0s autopkgtest [06:30:39]: starting date and time: 2024-03-24 06:30:39+0000 0s autopkgtest [06:30:39]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [06:30:39]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b_fga2wz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl,src:orthanc-python --apt-upgrade htslib --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2 orthanc-python/4.1+ds-2build3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-5.secgroup --name adt-noble-ppc64el-htslib-20240324-063039-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 175s autopkgtest [06:33:34]: testbed dpkg architecture: ppc64el 175s autopkgtest [06:33:34]: testbed apt version: 2.7.12 175s autopkgtest [06:33:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 176s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 176s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 176s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 176s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4009 kB] 176s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 177s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [698 kB] 177s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 177s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 177s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 177s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4267 kB] 177s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 177s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 177s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 180s Fetched 9723 kB in 2s (4214 kB/s) 180s Reading package lists... 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 183s Calculating upgrade... 183s The following packages will be REMOVED: 183s libssl3 183s The following NEW packages will be installed: 183s libssl3t64 183s The following packages have been kept back: 183s curl 183s The following packages will be upgraded: 183s openssl 183s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 183s Need to get 3151 kB of archives. 183s After this operation, 73.7 kB of additional disk space will be used. 183s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 184s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 185s Fetched 3151 kB in 1s (2373 kB/s) 185s (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 ... 70156 files and directories currently installed.) 185s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 185s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 185s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 185s wget depends on libssl3 (>= 3.0.0). 185s tnftp depends on libssl3 (>= 3.0.0). 185s tcpdump depends on libssl3 (>= 3.0.0). 185s systemd-resolved depends on libssl3 (>= 3.0.0). 185s systemd depends on libssl3 (>= 3.0.0). 185s sudo depends on libssl3 (>= 3.0.0). 185s rsync depends on libssl3 (>= 3.0.0). 185s python3-cryptography depends on libssl3 (>= 3.0.0). 185s openssh-server depends on libssl3 (>= 3.0.10). 185s openssh-client depends on libssl3 (>= 3.0.10). 185s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 185s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 185s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 185s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 185s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 185s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 185s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 185s libnvme1 depends on libssl3 (>= 3.0.0). 185s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 185s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 185s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 185s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 185s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 185s kmod depends on libssl3 (>= 3.0.0). 185s dhcpcd-base depends on libssl3 (>= 3.0.0). 185s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 185s 185s (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 ... 70156 files and directories currently installed.) 185s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 185s Selecting previously unselected package libssl3t64:ppc64el. 185s (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 ... 70145 files and directories currently installed.) 185s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 185s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 185s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 185s Setting up openssl (3.0.13-0ubuntu2) ... 185s Processing triggers for man-db (2.12.0-3) ... 186s Processing triggers for libc-bin (2.39-0ubuntu6) ... 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 186s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 187s sh: Attempting to set up Debian/Ubuntu apt sources automatically 187s sh: Distribution appears to be Ubuntu 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s eatmydata is already the newest version (131-1). 