.0). 164s sbsigntool depends on libssl3 (>= 3.0.0). 164s rsync depends on libssl3 (>= 3.0.0). 164s python3-cryptography depends on libssl3 (>= 3.0.0). 164s openssh-server depends on libssl3 (>= 3.0.10). 164s openssh-client depends on libssl3 (>= 3.0.10). 164s mtd-utils depends on libssl3 (>= 3.0.0). 164s mokutil depends on libssl3 (>= 3.0.0). 164s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 164s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 164s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 164s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 164s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 164s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 164s libnvme1 depends on libssl3 (>= 3.0.0). 164s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 164s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 164s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 164s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 164s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 164s kmod depends on libssl3 (>= 3.0.0). 164s dhcpcd-base depends on libssl3 (>= 3.0.0). 164s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 164s 164s (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 ... 74758 files and directories currently installed.) 164s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 164s Selecting previously unselected package libssl3t64:arm64. 164s (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 ... 74747 files and directories currently installed.) 164s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 164s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 164s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 164s Setting up openssl (3.0.13-0ubuntu2) ... 164s Processing triggers for man-db (2.12.0-3) ... 164s Processing triggers for libc-bin (2.39-0ubuntu2) ... 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s sh: Attempting to set up Debian/Ubuntu apt sources automatically 165s sh: Distribution appears to be Ubuntu 166s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 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... 177s dbus is already the newest version (1.14.10-4ubuntu1). 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... 177s rng-tools-debian is already the newest version (2.4). 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... 177s The following packages will be REMOVED: 177s cloud-init* python3-configobj* python3-debconf* 177s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 177s After this operation, 3252 kB disk space will be freed. 177s (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 ... 74760 files and directories currently installed.) 177s Removing cloud-init (24.1.1-0ubuntu1) ... 177s Removing python3-configobj (5.0.8-3) ... 177s Removing python3-debconf (1.5.86) ... 177s Processing triggers for man-db (2.12.0-3) ... 177s (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 ... 74371 files and directories currently installed.) 177s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 177s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 177s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 177s invoke-rc.d: policy-rc.d denied execution of try-restart. 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s linux-generic is already the newest version (6.8.0-11.11+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... 177s Calculating upgrade... 177s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 177s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 177s Reading package lists... 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... 182s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 182s autopkgtest [14:54:17]: rebooting testbed after setup commands that affected boot 367s autopkgtest [14:57:25]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 379s autopkgtest [14:57:38]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 390s Get:1 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (dsc) [2437 B] 390s Get:2 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (tar) [1469 kB] 390s Get:3 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (diff) [20.1 kB] 390s gpgv: Signature made Tue Nov 7 20:35:25 2023 UTC 390s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 390s gpgv: issuer "emollier@debian.org" 390s gpgv: Can't check signature: No public key 390s dpkg-source: warning: cannot verify inline signature for ./htslib_1.18+ds-1.dsc: no acceptable signature found 390s autopkgtest [14:57:45]: testing package htslib version 1.18+ds-1 391s autopkgtest [14:57:50]: build not needed 396s autopkgtest [14:57:55]: test run-unit-test: preparing testbed 401s Reading package lists... 402s Building dependency tree... 402s Reading state information... 402s Starting pkgProblemResolver with broken count: 1 402s Starting 2 pkgProblemResolver with broken count: 1 402s Investigating (0) libssl3t64:arm64 < 3.0.13-0ubuntu2 @ii mK Ib > 402s Broken libssl3t64:arm64 Breaks on libssl3:arm64 < none -> 3.0.10-1ubuntu4 @un pumN > (< 3.0.13-0ubuntu2) 402s Considering libssl3:arm64 150 as a solution to libssl3t64:arm64 146 402s Removing libssl3t64:arm64 rather than change libssl3:arm64 402s Investigating (0) openssl:arm64 < 3.0.13-0ubuntu2 @ii mK Ib > 402s Broken openssl:arm64 Depends on libssl3t64:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 402s Considering libssl3t64:arm64 146 as a solution to openssl:arm64 12 402s Removing openssl:arm64 rather than change libssl3t64:arm64 402s Investigating (1) ca-certificates:arm64 < 20240203 @ii mK Ib > 402s Broken ca-certificates:arm64 Depends on openssl:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 402s Considering openssl:arm64 12 as a solution to ca-certificates:arm64 137 402s Added openssl:arm64 to the remove list 402s Fixing ca-certificates:arm64 via keep of openssl:arm64 402s Investigating (1) openssl:arm64 < 3.0.13-0ubuntu2 @ii mK Ib > 402s Broken openssl:arm64 Depends on libssl3t64:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 402s Considering libssl3t64:arm64 146 as a solution to openssl:arm64 12 402s Removing openssl:arm64 rather than change libssl3t64:arm64 402s Investigating (2) ca-certificates:arm64 < 20240203 @ii mK Ib > 402s Broken ca-certificates:arm64 Depends on openssl:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 402s Considering openssl:arm64 12 as a solution to ca-certificates:arm64 137 402s Added openssl:arm64 to the remove list 402s Fixing ca-certificates:arm64 via keep of openssl:arm64 402s Investigating (2) openssl:arm64 < 3.0.13-0ubuntu2 @ii mK Ib > 402s Broken openssl:arm64 Depends on libssl3t64:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 402s Considering libssl3t64:arm64 146 as a solution to openssl:arm64 137 402s Removing openssl:arm64 rather than change libssl3t64:arm64 402s Investigating (3) ca-certificates:arm64 < 20240203 @ii mK Ib > 402s Broken ca-certificates:arm64 Depends on openssl:arm64 < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 402s Considering openssl:arm64 146 as a solution to ca-certificates:arm64 137 402s Removing ca-certificates:arm64 rather than change openssl:arm64 402s Investigating (3) python3-httplib2:arm64 < 0.20.4-3 @ii mK Ib > 402s Broken python3-httplib2:arm64 Depends on ca-certificates:arm64 < 20240203 @ii mR > 402s Considering ca-certificates:arm64 146 as a solution to python3-httplib2:arm64 6 402s Removing python3-httplib2:arm64 rather than change ca-certificates:arm64 402s Investigating (3) python3-apport:arm64 < 2.28.0-0ubuntu1 @ii mK Ib > 402s Broken python3-apport:arm64 Depends on python3-httplib2:arm64 < 0.20.4-3 @ii mR > 402s Considering python3-httplib2:arm64 146 as a solution to python3-apport:arm64 4 402s Removing python3-apport:arm64 rather than change python3-httplib2:arm64 402s Investigating (3) ssh-import-id:arm64 < 5.11-0ubuntu2 @ii mK Ib > 402s Broken ssh-import-id:arm64 Depends on ca-certificates:arm64 < 20240203 @ii mR > 402s Considering ca-certificates:arm64 146 as a solution to ssh-import-id:arm64 3 402s Removing ssh-import-id:arm64 rather than change ca-certificates:arm64 402s Investigating (3) python3-certifi:arm64 < 2023.11.17-1 @ii mK Ib > 402s Broken python3-certifi:arm64 Depends on ca-certificates:arm64 < 20240203 @ii mR > 402s Considering ca-certificates:arm64 146 as a solution to python3-certifi:arm64 2 402s Removing python3-certifi:arm64 rather than change ca-certificates:arm64 402s Investigating (3) python3-launchpadlib:arm64 < 1.11.0-6 @ii mK Ib > 402s Broken python3-launchpadlib:arm64 Depends on python3-httplib2:arm64 < 0.20.4-3 @ii mR > 402s Considering python3-httplib2:arm64 146 as a solution to python3-launchpadlib:arm64 2 402s Removing python3-launchpadlib:arm64 rather than change python3-httplib2:arm64 402s Investigating (3) python3-lazr.restfulclient:arm64 < 0.14.6-1 @ii mK Ib > 402s Broken python3-lazr.restfulclient:arm64 Depends on python3-httplib2:arm64 < 0.20.4-3 @ii mR > (>= 0.7.7) 402s Considering python3-httplib2:arm64 146 as a solution to python3-lazr.restfulclient:arm64 2 402s Removing python3-lazr.restfulclient:arm64 rather than change python3-httplib2:arm64 402s Investigating (3) python3-requests:arm64 < 2.31.0+dfsg-1ubuntu1 @ii mK Ib > 402s Broken python3-requests:arm64 Depends on python3-certifi:arm64 < 2023.11.17-1 @ii mR > 402s Considering python3-certifi:arm64 146 as a solution to python3-requests:arm64 2 402s Removing python3-requests:arm64 rather than change python3-certifi:arm64 402s Investigating (4) apport:arm64 < 2.28.0-0ubuntu1 @ii mK Ib > 402s Broken apport:arm64 Depends on python3-apport:arm64 < 2.28.0-0ubuntu1 @ii mR > (>= 2.28.0-0ubuntu1) 402s Considering python3-apport:arm64 146 as a solution to apport:arm64 6 402s Removing apport:arm64 rather than change python3-apport:arm64 402s Investigating (4) apport-core-dump-handler:arm64 < 2.28.0-0ubuntu1 @ii mK Ib > 402s Broken apport-core-dump-handler:arm64 Depends on apport:arm64 < 2.28.0-0ubuntu1 @ii mR > (>= 2.27.0-0ubuntu7~) 402s Considering apport:arm64 146 as a solution to apport-core-dump-handler:arm64 4 402s Removing apport-core-dump-handler:arm64 rather than change apport:arm64 402s Done 402s The following packages were automatically installed and are no longer required: 402s apport-symptoms python3-blinker python3-chardet python3-cryptography 402s python3-jwt python3-lazr.uri python3-oauthlib python3-openssl 402s python3-problem-report python3-pyparsing python3-six python3-systemd 402s python3-urllib3 python3-wadllib 402s Use 'sudo apt autoremove' to remove them. 402s The following additional packages will be installed: 402s autoconf automake autopoint autotools-dev build-essential cpp cpp-13 402s cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 402s dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 402s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 402s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext htslib-test 402s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 402s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 402s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 402s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 402s libhtscodecs-dev libhtscodecs2 libhwasan0 libisl23 libitm1 liblsan0 402s liblzma-dev libmpc3 libnsl-dev libssl-dev libssl3 libstdc++-13-dev 402s libsub-override-perl libtirpc-dev libtool libtsan2 libubsan1 linux-libc-dev 402s m4 po-debconf rpcsvc-proto tabix zlib1g-dev 402s Suggested packages: 402s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 402s cpp-13-doc dh-make gcc-13-doc gcc-multilib manpages-dev flex bison gdb 402s gcc-doc gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 402s glibc-doc libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev 402s librtmp-dev libssh2-1-dev pkg-config liblzma-doc libssl-doc libstdc++-13-doc 402s libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl 402s Recommended packages: 402s bzip2-doc manpages manpages-dev libc-devtools libarchive-cpio-perl 402s libltdl-dev libmail-sendmail-perl 402s The following packages will be REMOVED: 402s apport apport-core-dump-handler ca-certificates libssl3t64 openssl 402s python3-apport python3-certifi python3-httplib2 python3-launchpadlib 402s python3-lazr.restfulclient python3-requests ssh-import-id 402s The following NEW packages will be installed: 402s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 402s cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 402s debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 402s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 402s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext htslib-test 402s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 402s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 402s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 402s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 402s libhtscodecs-dev libhtscodecs2 libhwasan0 libisl23 libitm1 liblsan0 402s liblzma-dev libmpc3 libnsl-dev libssl-dev libssl3 libstdc++-13-dev 402s libsub-override-perl libtirpc-dev libtool libtsan2 libubsan1 linux-libc-dev 402s m4 po-debconf rpcsvc-proto tabix zlib1g-dev 402s 0 upgraded, 67 newly installed, 12 to remove and 0 not upgraded. 402s Need to get 82.8 MB/82.8 MB of archives. 402s After this operation, 274 MB of additional disk space will be used. 402s Get:1 /tmp/autopkgtest.Pl3h3g/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [816 B] 402s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libssl3 arm64 3.0.10-1ubuntu4 [1764 kB] 403s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4 [240 kB] 403s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB] 403s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB] 403s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 403s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 autopoint all 0.21-14ubuntu1 [422 kB] 403s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 403s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 403s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 403s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] 403s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 403s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 403s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 403s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 403s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 403s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 403s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 403s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 403s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 403s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 403s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 403s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 403s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 403s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 403s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 403s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 403s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 403s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 404s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 404s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 404s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 404s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 404s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 404s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 404s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 404s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 404s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 404s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 404s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 404s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 404s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7 [166 kB] 404s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB] 404s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 404s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB] 404s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 404s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] 404s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libdw1 arm64 0.190-1 [254 kB] 404s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] 404s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 dwz arm64 0.15-1 [110 kB] 404s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 gettext arm64 0.21-14ubuntu1 [846 kB] 404s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 404s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 404s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 debhelper all 13.14.1ubuntu1 [869 kB] 404s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 htslib-test all 1.18+ds-1 [1120 kB] 405s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 405s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libcurl4-gnutls-dev arm64 8.5.0-2ubuntu2 [448 kB] 405s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 405s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate-dev arm64 1.19-1 [51.2 kB] 405s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 405s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 405s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 405s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 405s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts-dev arm64 1.18+ds-1 [5806 kB] 405s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs-dev arm64 1.6.0-1 [2975 kB] 405s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libssl-dev arm64 3.0.10-1ubuntu4 [2330 kB] 405s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 tabix arm64 1.18+ds-1 [505 kB] 406s Fetched 82.8 MB in 3s (32.4 MB/s) 406s (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 ... 74316 files and directories currently installed.) 406s Removing ssh-import-id (5.11-0ubuntu2) ... 406s Removing apport-core-dump-handler (2.28.0-0ubuntu1) ... 406s Removing apport (2.28.0-0ubuntu1) ... 407s Removing python3-apport (2.28.0-0ubuntu1) ... 407s Removing python3-requests (2.31.0+dfsg-1ubuntu1) ... 407s dpkg: ca-certificates: dependency problems, but removing anyway as you requested: 407s python3-httplib2 depends on ca-certificates. 407s python3-certifi depends on ca-certificates. 407s 407s Removing ca-certificates (20240203) ... 407s Removing dangling symlinks from /etc/ssl/certs... done. 407s Removing openssl (3.0.13-0ubuntu2) ... 407s dpkg: libssl3t64:arm64: dependency problems, but removing anyway as you requested: 407s wget depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s u-boot-tools depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s tnftp depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s tcpdump depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s systemd-resolved depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s systemd depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s sudo depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s sbsigntool depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s rsync depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s python3-cryptography depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s openssh-server depends on libssl3 (>= 3.0.10); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s openssh-client depends on libssl3 (>= 3.0.10); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s mtd-utils depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s mokutil depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libssh-4:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libnvme1 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libkmod2:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libfido2-1:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libcurl4:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s kmod depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s dhcpcd-base depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s bind9-libs:arm64 depends on libssl3 (>= 3.0.0); however: 407s Package libssl3 is not installed. 407s Package libssl3t64:arm64 which provides libssl3 is to be removed. 407s 407s Removing libssl3t64:arm64 (3.0.13-0ubuntu2) ... 407s Selecting previously unselected package libssl3:arm64. 407s (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 ... 73655 files and directories currently installed.) 407s Preparing to unpack .../libssl3_3.0.10-1ubuntu4_arm64.deb ... 407s Unpacking libssl3:arm64 (3.0.10-1ubuntu4) ... 407s (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 ... 73666 files and directories currently installed.) 407s Removing python3-certifi (2023.11.17-1) ... 407s Removing python3-launchpadlib (1.11.0-6) ... 407s Removing python3-lazr.restfulclient (0.14.6-1) ... 408s Removing python3-httplib2 (0.20.4-3) ... 408s Selecting previously unselected package m4. 408s (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 ... 73552 files and directories currently installed.) 408s Preparing to unpack .../00-m4_1.4.19-4_arm64.deb ... 408s Unpacking m4 (1.4.19-4) ... 408s Selecting previously unselected package autoconf. 408s Preparing to unpack .../01-autoconf_2.71-3_all.deb ... 408s Unpacking autoconf (2.71-3) ... 415s Selecting previously unselected package autotools-dev. 415s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 415s Unpacking autotools-dev (20220109.1) ... 415s Selecting previously unselected package automake. 415s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 415s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 415s Selecting previously unselected package autopoint. 415s Preparing to unpack .../04-autopoint_0.21-14ubuntu1_all.deb ... 415s Unpacking autopoint (0.21-14ubuntu1) ... 415s Selecting previously unselected package libc-dev-bin. 415s Preparing to unpack .../05-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 415s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 415s Selecting previously unselected package linux-libc-dev:arm64. 415s Preparing to unpack .../06-linux-libc-dev_6.8.0-11.11_arm64.deb ... 415s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 415s Selecting previously unselected package libcrypt-dev:arm64. 415s Preparing to unpack .../07-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 415s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 415s Selecting previously unselected package libtirpc-dev:arm64. 415s Preparing to unpack .../08-libtirpc-dev_1.3.4+ds-1build1_arm64.deb ... 415s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 415s Selecting previously unselected package libnsl-dev:arm64. 415s Preparing to unpack .../09-libnsl-dev_1.3.0-3_arm64.deb ... 415s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 415s Selecting previously unselected package rpcsvc-proto. 415s Preparing to unpack .../10-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 415s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 415s Selecting previously unselected package libc6-dev:arm64. 415s Preparing to unpack .../11-libc6-dev_2.39-0ubuntu2_arm64.deb ... 415s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 415s Selecting previously unselected package libisl23:arm64. 415s Preparing to unpack .../12-libisl23_0.26-3_arm64.deb ... 415s Unpacking libisl23:arm64 (0.26-3) ... 415s Selecting previously unselected package libmpc3:arm64. 415s Preparing to unpack .../13-libmpc3_1.3.1-1_arm64.deb ... 415s Unpacking libmpc3:arm64 (1.3.1-1) ... 415s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 415s Preparing to unpack .../14-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 415s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 415s Selecting previously unselected package cpp-13. 415s Preparing to unpack .../15-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 415s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 415s Selecting previously unselected package cpp-aarch64-linux-gnu. 415s Preparing to unpack .../16-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 415s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 415s Selecting previously unselected package cpp. 415s Preparing to unpack .../17-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 415s Unpacking cpp (4:13.2.0-7ubuntu1) ... 415s Selecting previously unselected package libcc1-0:arm64. 415s Preparing to unpack .../18-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libgomp1:arm64. 415s Preparing to unpack .../19-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libitm1:arm64. 415s Preparing to unpack .../20-libitm1_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libatomic1:arm64. 415s Preparing to unpack .../21-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libasan8:arm64. 415s Preparing to unpack .../22-libasan8_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package liblsan0:arm64. 415s Preparing to unpack .../23-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libtsan2:arm64. 415s Preparing to unpack .../24-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libubsan1:arm64. 415s Preparing to unpack .../25-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libhwasan0:arm64. 415s Preparing to unpack .../26-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libgcc-13-dev:arm64. 415s Preparing to unpack .../27-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 415s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 415s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 415s Preparing to unpack .../28-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 415s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 415s Selecting previously unselected package gcc-13. 415s Preparing to unpack .../29-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 415s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 415s Selecting previously unselected package gcc-aarch64-linux-gnu. 415s Preparing to unpack .../30-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 415s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 415s Selecting previously unselected package gcc. 415s Preparing to unpack .../31-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 415s Unpacking gcc (4:13.2.0-7ubuntu1) ... 415s Selecting previously unselected package libstdc++-13-dev:arm64. 415s Preparing to unpack .../32-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 415s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 415s Selecting previously unselected package g++-13-aarch64-linux-gnu. 415s Preparing to unpack .../33-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 415s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 415s Selecting previously unselected package g++-13. 415s Preparing to unpack .../34-g++-13_13.2.0-17ubuntu2_arm64.deb ... 415s Unpacking g++-13 (13.2.0-17ubuntu2) ... 415s Selecting previously unselected package g++-aarch64-linux-gnu. 415s Preparing to unpack .../35-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 415s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 415s Selecting previously unselected package g++. 415s Preparing to unpack .../36-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 415s Unpacking g++ (4:13.2.0-7ubuntu1) ... 415s Selecting previously unselected package build-essential. 415s Preparing to unpack .../37-build-essential_12.10ubuntu1_arm64.deb ... 415s Unpacking build-essential (12.10ubuntu1) ... 415s Selecting previously unselected package libdebhelper-perl. 415s Preparing to unpack .../38-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 415s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 415s Selecting previously unselected package libtool. 415s Preparing to unpack .../39-libtool_2.4.7-7_all.deb ... 415s Unpacking libtool (2.4.7-7) ... 415s Selecting previously unselected package dh-autoreconf. 415s Preparing to unpack .../40-dh-autoreconf_20_all.deb ... 415s Unpacking dh-autoreconf (20) ... 415s Selecting previously unselected package libarchive-zip-perl. 415s Preparing to unpack .../41-libarchive-zip-perl_1.68-1_all.deb ... 415s Unpacking libarchive-zip-perl (1.68-1) ... 415s Selecting previously unselected package libsub-override-perl. 415s Preparing to unpack .../42-libsub-override-perl_0.10-1_all.deb ... 415s Unpacking libsub-override-perl (0.10-1) ... 415s Selecting previously unselected package libfile-stripnondeterminism-perl. 415s Preparing to unpack .../43-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 415s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 415s Selecting previously unselected package dh-strip-nondeterminism. 415s Preparing to unpack .../44-dh-strip-nondeterminism_1.13.1-1_all.deb ... 415s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 415s Selecting previously unselected package libdw1:arm64. 415s Preparing to unpack .../45-libdw1_0.190-1_arm64.deb ... 415s Unpacking libdw1:arm64 (0.190-1) ... 415s Selecting previously unselected package debugedit. 415s Preparing to unpack .../46-debugedit_1%3a5.0-5_arm64.deb ... 415s Unpacking debugedit (1:5.0-5) ... 415s Selecting previously unselected package dwz. 415s Preparing to unpack .../47-dwz_0.15-1_arm64.deb ... 415s Unpacking dwz (0.15-1) ... 415s Selecting previously unselected package gettext. 415s Preparing to unpack .../48-gettext_0.21-14ubuntu1_arm64.deb ... 415s Unpacking gettext (0.21-14ubuntu1) ... 415s Selecting previously unselected package intltool-debian. 415s Preparing to unpack .../49-intltool-debian_0.35.0+20060710.6_all.deb ... 415s Unpacking intltool-debian (0.35.0+20060710.6) ... 415s Selecting previously unselected package po-debconf. 415s Preparing to unpack .../50-po-debconf_1.0.21+nmu1_all.deb ... 415s Unpacking po-debconf (1.0.21+nmu1) ... 415s Selecting previously unselected package debhelper. 415s Preparing to unpack .../51-debhelper_13.14.1ubuntu1_all.deb ... 415s Unpacking debhelper (13.14.1ubuntu1) ... 415s Selecting previously unselected package htslib-test. 415s Preparing to unpack .../52-htslib-test_1.18+ds-1_all.deb ... 415s Unpacking htslib-test (1.18+ds-1) ... 415s Selecting previously unselected package libbz2-dev:arm64. 415s Preparing to unpack .../53-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 415s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 415s Selecting previously unselected package libcurl4-gnutls-dev:arm64. 415s Preparing to unpack .../54-libcurl4-gnutls-dev_8.5.0-2ubuntu2_arm64.deb ... 415s Unpacking libcurl4-gnutls-dev:arm64 (8.5.0-2ubuntu2) ... 415s Selecting previously unselected package libdeflate0:arm64. 415s Preparing to unpack .../55-libdeflate0_1.19-1_arm64.deb ... 415s Unpacking libdeflate0:arm64 (1.19-1) ... 415s Selecting previously unselected package libdeflate-dev:arm64. 415s Preparing to unpack .../56-libdeflate-dev_1.19-1_arm64.deb ... 415s Unpacking libdeflate-dev:arm64 (1.19-1) ... 415s Selecting previously unselected package libhtscodecs2:arm64. 415s Preparing to unpack .../57-libhtscodecs2_1.6.0-1_arm64.deb ... 415s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 415s Selecting previously unselected package libhts3:arm64. 415s Preparing to unpack .../58-libhts3_1.18+ds-1_arm64.deb ... 415s Unpacking libhts3:arm64 (1.18+ds-1) ... 415s Selecting previously unselected package liblzma-dev:arm64. 415s Preparing to unpack .../59-liblzma-dev_5.4.5-0.3_arm64.deb ... 415s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 415s Selecting previously unselected package zlib1g-dev:arm64. 415s Preparing to unpack .../60-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 415s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 415s Selecting previously unselected package libhts-dev:arm64. 415s Preparing to unpack .../61-libhts-dev_1.18+ds-1_arm64.deb ... 415s Unpacking libhts-dev:arm64 (1.18+ds-1) ... 415s Selecting previously unselected package libhtscodecs-dev:arm64. 415s Preparing to unpack .../62-libhtscodecs-dev_1.6.0-1_arm64.deb ... 415s Unpacking libhtscodecs-dev:arm64 (1.6.0-1) ... 415s Selecting previously unselected package libssl-dev:arm64. 415s Preparing to unpack .../63-libssl-dev_3.0.10-1ubuntu4_arm64.deb ... 