188s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s dbus is already the newest version (1.14.10-4ubuntu1). 188s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s rng-tools-debian is already the newest version (2.4). 189s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s The following packages will be REMOVED: 189s cloud-init* python3-configobj* python3-debconf* 189s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 189s After this operation, 3256 kB disk space will be freed. 189s (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 ... 70158 files and directories currently installed.) 189s Removing cloud-init (24.1.2-0ubuntu1) ... 190s Removing python3-configobj (5.0.8-3) ... 190s Removing python3-debconf (1.5.86) ... 190s Processing triggers for man-db (2.12.0-3) ... 190s (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 ... 69769 files and directories currently installed.) 190s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 191s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 191s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 191s invoke-rc.d: policy-rc.d denied execution of try-restart. 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 191s linux-generic is already the newest version (6.8.0-11.11+1). 191s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 192s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 192s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 194s Reading package lists... 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s Calculating upgrade... 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 195s Reading package lists... 195s Building dependency tree... 195s Reading state information... 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 195s autopkgtest [06:33:54]: rebooting testbed after setup commands that affected boot 361s autopkgtest [06:36:40]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 364s autopkgtest [06:36:43]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 368s Get:1 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (dsc) [2437 B] 368s Get:2 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (tar) [1469 kB] 368s Get:3 http://ftpmaster.internal/ubuntu noble/universe htslib 1.18+ds-1 (diff) [20.1 kB] 368s gpgv: Signature made Tue Nov 7 20:35:25 2023 UTC 368s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 368s gpgv: issuer "emollier@debian.org" 368s gpgv: Can't check signature: No public key 368s dpkg-source: warning: cannot verify inline signature for ./htslib_1.18+ds-1.dsc: no acceptable signature found 369s autopkgtest [06:36:48]: testing package htslib version 1.18+ds-1 369s autopkgtest [06:36:48]: build not needed 372s autopkgtest [06:36:51]: test run-unit-test: preparing testbed 377s Reading package lists... 377s Building dependency tree... 377s Reading state information... 378s Starting pkgProblemResolver with broken count: 1 378s Starting 2 pkgProblemResolver with broken count: 1 378s Investigating (0) libssl3t64:ppc64el < 3.0.13-0ubuntu2 @ii mK Ib > 378s Broken libssl3t64:ppc64el Breaks on libssl3:ppc64el < none -> 3.0.10-1ubuntu4 @un pumN > (< 3.0.13-0ubuntu2) 378s Considering libssl3:ppc64el 147 as a solution to libssl3t64:ppc64el 143 378s Removing libssl3t64:ppc64el rather than change libssl3:ppc64el 378s Investigating (0) openssl:ppc64el < 3.0.13-0ubuntu2 @ii mK Ib > 378s Broken openssl:ppc64el Depends on libssl3t64:ppc64el < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 378s Considering libssl3t64:ppc64el 143 as a solution to openssl:ppc64el 13 378s Removing openssl:ppc64el rather than change libssl3t64:ppc64el 378s Investigating (1) ca-certificates:ppc64el < 20240203 @ii mK Ib > 378s Broken ca-certificates:ppc64el Depends on openssl:ppc64el < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 378s Considering openssl:ppc64el 13 as a solution to ca-certificates:ppc64el 142 378s Added openssl:ppc64el to the remove list 378s Fixing ca-certificates:ppc64el via keep of openssl:ppc64el 378s Investigating (1) openssl:ppc64el < 3.0.13-0ubuntu2 @ii mK Ib > 378s Broken openssl:ppc64el Depends on libssl3t64:ppc64el < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 378s Considering libssl3t64:ppc64el 143 as a solution to openssl:ppc64el 13 378s Removing openssl:ppc64el rather than change libssl3t64:ppc64el 378s Investigating (2) ca-certificates:ppc64el < 20240203 @ii mK Ib > 378s Broken ca-certificates:ppc64el Depends on openssl:ppc64el < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 378s Considering openssl:ppc64el 13 as a solution to ca-certificates:ppc64el 142 378s Added