415s Unpacking libssl-dev:arm64 (3.0.10-1ubuntu4) ... 415s Selecting previously unselected package tabix. 415s Preparing to unpack .../64-tabix_1.18+ds-1_arm64.deb ... 415s Unpacking tabix (1.18+ds-1) ... 415s Selecting previously unselected package autopkgtest-satdep. 415s Preparing to unpack .../65-1-autopkgtest-satdep.deb ... 415s Unpacking autopkgtest-satdep (0) ... 415s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 415s Setting up libdw1:arm64 (0.190-1) ... 415s Setting up libarchive-zip-perl (1.68-1) ... 415s Setting up htslib-test (1.18+ds-1) ... 415s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 415s Setting up libssl3:arm64 (3.0.10-1ubuntu4) ... 415s Setting up libdeflate0:arm64 (1.19-1) ... 415s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 415s Setting up m4 (1.4.19-4) ... 415s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 415s Setting up libcurl4-gnutls-dev:arm64 (8.5.0-2ubuntu2) ... 415s Setting up libhtscodecs-dev:arm64 (1.6.0-1) ... 415s Setting up autotools-dev (20220109.1) ... 415s Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 415s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 415s Setting up libssl-dev:arm64 (3.0.10-1ubuntu4) ... 415s Setting up libmpc3:arm64 (1.3.1-1) ... 415s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 415s Setting up autopoint (0.21-14ubuntu1) ... 415s Setting up autoconf (2.71-3) ... 415s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 415s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 415s Setting up dwz (0.15-1) ... 415s Setting up libnsl-dev:arm64 (1.3.0-3) ... 415s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 415s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 415s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 415s Setting up debugedit (1:5.0-5) ... 415s Setting up libsub-override-perl (0.10-1) ... 415s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 415s Setting up libisl23:arm64 (0.26-3) ... 415s Setting up libc-dev-bin (2.39-0ubuntu2) ... 415s Setting up libdeflate-dev:arm64 (1.19-1) ... 415s Setting up tabix (1.18+ds-1) ... 415s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 415s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 415s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 415s Setting up automake (1:1.16.5-1.3ubuntu1) ... 415s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 415s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 415s Setting up libhts3:arm64 (1.18+ds-1) ... 415s Setting up gettext (0.21-14ubuntu1) ... 415s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 415s Setting up intltool-debian (0.35.0+20060710.6) ... 415s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 415s Setting up dh-strip-nondeterminism (1.13.1-1) ... 415s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 415s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 415s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 415s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 415s Setting up cpp-13 (13.2.0-17ubuntu2) ... 415s Setting up po-debconf (1.0.21+nmu1) ... 415s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 415s Setting up gcc-13 (13.2.0-17ubuntu2) ... 415s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 415s Setting up cpp (4:13.2.0-7ubuntu1) ... 415s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 415s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 415s Setting up g++-13 (13.2.0-17ubuntu2) ... 415s Setting up libtool (2.4.7-7) ... 415s Setting up libhts-dev:arm64 (1.18+ds-1) ... 415s Setting up gcc (4:13.2.0-7ubuntu1) ... 415s Setting up dh-autoreconf (20) ... 415s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 415s Setting up debhelper (13.14.1ubuntu1) ... 415s Setting up g++ (4:13.2.0-7ubuntu1) ... 415s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 415s Setting up build-essential (12.10ubuntu1) ... 415s Setting up autopkgtest-satdep (0) ... 415s Processing triggers for man-db (2.12.0-3) ... 415s Processing triggers for install-info (7.1-3) ... 415s Processing triggers for libc-bin (2.39-0ubuntu2) ... 419s (Reading database ... 78489 files and directories currently installed.) 419s Removing autopkgtest-satdep (0) ... 420s autopkgtest [14:58:19]: test run-unit-test: [----------------------- 420s + pkg=htslib 420s + '[' /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp = '' ']' 420s + 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.Pl3h3g/autopkgtest_tmp 420s + cp -aL htslib.pc.in /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp 420s + cp -aL htslib.map /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp 420s + cd /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp 420s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 420s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 420s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 420s + grep sse /proc/cpuinfo 420s + export CFLAGS 420s + make -e check 420s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c 421s : warning: "_FORTIFY_SOURCE" redefined 421s : note: this is the location of the previous definition 422s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c 422s : warning: "_FORTIFY_SOURCE" redefined 422s : note: this is the location of the previous definition 422s 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 422s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c 422s : warning: "_FORTIFY_SOURCE" redefined 422s : note: this is the location of the previous definition 422s : warning: "_FORTIFY_SOURCE" redefined 422s : note: this is the location of the previous definition 423s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c 423s : warning: "_FORTIFY_SOURCE" redefined 423s : note: this is the location of the previous definition 423s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c 423s : warning: "_FORTIFY_SOURCE" redefined 423s : note: this is the location of the previous definition 424s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c 424s : warning: "_FORTIFY_SOURCE" redefined 424s : note: this is the location of the previous definition 427s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c 427s : warning: "_FORTIFY_SOURCE" redefined 427s : note: this is the location of the previous definition 427s : warning: "_FORTIFY_SOURCE" redefined 427s : note: this is the location of the previous definition 427s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c 428s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c 428s : warning: "_FORTIFY_SOURCE" redefined 428s : note: this is the location of the previous definition 429s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c 429s : warning: "_FORTIFY_SOURCE" redefined 429s : note: this is the location of the previous definition 429s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c 429s : warning: "_FORTIFY_SOURCE" redefined 429s : note: this is the location of the previous definition 429s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c 429s : warning: "_FORTIFY_SOURCE" redefined 429s : note: this is the location of the previous definition 429s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c 429s : warning: "_FORTIFY_SOURCE" redefined 429s : note: this is the location of the previous definition 429s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c 429s : warning: "_FORTIFY_SOURCE" redefined 429s : note: this is the location of the previous definition 429s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c 429s : warning: "_FORTIFY_SOURCE" redefined 429s : note: this is the location of the previous definition 430s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c 430s : warning: "_FORTIFY_SOURCE" redefined 430s : note: this is the location of the previous definition 430s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c 430s : warning: "_FORTIFY_SOURCE" redefined 430s : note: this is the location of the previous definition 435s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c 435s : warning: "_FORTIFY_SOURCE" redefined 435s : note: this is the location of the previous definition 435s 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 435s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c 435s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c 435s : warning: "_FORTIFY_SOURCE" redefined 435s : note: this is the location of the previous definition 435s : warning: "_FORTIFY_SOURCE" redefined 435s : note: this is the location of the previous definition 435s : warning: "_FORTIFY_SOURCE" redefined 435s : note: this is the location of the previous definition 435s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c 435s : warning: "_FORTIFY_SOURCE" redefined 435s : note: this is the location of the previous definition 435s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c 435s : warning: "_FORTIFY_SOURCE" redefined 435s : note: this is the location of the previous definition 436s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c 436s : warning: "_FORTIFY_SOURCE" redefined 436s : note: this is the location of the previous definition 440s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c 440s : warning: "_FORTIFY_SOURCE" redefined 440s : note: this is the location of the previous definition 441s 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 441s : warning: "_FORTIFY_SOURCE" redefined 441s : note: this is the location of the previous definition 442s 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 442s : warning: "_FORTIFY_SOURCE" redefined 442s : note: this is the location of the previous definition 446s 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 446s : warning: "_FORTIFY_SOURCE" redefined 446s : note: this is the location of the previous definition 446s 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 447s : warning: "_FORTIFY_SOURCE" redefined 447s : note: this is the location of the previous definition 447s 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 447s : warning: "_FORTIFY_SOURCE" redefined 447s : note: this is the location of the previous definition 450s 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 450s : warning: "_FORTIFY_SOURCE" redefined 450s : note: this is the location of the previous definition 450s 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 450s : warning: "_FORTIFY_SOURCE" redefined 450s : note: this is the location of the previous definition 450s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c 450s : warning: "_FORTIFY_SOURCE" redefined 450s : note: this is the location of the previous definition 450s 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 450s : warning: "_FORTIFY_SOURCE" redefined 450s : note: this is the location of the previous definition 450s 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 450s : warning: "_FORTIFY_SOURCE" redefined 450s : note: this is the location of the previous definition 450s 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 450s : warning: "_FORTIFY_SOURCE" redefined 450s : note: this is the location of the previous definition 450s 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 450s : warning: "_FORTIFY_SOURCE" redefined 450s : note: this is the location of the previous definition 451s 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 451s ranlib libhts.a 451s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c 451s : warning: "_FORTIFY_SOURCE" redefined 451s : note: this is the location of the previous definition 451s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c 451s : warning: "_FORTIFY_SOURCE" redefined 451s : note: this is the location of the previous definition 451s 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 451s : warning: "_FORTIFY_SOURCE" redefined 451s : note: this is the location of the previous definition 452s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c 452s : warning: "_FORTIFY_SOURCE" redefined 452s : note: this is the location of the previous definition 453s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c 453s : warning: "_FORTIFY_SOURCE" redefined 453s : note: this is the location of the previous definition 453s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c 453s : warning: "_FORTIFY_SOURCE" redefined 453s : note: this is the location of the previous definition 453s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c 453s : warning: "_FORTIFY_SOURCE" redefined 453s : note: this is the location of the previous definition 455s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c 455s : warning: "_FORTIFY_SOURCE" redefined 455s : note: this is the location of the previous definition 455s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c 455s : warning: "_FORTIFY_SOURCE" redefined 455s : note: this is the location of the previous definition 458s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c 458s : warning: "_FORTIFY_SOURCE" redefined 458s : note: this is the location of the previous definition 458s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c 458s : warning: "_FORTIFY_SOURCE" redefined 458s : note: this is the location of the previous definition 458s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c 458s : warning: "_FORTIFY_SOURCE" redefined 458s : note: this is the location of the previous definition 458s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c 458s : warning: "_FORTIFY_SOURCE" redefined 458s : note: this is the location of the previous definition 459s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c 459s : warning: "_FORTIFY_SOURCE" redefined 459s : note: this is the location of the previous definition 459s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c 459s : warning: "_FORTIFY_SOURCE" redefined 459s : note: this is the location of the previous definition 459s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c 459s : warning: "_FORTIFY_SOURCE" redefined 459s : note: this is the location of the previous definition 459s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c 459s : warning: "_FORTIFY_SOURCE" redefined 459s : note: this is the location of the previous definition 460s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c 460s : warning: "_FORTIFY_SOURCE" redefined 460s : note: this is the location of the previous definition 463s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c 463s : warning: "_FORTIFY_SOURCE" redefined 463s : note: this is the location of the previous definition 463s 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 463s : warning: "_FORTIFY_SOURCE" redefined 463s : note: this is the location of the previous definition 464s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 464s : warning: "_FORTIFY_SOURCE" redefined 464s : note: this is the location of the previous definition 464s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c 464s : warning: "_FORTIFY_SOURCE" redefined 464s : note: this is the location of the previous definition 465s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c 465s : warning: "_FORTIFY_SOURCE" redefined 465s : note: this is the location of the previous definition 465s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c 465s : warning: "_FORTIFY_SOURCE" redefined 465s : note: this is the location of the previous definition 465s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c 465s : warning: "_FORTIFY_SOURCE" redefined 465s : note: this is the location of the previous definition 469s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c 469s : warning: "_FORTIFY_SOURCE" redefined 469s : 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 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c 473s : warning: "_FORTIFY_SOURCE" redefined 473s : note: this is the location of the previous definition 473s : warning: "_FORTIFY_SOURCE" redefined 473s : 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 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c 473s 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 473s : warning: "_FORTIFY_SOURCE" redefined 473s : 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 -fPIC -c -o cram/cram_external.pico cram/cram_external.c 476s : warning: "_FORTIFY_SOURCE" redefined 476s : 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 -fPIC -c -o cram/cram_index.pico cram/cram_index.c 476s : warning: "_FORTIFY_SOURCE" redefined 476s : note: this is the location of the previous definition 477s 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 477s : warning: "_FORTIFY_SOURCE" redefined 477s : note: this is the location of the previous definition 479s 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 479s : warning: "_FORTIFY_SOURCE" redefined 479s : note: this is the location of the previous definition 479s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c 479s : warning: "_FORTIFY_SOURCE" redefined 479s : note: this is the location of the previous definition 479s 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 479s : warning: "_FORTIFY_SOURCE" redefined 479s : note: this is the location of the previous definition 479s 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 479s : warning: "_FORTIFY_SOURCE" redefined 479s : note: this is the location of the previous definition 479s 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 479s : warning: "_FORTIFY_SOURCE" redefined 479s : note: this is the location of the previous definition 480s 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 480s : warning: "_FORTIFY_SOURCE" redefined 480s : note: this is the location of the previous definition 480s 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 480s ln -sf libhts.so libhts.so.3 480s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c 480s : warning: "_FORTIFY_SOURCE" redefined 480s : note: this is the location of the previous definition 480s 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 480s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c 480s : warning: "_FORTIFY_SOURCE" redefined 480s : note: this is the location of the previous definition 480s 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 480s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c 480s : warning: "_FORTIFY_SOURCE" redefined 480s : note: this is the location of the previous definition 481s 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 481s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 481s : warning: "_FORTIFY_SOURCE" redefined 481s : note: this is the location of the previous definition 482s 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 482s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 482s : warning: "_FORTIFY_SOURCE" redefined 482s : note: this is the location of the previous definition 482s 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 482s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c 482s : warning: "_FORTIFY_SOURCE" redefined 482s : note: this is the location of the previous definition 484s 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 484s : warning: "_FORTIFY_SOURCE" redefined 484s : note: this is the location of the previous definition 484s 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 484s 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 484s 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 484s 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 484s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c 484s 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 484s : warning: "_FORTIFY_SOURCE" redefined 484s : note: this is the location of the previous definition 484s : warning: "_FORTIFY_SOURCE" redefined 484s : note: this is the location of the previous definition 484s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c 484s : warning: "_FORTIFY_SOURCE" redefined 484s : note: this is the location of the previous definition 484s 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 484s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c 484s : warning: "_FORTIFY_SOURCE" redefined 484s : note: this is the location of the previous definition 484s 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 484s 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 484s : warning: "_FORTIFY_SOURCE" redefined 484s : note: this is the location of the previous definition 484s 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 484s 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 484s : warning: "_FORTIFY_SOURCE" redefined 484s : note: this is the location of the previous definition 484s 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 484s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c 484s : warning: "_FORTIFY_SOURCE" redefined 484s : note: this is the location of the previous definition 485s 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 485s 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 485s : warning: "_FORTIFY_SOURCE" redefined 485s : note: this is the location of the previous definition 486s 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 486s 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 486s : warning: "_FORTIFY_SOURCE" redefined 486s : note: this is the location of the previous definition 486s 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 486s 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 486s : warning: "_FORTIFY_SOURCE" redefined 486s : note: this is the location of the previous definition 486s 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 486s 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 486s : warning: "_FORTIFY_SOURCE" redefined 486s : note: this is the location of the previous definition 486s 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 486s 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 486s : warning: "_FORTIFY_SOURCE" redefined 486s : note: this is the location of the previous definition 487s 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 487s 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 487s : warning: "_FORTIFY_SOURCE" redefined 487s : note: this is the location of the previous definition 487s 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 487s 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 487s : warning: "_FORTIFY_SOURCE" redefined 487s : note: this is the location of the previous definition 487s 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 487s : warning: "_FORTIFY_SOURCE" redefined 487s : note: this is the location of the previous definition 487s 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 487s 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 487s 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 487s : warning: "_FORTIFY_SOURCE" redefined 487s : note: this is the location of the previous definition 487s 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 487s 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 487s : warning: "_FORTIFY_SOURCE" redefined 487s : note: this is the location of the previous definition 487s 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 488s 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 488s : warning: "_FORTIFY_SOURCE" redefined 488s : note: this is the location of the previous definition 488s 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 488s 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 488s : warning: "_FORTIFY_SOURCE" redefined 488s : note: this is the location of the previous definition 488s 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 488s 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 488s : warning: "_FORTIFY_SOURCE" redefined 488s : note: this is the location of the previous definition 488s 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 488s 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 488s : warning: "_FORTIFY_SOURCE" redefined 488s : note: this is the location of the previous definition 488s 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 488s 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 488s : warning: "_FORTIFY_SOURCE" redefined 488s : note: this is the location of the previous definition 489s 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 489s 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 489s : warning: "_FORTIFY_SOURCE" redefined 489s : note: this is the location of the previous definition 489s 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 489s : warning: "_FORTIFY_SOURCE" redefined 489s : note: this is the location of the previous definition 489s 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 489s 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 489s : warning: "_FORTIFY_SOURCE" redefined 489s : note: this is the location of the previous definition 489s 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 489s 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 489s : warning: "_FORTIFY_SOURCE" redefined 489s : note: this is the location of the previous definition 489s 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 489s 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 489s : warning: "_FORTIFY_SOURCE" redefined 489s : note: this is the location of the previous definition 493s 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 493s sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 493s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 493s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 493s test/hts_endian 493s test/test_expr 493s test/test_kfunc 493s test/test_kstring 493s test/test_str2int 493s test/test_time_funcs 494s test/fieldarith test/fieldarith.sam 494s test/hfile 494s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 494s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 494s fi 494s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 494s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 494s fi 494s test/test_bgzf test/bgziptest.txt 495s test/test-parse-reg -t test/colons.bam 495s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 495s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 495s Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" 495s Expected error: [E::hts_parse_region] Unexpected string "x" after region 495s Expected error: [E::hts_parse_region] Unexpected string "y" after region 495s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 495s cd test/faidx && ./test-faidx.sh faidx.tst 495s Testing faidx... 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 495s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 495s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 495s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 495s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 495s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 495s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 495s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 495s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 495s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 495s 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 495s 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 495s 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 495s 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 495s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 495s 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 495s 495s Expected passes: 25 495s Unexpected passes: 0 495s Expected failures: 0 495s Unexpected failures: 0 495s cd test/sam_filter && ./filter.sh filter.tst 495s Testing sam_filter... 495s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 495s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 495s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 495s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 495s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 495s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 495s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 495s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 495s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 495s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 495s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 495s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 495s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 495s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 495s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 495s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 495s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 495s 495s Expected passes: 17 495s Unexpected passes: 0 495s Expected failures: 0 495s Unexpected failures: 0 495s cd test/tabix && ./test-tabix.sh tabix.tst 495s Testing tabix... 495s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 495s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 495s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 495s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 495s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 495s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 495s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 495s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 495s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 495s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 495s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 495s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 495s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 495s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 495s 495s Expected passes: 14 495s Unexpected passes: 0 495s Expected failures: 0 495s Unexpected failures: 0 495s cd test/mpileup && ./test-pileup.sh mpileup.tst 495s Testing (m)pileup... 495s PASS : $pileup mp_D.sam 495s PASS : $pileup -m mp_D.sam 495s PASS : $pileup mp_DI.sam 495s PASS : $pileup -m mp_DI.sam 495s PASS : $pileup mp_I.sam 495s PASS : $pileup -m mp_I.sam 495s PASS : $pileup mp_P.sam 495s PASS : $pileup -m mp_P.sam 495s PASS : $pileup mp_ID.sam 495s PASS : $pileup -m mp_ID.sam 495s PASS : $pileup mp_N.sam 495s PASS : $pileup -m mp_N.sam 495s PASS : $pileup mp_N2.sam 495s PASS : $pileup -m mp_N2.sam 495s PASS : $pileup c1#pad1.sam 495s PASS : $pileup -m c1#pad1.sam 495s PASS : $pileup c1#pad2.sam 495s PASS : $pileup -m c1#pad2.sam 495s PASS : $pileup c1#pad3.sam 495s PASS : $pileup -m c1#pad3.sam 495s PASS : $pileup -m small.bam 495s 495s Expected passes: 21 495s Unexpected passes: 0 495s Expected failures: 0 495s Unexpected failures: 0 495s cd test/fastq && ./test-fastq.sh 495s Testing fastq support 495s PASS : $tview minimal.fq 495s PASS : $tview minimal.fa 495s PASS : $tview multiline.fq 495s PASS : $tview multiline.fa 496s PASS : $tview -i fastq_aux longline.fq 496s PASS : $tview single.fq 496s PASS : $tview single.fa 496s PASS : $tview -i fastq_aux single.fq 496s PASS : $tview -i fastq_aux single.fa 496s PASS : $tview interleaved.fq 496s PASS : $tview interleaved.fa 496s PASS : $tview -i fastq_aux interleaved.fq 496s PASS : $tview -i fastq_aux interleaved.fa 496s PASS : $tview -i fastq_casava interleaved_casava.fq 496s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 496s PASS : $tview -i fastq_casava interleaved_casava.fa 496s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 496s PASS : $tview -i fastq_casava filter_casava.fq 496s PASS : $tview -i fastq_casava filter_casava.fa 496s PASS : $tview -i fastq_aux r1.fq 496s PASS : $tview -i fastq_aux r2.fq 496s PASS : $tview -i fastq_aux r1.fa 496s PASS : $tview -i fastq_aux r2.fa 496s PASS : $tview -i fastq_name2 name2.fq 496s PASS : $tview -i fastq_name2 name2.fa 496s PASS : $tview -f minimal.sam 496s PASS : $tview -F minimal.sam 496s PASS : $tview -f -o fastq_aux single_aux.sam 496s PASS : $tview -F -o fastq_aux single_aux.sam 496s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 496s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 496s PASS : $tview -f -o fastq_casava inter_casava.sam 496s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 496s PASS : $tview -F -o fastq_casava inter_casava.sam 496s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 496s PASS : $tview -f -o fastq_casava filter_casava.sam 496s PASS : $tview -F -o fastq_casava filter_casava.sam 496s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 496s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 496s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 496s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 496s 496s Expected passes: 41 496s Unexpected passes: 0 496s Expected failures: 0 496s Unexpected failures: 0 496s cd test/base_mods && ./base-mods.sh base-mods.tst 496s Testing base-modifications... 