openssl:ppc64el to the remove list 378s Fixing ca-certificates:ppc64el via keep of openssl:ppc64el 378s Investigating (2) openssl:ppc64el < 3.0.13-0ubuntu2 @ii mK Ib > 378s Broken openssl:ppc64el Depends on libssl3t64:ppc64el < 3.0.13-0ubuntu2 @ii mR > (>= 3.0.9) 378s Considering libssl3t64:ppc64el 143 as a solution to openssl:ppc64el 142 378s Removing openssl:ppc64el rather than change libssl3t64:ppc64el 378s Investigating (3) ca-certificates:ppc64el < 20240203 @ii mK Ib > 378s Broken ca-certificates:ppc64el Depends on openssl:ppc64el < 3.0.13-0ubuntu2 @ii mR > (>= 1.1.1) 378s Considering openssl:ppc64el 143 as a solution to ca-certificates:ppc64el 142 378s Removing ca-certificates:ppc64el rather than change openssl:ppc64el 378s Investigating (3) python3-httplib2:ppc64el < 0.20.4-3 @ii mK Ib > 378s Broken python3-httplib2:ppc64el Depends on ca-certificates:ppc64el < 20240203 @ii mR > 378s Considering ca-certificates:ppc64el 143 as a solution to python3-httplib2:ppc64el 6 378s Removing python3-httplib2:ppc64el rather than change ca-certificates:ppc64el 378s Investigating (3) python3-apport:ppc64el < 2.28.0-0ubuntu1 @ii mK Ib > 378s Broken python3-apport:ppc64el Depends on python3-httplib2:ppc64el < 0.20.4-3 @ii mR > 378s Considering python3-httplib2:ppc64el 143 as a solution to python3-apport:ppc64el 4 378s Removing python3-apport:ppc64el rather than change python3-httplib2:ppc64el 378s Investigating (3) ssh-import-id:ppc64el < 5.11-0ubuntu2 @ii mK Ib > 378s Broken ssh-import-id:ppc64el Depends on ca-certificates:ppc64el < 20240203 @ii mR > 378s Considering ca-certificates:ppc64el 143 as a solution to ssh-import-id:ppc64el 3 378s Removing ssh-import-id:ppc64el rather than change ca-certificates:ppc64el 378s Investigating (3) python3-launchpadlib:ppc64el < 1.11.0-6 @ii mK Ib > 378s Broken python3-launchpadlib:ppc64el Depends on python3-httplib2:ppc64el < 0.20.4-3 @ii mR > 378s Considering python3-httplib2:ppc64el 143 as a solution to python3-launchpadlib:ppc64el 2 378s Removing python3-launchpadlib:ppc64el rather than change python3-httplib2:ppc64el 378s Investigating (3) python3-lazr.restfulclient:ppc64el < 0.14.6-1 @ii mK Ib > 378s Broken python3-lazr.restfulclient:ppc64el Depends on python3-httplib2:ppc64el < 0.20.4-3 @ii mR > (>= 0.7.7) 378s Considering python3-httplib2:ppc64el 143 as a solution to python3-lazr.restfulclient:ppc64el 2 378s Removing python3-lazr.restfulclient:ppc64el rather than change python3-httplib2:ppc64el 378s Investigating (3) python3-certifi:ppc64el < 2023.11.17-1 @ii mK Ib > 378s Broken python3-certifi:ppc64el Depends on ca-certificates:ppc64el < 20240203 @ii mR > 378s Considering ca-certificates:ppc64el 143 as a solution to python3-certifi:ppc64el 2 378s Removing python3-certifi:ppc64el rather than change ca-certificates:ppc64el 378s Investigating (3) python3-requests:ppc64el < 2.31.0+dfsg-1ubuntu1 @ii mK Ib > 378s Broken python3-requests:ppc64el Depends on python3-certifi:ppc64el < 2023.11.17-1 @ii mR > 378s Considering python3-certifi:ppc64el 143 as a solution to python3-requests:ppc64el 2 378s Removing python3-requests:ppc64el rather than change python3-certifi:ppc64el 378s Investigating (4) apport:ppc64el < 2.28.0-0ubuntu1 @ii mK Ib > 378s Broken apport:ppc64el Depends on python3-apport:ppc64el < 2.28.0-0ubuntu1 @ii mR > (>= 2.28.0-0ubuntu1) 378s Considering python3-apport:ppc64el 143 as a solution to apport:ppc64el 6 378s Removing apport:ppc64el rather than change python3-apport:ppc64el 378s Investigating (4) apport-core-dump-handler:ppc64el < 2.28.0-0ubuntu1 @ii mK Ib > 378s Broken apport-core-dump-handler:ppc64el Depends on apport:ppc64el < 2.28.0-0ubuntu1 @ii mR > (>= 2.27.0-0ubuntu7~) 378s Considering apport:ppc64el 143 as a solution to apport-core-dump-handler:ppc64el 4 378s Removing apport-core-dump-handler:ppc64el rather than change apport:ppc64el 378s Done 378s The following packages were automatically installed and are no longer required: 378s apport-symptoms python3-blinker python3-chardet python3-cryptography 378s python3-jwt python3-lazr.uri python3-oauthlib python3-openssl 378s python3-problem-report python3-pyparsing python3-six python3-systemd 378s python3-urllib3 python3-wadllib 378s Use 'sudo apt autoremove' to remove them. 378s The following additional packages will be installed: 378s autoconf automake autopoint autotools-dev build-essential cpp cpp-13 378s cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper debugedit 378s dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 378s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 378s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext htslib-test 378s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 378s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 