496s PASS : $test_mod MM-chebi.sam 496s PASS : $test_mod MM-double.sam 496s PASS : $test_mod MM-multi.sam 496s PASS : $test_mod MM-explicit.sam 496s PASS : $test_mod -x MM-explicit.sam 496s PASS : $test_mod -f 1 MM-explicit.sam 496s PASS : $test_mod MM-not-all-modded.sam 496s PASS : $pileup_mod < MM-pileup.sam 496s PASS : $pileup_mod < MM-pileup2.sam 496s PASS : $pileup_mod < MM-MNp.sam 496s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 496s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 496s 496s Expected passes: 12 496s Unexpected passes: 0 496s Expected failures: 0 496s Unexpected failures: 0 496s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 496s (Expect trailing 'x' message for " -1,001x") 496s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 496s (Expect trailing 'k' message for "1.5e+3k") 496s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 496s (Expect dropped fraction message for "12.3456k") 496s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 496s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 496s (Expect invalid numeric message for "A") 496s [W::hts_parse_decimal] Invalid numeric value A[truncated] 496s (Expect invalid numeric message for "G") 496s [W::hts_parse_decimal] Invalid numeric value G[truncated] 496s (Expect invalid numeric message for " +/-") 496s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 496s (Expect invalid numeric message for " -.e+9999") 496s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 496s test/test-regidx 496s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 496s bgzip round-trip no threads: .. ok 496s 497s bgzip text mode round-trip no threads: .. ok 497s 497s bgzip -b no threads: .. ok 497s 497s bgzip -b -I no threads: .. ok 497s 497s bgzip round-trip 4 threads: .. ok 497s 497s bgzip text mode round-trip 4 threads: .. ok 497s 497s bgzip -b 4 threads: .. ok 497s 497s bgzip -b -I 4 threads: .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/arqwdNIWgv/index.bam.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.bam 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.bam 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/arqwdNIWgv/index.bam.bai /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.bam 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -b /tmp/arqwdNIWgv/index.bam 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/arqwdNIWgv/index.sam.gz.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/arqwdNIWgv/index.sam.gz.bai /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -b /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/arqwdNIWgv/index.sam.gz.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index_dos.sam > /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/arqwdNIWgv/index.sam.gz.bai /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index_dos.sam > /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -b /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/arqwdNIWgv/index.cram.crai /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.cram 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index /tmp/arqwdNIWgv/index.cram 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/arqwdNIWgv/index.bcf.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.vcf > /tmp/arqwdNIWgv/index.bcf 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.bcf 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/arqwdNIWgv/index.vcf.gz.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.vcf > /tmp/arqwdNIWgv/index.vcf.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.vcf.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/arqwdNIWgv/index.vcf.gz.tbi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.vcf > /tmp/arqwdNIWgv/index.vcf.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -t /tmp/arqwdNIWgv/index.vcf.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/tabix /tmp/arqwdNIWgv/index.vcf.gz##idx##/tmp/arqwdNIWgv/index.vcf.gz.tbi 1:10000060-10000060 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/arqwdNIWgv/index2.bam 1:1000000-1000000 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/arqwdNIWgv/index2.bam 1:2000000-2000000 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/arqwdNIWgv/index2.bam 2:1000000-1000000 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/arqwdNIWgv/index2.bam 2:2000000-2000000 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/arqwdNIWgv/index.bam.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.bam 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.bam 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/arqwdNIWgv/index.bam.bai /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.bam 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -b /tmp/arqwdNIWgv/index.bam 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/arqwdNIWgv/index.sam.gz.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/arqwdNIWgv/index.sam.gz.bai /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -b /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/arqwdNIWgv/index.sam.gz.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index_dos.sam > /tmp/arqwdNIWgv/index.sam.gz 497s .. ok 497s 497s test_index: 497s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.sam.gz 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/arqwdNIWgv/index.sam.gz.bai /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index_dos.sam > /tmp/arqwdNIWgv/index.sam.gz 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -b /tmp/arqwdNIWgv/index.sam.gz 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/arqwdNIWgv/index.cram.crai /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.sam > /tmp/arqwdNIWgv/index.cram 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index /tmp/arqwdNIWgv/index.cram 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/arqwdNIWgv/index.bcf.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.vcf > /tmp/arqwdNIWgv/index.bcf 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.bcf 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/arqwdNIWgv/index.vcf.gz.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.vcf > /tmp/arqwdNIWgv/index.vcf.gz 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c /tmp/arqwdNIWgv/index.vcf.gz 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/arqwdNIWgv/index.vcf.gz.tbi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/index.vcf > /tmp/arqwdNIWgv/index.vcf.gz 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -t /tmp/arqwdNIWgv/index.vcf.gz 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/tabix /tmp/arqwdNIWgv/index.vcf.gz##idx##/tmp/arqwdNIWgv/index.vcf.gz.tbi 1:10000060-10000060 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/arqwdNIWgv/index2.bam 1:1000000-1000000 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/arqwdNIWgv/index2.bam 1:2000000-2000000 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/arqwdNIWgv/index2.bam 2:1000000-1000000 498s .. ok 498s 498s test_index: 498s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/arqwdNIWgv/index2.bam 2:2000000-2000000 498s .. ok 498s 498s test_view testing multi-ref CRAM modes: 498s ./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 498s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 498s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 499s ./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 499s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 499s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 499s ./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 499s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 499s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 499s .. ok 499s 499s test_view testing multi-ref CRAM modes: 499s ./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 499s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 499s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 499s ./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 499s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 499s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 499s ./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 499s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 499s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 499s .. ok 499s 499s test_view testing auxf#values.sam, ref auxf.fa: 499s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 499s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 499s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 499s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 499s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 499s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 499s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 499s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 499s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 499s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 499s .. ok 499s 499s test_view testing c1#bounds.sam, ref c1.fa: 499s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 499s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 499s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 499s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 499s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 499s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 499s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 499s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing c1#clip.sam, ref c1.fa: 499s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 499s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 499s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 499s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 499s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 499s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 499s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 499s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing c1#noseq.sam, ref c1.fa: 499s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 499s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 499s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 499s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 499s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 499s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 499s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 499s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing c1#pad1.sam, ref c1.fa: 499s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 499s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 499s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 499s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 499s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 499s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 499s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 499s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing c1#pad2.sam, ref c1.fa: 499s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 499s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 499s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 499s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 499s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 499s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 499s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 499s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing c1#pad3.sam, ref c1.fa: 499s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 499s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 499s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 499s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 499s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 499s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 499s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 499s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing c1#unknown.sam, ref c1.fa: 499s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 499s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 499s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 499s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 499s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 499s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 499s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 499s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing c2#pad.sam, ref c2.fa: 499s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 499s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 499s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 499s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 499s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 499s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 499s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 499s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing ce#1.sam, ref ce.fa: 499s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 499s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 499s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 499s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 499s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 499s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 499s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 499s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 499s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 499s .. ok 499s 499s test_view testing ce#1000.sam, ref ce.fa: 499s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 499s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 499s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 499s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 499s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 499s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 499s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 499s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 499s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 499s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 500s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 500s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 500s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 500s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 500s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 500s .. ok 500s 500s test_view testing ce#2.sam, ref ce.fa: 500s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 500s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 500s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 500s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 500s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 500s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 500s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 500s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 500s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 500s .. ok 500s 500s test_view testing ce#5.sam, ref ce.fa: 500s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 500s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 500s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 500s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 500s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 500s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 500s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 500s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 500s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 500s .. ok 500s 500s test_view testing ce#5b.sam, ref ce.fa: 500s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 500s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 500s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 500s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 500s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 500s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 500s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 500s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 500s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 500s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 500s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 500s .. ok 500s 500s test_view testing ce#large_seq.sam, ref ce.fa: 500s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 500s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 500s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 500s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 500s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 500s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 500s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 500s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 500s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 500s .. ok 500s 500s test_view testing ce#supp.sam, ref ce.fa: 500s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 500s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 500s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 500s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 500s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 500s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 500s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 500s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 500s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 500s .. ok 500s 500s test_view testing ce#tag_depadded.sam, ref ce.fa: 500s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 500s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 500s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 500s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 501s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 501s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 501s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 501s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 501s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 501s .. ok 501s 501s test_view testing ce#tag_padded.sam, ref ce.fa: 501s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 501s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 501s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 501s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 501s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 501s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 501s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 501s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 501s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 501s .. ok 501s 501s test_view testing ce#unmap.sam, ref ce.fa: 501s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 501s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 501s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 501s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 501s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 501s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 501s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 501s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 501s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 501s .. ok 501s 501s test_view testing ce#unmap1.sam, ref ce.fa: 501s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 501s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 501s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 501s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 501s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 501s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 501s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 501s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 501s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 501s .. ok 501s 501s test_view testing ce#unmap2.sam, ref ce.fa: 501s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 501s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 501s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 501s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 501s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 501s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 501s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 501s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 501s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 501s .. ok 501s 501s test_view testing md#1.sam, ref md.fa: 501s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 501s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 501s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 501s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 501s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 501s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 501s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 501s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 501s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 501s .. ok 501s 501s test_view testing xx#blank.sam, ref xx.fa: 501s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 501s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 501s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 501s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 501s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 501s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 501s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 501s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 501s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 501s .. ok 501s 501s test_view testing xx#large_aux.sam, ref xx.fa: 501s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 501s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 501s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 501s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 501s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 501s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 501s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 501s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 501s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 501s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 501s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 501s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 502s .. ok 502s 502s test_view testing xx#large_aux2.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 502s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 502s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 502s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 502s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#MD.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 502s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 502s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 502s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 502s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#MD2.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 502s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 502s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 502s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 502s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#minimal.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 502s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 502s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 502s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 502s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#pair.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 502s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 502s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 502s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 502s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#repeated.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 502s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 502s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 502s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 502s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#rg.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 502s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 502s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 502s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 502s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#tlen.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 502s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 502s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 502s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 502s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#tlen2.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 502s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 502s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 502s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 502s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 502s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 502s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 502s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 502s .. ok 502s 502s test_view testing xx#triplet.sam, ref xx.fa: 502s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 502s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 502s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 502s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 503s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 503s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 503s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 503s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 503s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 503s .. ok 503s 503s test_view testing xx#unsorted.sam, ref xx.fa: 503s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 503s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 503s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 503s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 503s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 503s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 503s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 503s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 503s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 503s .. ok 503s 503s test_view testing embed_ref=2: 503s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 503s [W::cram_get_ref] Failed to populate reference for id 0 503s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 503s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 503s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 503s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 503s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 503s .. ok 503s 503s test_view testing region queries: 503s ./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 503s ./compare_sam.pl range.tmp range.out 503s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 503s ./compare_sam.pl range.tmp range.out 503s .. ok 503s 503s test_view testing BAM files with absent @SQ lines: 503s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 503s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 503s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 503s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 503s .. ok 503s 503s test_view testing large (> 2Gbases) positions: 503s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 503s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 503s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 503s test_view: 503s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 503s .. ok 503s 503s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 503s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 503s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 503s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 503s .. ok 503s 503s test_view testing auxf#values.sam, ref auxf.fa: 503s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 503s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 503s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 503s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 503s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 503s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 503s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 503s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 503s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 504s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 504s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 504s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 504s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 504s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 504s This is a technology demonstration that should not be used for archival data. 504s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 504s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 504s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 504s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 504s .. ok 504s 504s test_view testing c1#bounds.sam, ref c1.fa: 504s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 504s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 504s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 504s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 504s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 504s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 504s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 504s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 504s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 504s .. ok 504s 504s test_view testing c1#clip.sam, ref c1.fa: 504s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 504s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 504s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 504s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 504s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 504s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 504s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 504s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 504s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 504s .. ok 504s 504s test_view testing c1#noseq.sam, ref c1.fa: 504s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 504s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 504s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 504s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 504s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 504s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 504s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 504s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 504s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 504s .. ok 504s 504s test_view testing c1#pad1.sam, ref c1.fa: 504s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 504s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 504s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 504s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 504s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 504s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 504s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 504s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 505s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 505s .. ok 505s 505s test_view testing c1#pad2.sam, ref c1.fa: 505s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 505s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 505s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 505s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 505s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 505s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 505s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 