378s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 378s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 378s libhtscodecs-dev libhtscodecs2 libisl23 libitm1 liblsan0 liblzma-dev libmpc3 378s libquadmath0 libssl-dev libssl3 libstdc++-13-dev libsub-override-perl 378s libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf rpcsvc-proto tabix 378s zlib1g-dev 378s Suggested packages: 378s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 378s cpp-13-doc dh-make gcc-13-doc gcc-multilib manpages-dev flex bison gdb 378s gcc-doc gdb-powerpc64le-linux-gnu gettext-doc libasprintf-dev 378s libgettextpo-dev glibc-doc libcurl4-doc libgnutls28-dev libidn-dev 378s libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc 378s libssl-doc libstdc++-13-doc libtool-doc gfortran | fortran95-compiler 378s gcj-jdk m4-doc libmail-box-perl 378s Recommended packages: 378s bzip2-doc manpages manpages-dev libc-devtools libarchive-cpio-perl 378s libltdl-dev libmail-sendmail-perl 378s The following packages will be REMOVED: 378s apport apport-core-dump-handler ca-certificates libssl3t64 openssl 378s python3-apport python3-certifi python3-httplib2 python3-launchpadlib 378s python3-lazr.restfulclient python3-requests ssh-import-id 378s The following NEW packages will be installed: 378s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 378s cpp cpp-13 cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper 378s debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 378s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 378s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext htslib-test 378s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 378s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 378s libdebhelper-perl libdeflate-dev libdeflate0 libdw1 378s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 378s libhtscodecs-dev libhtscodecs2 libisl23 libitm1 liblsan0 liblzma-dev libmpc3 378s libquadmath0 libssl-dev libssl3 libstdc++-13-dev libsub-override-perl 378s libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf rpcsvc-proto tabix 378s zlib1g-dev 378s 0 upgraded, 65 newly installed, 12 to remove and 0 not upgraded. 378s Need to get 84.6 MB/84.6 MB of archives. 378s After this operation, 298 MB of additional disk space will be used. 378s Get:1 /tmp/autopkgtest.VEmnT6/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [812 B] 378s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libssl3 ppc64el 3.0.10-1ubuntu4 [2164 kB] 379s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el m4 ppc64el 1.4.19-4 [275 kB] 379s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el autoconf all 2.71-3 [339 kB] 379s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 379s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 379s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el autopoint all 0.21-14ubuntu1 [422 kB] 380s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu6 [21.3 kB] 380s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-11.11 [1585 kB] 380s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 380s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 380s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu6 [2102 kB] 380s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libisl23 ppc64el 0.26-3 [864 kB] 380s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libmpc3 ppc64el 1.3.1-1 [61.2 kB] 380s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [10.7 MB] 382s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13 ppc64el 13.2.0-17ubuntu2 [1038 B] 382s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] 382s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] 382s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libcc1-0 ppc64el 14-20240303-1ubuntu1 [48.1 kB] 382s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 382s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libitm1 ppc64el 14-20240303-1ubuntu1 [32.4 kB] 382s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libatomic1 ppc64el 14-20240303-1ubuntu1 [10.7 kB] 382s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libasan8 ppc64el 14-20240303-1ubuntu1 [2973 kB] 382s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el liblsan0 ppc64el 14-20240303-1ubuntu1 [1325 kB] 382s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libtsan2 ppc64el 14-20240303-1ubuntu1 [2734 kB] 382s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libubsan1 ppc64el 14-20240303-1ubuntu1 [1194 kB] 382s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libquadmath0 ppc64el 14-20240303-1ubuntu1 [158 kB] 382s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcc-13-dev ppc64el 13.2.0-17ubuntu2 [1581 kB] 382s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [20.6 MB] 