505s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 505s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 505s .. ok 505s 505s test_view testing c1#pad3.sam, ref c1.fa: 505s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 505s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 505s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 505s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 505s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 505s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 505s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 505s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 505s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 505s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 505s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 505s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 505s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 505s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 505s This is a technology demonstration that should not be used for archival data. 505s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 505s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 508s .. ok 508s 508s test_view testing c1#unknown.sam, ref c1.fa: 508s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 508s [W::cram_set_voption] ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 508s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 508s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 508s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 508s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 508s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 508s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 508s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 508s .. ok 508s 508s test_view testing c2#pad.sam, ref c2.fa: 508s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 508s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 508s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 508s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 508s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 508s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 508s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 508s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 508s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 508s .. ok 508s 508s test_view testing ce#1.sam, ref ce.fa: 508s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 508s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 508s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 508s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 508s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 508s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 508s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 508s .. ok 508s 508s test_view testing ce#1000.sam, ref ce.fa: 508s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 508s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 508s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 508s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 508s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 508s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 508s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 508s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 508s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 508s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 508s ./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 508s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 508s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 508s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 508s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 508s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 508s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 508s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 508s .. ok 508s 508s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 508s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 508s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 508s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 508s ./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 508s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 508s ./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 508s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 508s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 508s .. ok 508s 508s test_view testing ce#2.sam, ref ce.fa: 508s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 508s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 508s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 508s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 508s CRAM version 4.0 is still a draft and subject to change. 508s This is a technology demonstration that should not be used for archival data. 508s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 508s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 508s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 508s .. ok 508s 508s test_view testing ce#5.sam, ref ce.fa: 508s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 508s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 508s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 508s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 508s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 508s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 508s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 508s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 508s ./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 508s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 508s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 508s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 508s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 508s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 509s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 509s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 509s This is a technology demonstration that should not be used for archival data. 509s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 509s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 509s .. ok 509s 509s test_view testing ce#5b.sam, ref ce.fa: 509s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 509s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 509s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 509s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 509s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 509s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 509s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 509s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 509s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 509s ./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 509s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 509s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 509s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 509s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 509s .. ok 509s 509s test_view testing ce#large_seq.sam, ref ce.fa: 509s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 509s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 509s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 509s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 509s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 509s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 509s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 509s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 510s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 510s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 512s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 512s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 512s This is a technology demonstration that should not be used for archival data. 512s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 512s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 512s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 512s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 512s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 512s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 512s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 512s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 512s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 512s .. ok 512s 512s test_view testing ce#supp.sam, ref ce.fa: 512s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 512s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 512s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 512s This is a technology demonstration that should not be used for archival data. 512s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 512s This is a technology demonstration that should not be used for archival data. 512s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 512s This is a technology demonstration that should not be used for archival data. 512s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 512s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 512s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 512s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 512s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 512s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 512s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 512s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 512s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 512s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 512s This is a technology demonstration that should not be used for archival data. 512s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 512s .. ok 512s 512s test_view testing ce#tag_depadded.sam, ref ce.fa: 512s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 512s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 512s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 512s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 512s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 512s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 512s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 512s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 512s .. ok 512s 512s test_view testing ce#tag_padded.sam, ref ce.fa: 512s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 512s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 512s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 512s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 512s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 512s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 512s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 512s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 512s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 513s .. ok 513s 513s test_view testing ce#unmap.sam, ref ce.fa: 513s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 513s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 513s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 513s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 513s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 513s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 513s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 513s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 513s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 513s ./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 513s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 513s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 513s .. ok 513s 513s test_view testing ce#unmap1.sam, ref ce.fa: 513s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 513s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 513s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 513s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 513s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 513s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 513s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 513s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 513s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 513s ./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 513s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 513s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 513s .. ok 513s 513s test_view testing ce#unmap2.sam, ref ce.fa: 513s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 513s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 513s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 513s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 513s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 514s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 514s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 516s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 516s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 516s This is a technology demonstration that should not be used for archival data. 516s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 516s ./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 516s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 516s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 516s .. ok 516s 516s test_view testing md#1.sam, ref md.fa: 516s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 516s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 516s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 516s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 516s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 516s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 516s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 516s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 516s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 516s .. ok 516s 516s test_view testing xx#blank.sam, ref xx.fa: 516s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 516s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 516s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 516s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 516s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 516s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 516s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 516s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 516s ./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 516s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 516s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 516s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 516s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 516s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 516s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 516s .. ok 516s 516s test_view testing xx#large_aux.sam, ref xx.fa: 516s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 516s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 516s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 516s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 516s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 516s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 516s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 516s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 516s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 516s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 516s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 516s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 516s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 516s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 516s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 516s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 516s This is a technology demonstration that should not be used for archival data. 