384s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13 ppc64el 13.2.0-17ubuntu2 [477 kB] 384s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] 384s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] 384s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libstdc++-13-dev ppc64el 13.2.0-17ubuntu2 [2445 kB] 384s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [12.2 MB] 384s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13 ppc64el 13.2.0-17ubuntu2 [14.5 kB] 384s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] 384s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] 384s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 384s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 384s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libtool all 2.4.7-7 [166 kB] 384s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-autoreconf all 20 [16.1 kB] 384s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 384s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libsub-override-perl all 0.10-1 [10.0 kB] 384s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 384s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] 384s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libdw1 ppc64el 0.190-1 [294 kB] 384s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el debugedit ppc64el 1:5.0-5 [51.1 kB] 384s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el dwz ppc64el 0.15-1 [139 kB] 384s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext ppc64el 0.21-14ubuntu1 [979 kB] 384s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 384s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 384s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el debhelper all 13.14.1ubuntu1 [869 kB] 384s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el htslib-test all 1.18+ds-1 [1120 kB] 384s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el libbz2-dev ppc64el 1.0.8-5ubuntu1 [51.2 kB] 384s Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el libcurl4-gnutls-dev ppc64el 8.5.0-2ubuntu2 [530 kB] 384s Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 384s Get:57 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate-dev ppc64el 1.19-1 [69.7 kB] 384s Get:58 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 384s Get:59 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 384s Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el liblzma-dev ppc64el 5.4.5-0.3 [243 kB] 384s Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3ubuntu1 [902 kB] 384s Get:62 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts-dev ppc64el 1.18+ds-1 [6252 kB] 385s Get:63 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs-dev ppc64el 1.6.0-1 [3007 kB] 385s Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el libssl-dev ppc64el 3.0.10-1ubuntu4 [2664 kB] 385s Get:65 http://ftpmaster.internal/ubuntu noble/universe ppc64el tabix ppc64el 1.18+ds-1 [692 kB] 386s Fetched 84.6 MB in 7s (11.3 MB/s) 386s (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 ... 69714 files and directories currently installed.) 386s Removing ssh-import-id (5.11-0ubuntu2) ... 386s Removing apport-core-dump-handler (2.28.0-0ubuntu1) ... 386s Removing apport (2.28.0-0ubuntu1) ... 387s Removing python3-apport (2.28.0-0ubuntu1) ... 387s Removing python3-requests (2.31.0+dfsg-1ubuntu1) ... 387s dpkg: ca-certificates: dependency problems, but removing anyway as you requested: 387s python3-httplib2 depends on ca-certificates. 387s python3-certifi depends on ca-certificates. 387s 387s Removing ca-certificates (20240203) ... 387s Removing dangling symlinks from /etc/ssl/certs... done. 387s Removing openssl (3.0.13-0ubuntu2) ... 387s dpkg: libssl3t64:ppc64el: dependency problems, but removing anyway as you requested: 387s wget depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s tnftp depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s tcpdump depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s systemd-resolved depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s systemd depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s sudo depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s rsync depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s python3-cryptography depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s openssh-server depends on libssl3 (>= 3.0.10); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s openssh-client depends on libssl3 (>= 3.0.10); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libssh-4:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libnvme1 depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libkmod2:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libcurl4:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s kmod depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s dhcpcd-base depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0); however: 387s Package libssl3 is not installed. 387s Package libssl3t64:ppc64el which provides libssl3 is to be removed. 387s 387s Removing libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 387s Selecting previously unselected package libssl3:ppc64el. 387s (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 ... 69053 files and directories currently installed.) 387s Preparing to unpack .../libssl3_3.0.10-1ubuntu4_ppc64el.deb ... 387s Unpacking libssl3:ppc64el (3.0.10-1ubuntu4) ... 387s (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 ... 69064 files and directories currently installed.) 387s Removing python3-certifi (2023.11.17-1) ... 387s Removing python3-launchpadlib (1.11.0-6) ... 387s Removing python3-lazr.restfulclient (0.14.6-1) ... 387s Removing python3-httplib2 (0.20.4-3) ... 388s Selecting previously unselected package m4. 388s (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 ... 68950 files and directories currently installed.) 388s Preparing to unpack .../00-m4_1.4.19-4_ppc64el.deb ... 388s Unpacking m4 (1.4.19-4) ... 388s Selecting previously unselected package autoconf. 388s Preparing to unpack .../01-autoconf_2.71-3_all.deb ... 388s Unpacking autoconf (2.71-3) ... 388s Selecting previously unselected package autotools-dev. 388s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 388s Unpacking autotools-dev (20220109.1) ... 388s Selecting previously unselected package automake. 388s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 388s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 388s Selecting previously unselected package autopoint. 388s Preparing to unpack .../04-autopoint_0.21-14ubuntu1_all.deb ... 388s Unpacking autopoint (0.21-14ubuntu1) ... 388s Selecting previously unselected package libc-dev-bin. 388s Preparing to unpack .../05-libc-dev-bin_2.39-0ubuntu6_ppc64el.deb ... 388s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 388s Selecting previously unselected package linux-libc-dev:ppc64el. 388s Preparing to unpack .../06-linux-libc-dev_6.8.0-11.11_ppc64el.deb ... 388s Unpacking linux-libc-dev:ppc64el (6.8.0-11.11) ... 388s Selecting previously unselected package libcrypt-dev:ppc64el. 388s Preparing to unpack .../07-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 388s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 388s Selecting previously unselected package rpcsvc-proto. 388s Preparing to unpack .../08-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 388s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 388s Selecting previously unselected package libc6-dev:ppc64el. 388s Preparing to unpack .../09-libc6-dev_2.39-0ubuntu6_ppc64el.deb ... 388s Unpacking libc6-dev:ppc64el (2.39-0ubuntu6) ... 388s Selecting previously unselected package libisl23:ppc64el. 388s Preparing to unpack .../10-libisl23_0.26-3_ppc64el.deb ... 388s Unpacking libisl23:ppc64el (0.26-3) ... 388s Selecting previously unselected package libmpc3:ppc64el. 388s Preparing to unpack .../11-libmpc3_1.3.1-1_ppc64el.deb ... 388s Unpacking libmpc3:ppc64el (1.3.1-1) ... 388s Selecting previously unselected package cpp-13-powerpc64le-linux-gnu. 388s Preparing to unpack .../12-cpp-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 388s Unpacking cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 388s Selecting previously unselected package cpp-13. 388s Preparing to unpack .../13-cpp-13_13.2.0-17ubuntu2_ppc64el.deb ... 388s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 388s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 388s Preparing to unpack .../14-cpp-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 388s Unpacking cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 388s Selecting previously unselected package cpp. 388s Preparing to unpack .../15-cpp_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 388s Unpacking cpp (4:13.2.0-7ubuntu1) ... 388s Selecting previously unselected package libcc1-0:ppc64el. 388s Preparing to unpack .../16-libcc1-0_14-20240303-1ubuntu1_ppc64el.deb ... 388s Unpacking libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 388s Selecting previously unselected package libgomp1:ppc64el. 388s Preparing to unpack .../17-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 388s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 388s Selecting previously unselected package libitm1:ppc64el. 388s Preparing to unpack .../18-libitm1_14-20240303-1ubuntu1_ppc64el.deb ... 388s Unpacking libitm1:ppc64el (14-20240303-1ubuntu1) ... 389s Selecting previously unselected package libatomic1:ppc64el. 389s Preparing to unpack .../19-libatomic1_14-20240303-1ubuntu1_ppc64el.deb ... 