516s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 516s This is a technology demonstration that should not be used for archival data. 516s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 516s This is a technology demonstration that should not be used for archival data. 516s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 516s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 516s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 516s This is a technology demonstration that should not be used for archival data. 516s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 516s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 516s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 516s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 516s .. ok 516s 516s test_view testing xx#large_aux2.sam, ref xx.fa: 516s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 516s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 516s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 516s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 516s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 516s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 516s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 516s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 516s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 516s .. ok 516s 516s test_view testing xx#MD.sam, ref xx.fa: 516s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 517s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 517s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 517s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 517s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 517s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 517s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 517s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 517s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 517s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 517s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 517s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 517s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 517s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 517s This is a technology demonstration that should not be used for archival data. 517s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 517s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 517s .. ok 517s 517s test_view testing xx#MD2.sam, ref xx.fa: 517s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 517s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 517s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 517s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 521s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 521s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 521s This is a technology demonstration that should not be used for archival data. 521s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 521s This is a technology demonstration that should not be used for archival data. 521s [W::cram_get_ref] Failed to populate reference for id 0 521s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 521s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 521s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 521s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 521s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 521s .. ok 521s 521s test_view testing xx#minimal.sam, ref xx.fa: 521s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 521s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 521s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 521s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 521s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 521s ./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 521s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 521s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 521s .. ok 521s 521s test_view testing xx#pair.sam, ref xx.fa: 521s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 521s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 521s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 521s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 521s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 521s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 521s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 521s .. ok 521s 521s test_view testing xx#repeated.sam, ref xx.fa: 521s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 521s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 521s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 521s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 521s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 521s .. ok 521s 521s test_view testing xx#rg.sam, ref xx.fa: 521s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 521s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 521s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 521s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 521s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 521s .. ok 521s 521s test_view testing xx#tlen.sam, ref xx.fa: 521s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 521s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 521s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 521s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 521s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 521s ./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 521s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 521s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 521s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 521s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 521s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 521s .. ok 521s 521s test_view testing xx#tlen2.sam, ref xx.fa: 521s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 521s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 521s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 521s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 521s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 521s ./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 521s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 521s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 521s .. ok 521s 521s test_view testing xx#triplet.sam, ref xx.fa: 521s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 521s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 521s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 521s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 521s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 521s ./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 521s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 521s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 521s .. ok 521s 521s test_view testing xx#unsorted.sam, ref xx.fa: 521s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 521s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 521s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 521s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 521s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 521s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 521s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 521s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 521s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 521s .. ok 521s 521s test_view testing embed_ref=2: 521s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 521s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 521s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 521s .. ok 521s 521s test_view testing region queries: 521s ./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 521s ./compare_sam.pl range.tmp range.out 521s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 521s ./compare_sam.pl range.tmp range.out 521s .. ok 521s 521s test_view testing BAM files with absent @SQ lines: 521s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 521s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 521s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 521s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 521s .. ok 521s 521s test_view testing large (> 2Gbases) positions: 521s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 521s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 521s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 521s test_view: 521s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 521s .. ok 521s 521s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 521s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 521s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 521s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 521s .. ok 521s 521s 521s test_MD testing xx#MD.sam, ref xx.fa: 521s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 521s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 521s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 521s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 521s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 521s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 521s Checking for MD/NM in xx#MD.sam 521s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 521s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 521s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 522s .. ok 522s 522s 522s test_MD testing xx#MD2.sam, ref xx.fa: 522s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 522s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 522s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 522s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 522s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 522s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 522s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 522s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 522s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 522s .. ok 522s 522s test_vcf_api: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-vcf-api /tmp/arqwdNIWgv/test-vcf-api.bcf 522s [W::bcf_record_check] Bad BCF record at 1:1: No REF allele 522s .. ok 522s 522s test_bcf2vcf: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/tabix/vcf_file.bcf 522s [E::bcf_index_build3] TBI indices for BCF files are not supported 522s [E::idx_find_and_load] Could not retrieve index file for '/tmp/arqwdNIWgv/test-vcf-api.bcf' 522s .. ok 522s 522s test_vcf_sweep: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-vcf-sweep /tmp/arqwdNIWgv/test-vcf-api.bcf 522s .. ok 522s 522s test_vcf_various: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 522s .. ok 522s 522s test_vcf_various: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/formatcols.vcf 522s .. ok 522s 522s test_vcf_various: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/noroundtrip.vcf 522s .. ok 522s 522s test_vcf_various: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/formatmissing.vcf 522s .. ok 522s 522s test_vcf_various: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/vcf_meta_meta.vcf 522s .. ok 522s 522s test_vcf_various: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 522s .. ok 522s 522s test-bcf-sr: 522s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 74452500 523s .. ok 523s 523s test-bcf-sr: 523s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 34270147 523s .. ok 523s 523s test-bcf-sr: 523s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 11108528 524s .. ok 524s 524s test-bcf-sr: 524s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 42233895 524s .. ok 524s 524s test-bcf-sr: 524s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 8111117 525s .. ok 525s 525s test-bcf-sr: 525s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 85644070 525s .. ok 525s 525s test-bcf-sr: 525s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 49879942 526s .. ok 526s 526s test-bcf-sr: 526s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 47881429 526s .. ok 526s 526s test-bcf-sr: 526s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 69081244 526s .. ok 526s 526s test-bcf-sr: 526s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/arqwdNIWgv -s 83459376 527s .. ok 527s 527s test_bcf_sr_no_index: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/arqwdNIWgv/no_index_1.err 527s .. ok 527s 527s test_bcf_sr_no_index: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/arqwdNIWgv/no_index_2.out 2> /tmp/arqwdNIWgv/no_index_2.err (expected fail) 527s .. ok 527s 527s test_bcf_sr_no_index: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/arqwdNIWgv/no_index_3.out 2> /tmp/arqwdNIWgv/no_index_3.err (expected fail) 527s .. ok 527s 527s test_bcf_sr_no_index: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/arqwdNIWgv/no_index_4.out 2> /tmp/arqwdNIWgv/no_index_4.err (expected fail) 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -b -p /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf -x /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_1.out.vcf -r '1' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_2.out.vcf -r '1:1-2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_4.out.vcf -r '1:1-1' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_5.out.vcf -r '{1:1}' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf (expected fail) 527s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 527s Failed to set regions 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_14.out.vcf -t '1' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_15.out.vcf -t '1:1-2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_17.out.vcf -t '1:1-1' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_18.out.vcf -t '{1:1}' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf 527s .. ok 527s 527s test_bcf_sr_range: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/arqwdNIWgv/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/arqwdNIWgv/weird-chr-names.vcf.bcf (expected fail) 527s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 527s Failed to set targets 527s .. ok 527s 527s test_command: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf-translate - 527s .. ok 527s 527s test_convert_padded_header: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/arqwdNIWgv/headernul0.bam 527s .. ok 527s 527s test_convert_padded_header: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/arqwdNIWgv/headernul1.bam 527s .. ok 527s 527s test_convert_padded_header: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/arqwdNIWgv/headernul678.bam 527s .. ok 527s 527s test_rebgzip: Alternate zlib/deflate library detected 527s test_rebgzip: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/bgziptest.txt 527s .. ok 527s 527s test-logging: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-logging.pl 527s .. ok 527s 527s test_plugin_loading: 527s HTS_PATH=/tmp/autopkgtest.Pl3h3g/autopkgtest_tmp /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn01.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn01.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn01.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02-r.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02_exp.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn02_exp-a.sam -o - 527s .. ok 527s 527s test_realn: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/realn03.sam -o - 527s .. ok 527s 527s test-bcf_set_variant_type: 527s /tmp/autopkgtest.Pl3h3g/autopkgtest_tmp/test/test-bcf_set_variant_type 527s .. ok 527s 527s 527s Number of tests: 527s total .. 211 527s passed .. 211 527s failed .. 0 527s 528s PASS 528s + echo PASS 528s autopkgtest [15:00:07]: test run-unit-test: -----------------------] 530s run-unit-test PASS 530s autopkgtest [15:00:09]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 531s autopkgtest [15:00:10]: @@@@@@@@@@@@@@@@@@@@ summary 531s run-unit-test PASS 544s Creating nova instance adt-noble-arm64-htslib-20240318-145118-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...