389s Unpacking libatomic1:ppc64el (14-20240303-1ubuntu1) ... 389s Selecting previously unselected package libasan8:ppc64el. 389s Preparing to unpack .../20-libasan8_14-20240303-1ubuntu1_ppc64el.deb ... 389s Unpacking libasan8:ppc64el (14-20240303-1ubuntu1) ... 389s Selecting previously unselected package liblsan0:ppc64el. 389s Preparing to unpack .../21-liblsan0_14-20240303-1ubuntu1_ppc64el.deb ... 389s Unpacking liblsan0:ppc64el (14-20240303-1ubuntu1) ... 389s Selecting previously unselected package libtsan2:ppc64el. 389s Preparing to unpack .../22-libtsan2_14-20240303-1ubuntu1_ppc64el.deb ... 389s Unpacking libtsan2:ppc64el (14-20240303-1ubuntu1) ... 389s Selecting previously unselected package libubsan1:ppc64el. 389s Preparing to unpack .../23-libubsan1_14-20240303-1ubuntu1_ppc64el.deb ... 389s Unpacking libubsan1:ppc64el (14-20240303-1ubuntu1) ... 389s Selecting previously unselected package libquadmath0:ppc64el. 389s Preparing to unpack .../24-libquadmath0_14-20240303-1ubuntu1_ppc64el.deb ... 389s Unpacking libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 389s Selecting previously unselected package libgcc-13-dev:ppc64el. 389s Preparing to unpack .../25-libgcc-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 389s Unpacking libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 389s Selecting previously unselected package gcc-13-powerpc64le-linux-gnu. 389s Preparing to unpack .../26-gcc-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 389s Unpacking gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 389s Selecting previously unselected package gcc-13. 389s Preparing to unpack .../27-gcc-13_13.2.0-17ubuntu2_ppc64el.deb ... 389s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 389s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 389s Preparing to unpack .../28-gcc-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 389s Unpacking gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 389s Selecting previously unselected package gcc. 389s Preparing to unpack .../29-gcc_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 389s Unpacking gcc (4:13.2.0-7ubuntu1) ... 389s Selecting previously unselected package libstdc++-13-dev:ppc64el. 389s Preparing to unpack .../30-libstdc++-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 389s Unpacking libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 390s Selecting previously unselected package g++-13-powerpc64le-linux-gnu. 390s Preparing to unpack .../31-g++-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 390s Unpacking g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 390s Selecting previously unselected package g++-13. 390s Preparing to unpack .../32-g++-13_13.2.0-17ubuntu2_ppc64el.deb ... 390s Unpacking g++-13 (13.2.0-17ubuntu2) ... 390s Selecting previously unselected package g++-powerpc64le-linux-gnu. 390s Preparing to unpack .../33-g++-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 390s Unpacking g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 390s Selecting previously unselected package g++. 390s Preparing to unpack .../34-g++_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 390s Unpacking g++ (4:13.2.0-7ubuntu1) ... 390s Selecting previously unselected package build-essential. 390s Preparing to unpack .../35-build-essential_12.10ubuntu1_ppc64el.deb ... 390s Unpacking build-essential (12.10ubuntu1) ... 390s Selecting previously unselected package libdebhelper-perl. 390s Preparing to unpack .../36-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 390s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 390s Selecting previously unselected package libtool. 390s Preparing to unpack .../37-libtool_2.4.7-7_all.deb ... 390s Unpacking libtool (2.4.7-7) ... 390s Selecting previously unselected package dh-autoreconf. 390s Preparing to unpack .../38-dh-autoreconf_20_all.deb ... 390s Unpacking dh-autoreconf (20) ... 390s Selecting previously unselected package libarchive-zip-perl. 390s Preparing to unpack .../39-libarchive-zip-perl_1.68-1_all.deb ... 390s Unpacking libarchive-zip-perl (1.68-1) ... 390s Selecting previously unselected package libsub-override-perl. 390s Preparing to unpack .../40-libsub-override-perl_0.10-1_all.deb ... 390s Unpacking libsub-override-perl (0.10-1) ... 390s Selecting previously unselected package libfile-stripnondeterminism-perl. 390s Preparing to unpack .../41-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 390s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 390s Selecting previously unselected package dh-strip-nondeterminism. 390s Preparing to unpack .../42-dh-strip-nondeterminism_1.13.1-1_all.deb ... 390s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 390s Selecting previously unselected package libdw1:ppc64el. 390s Preparing to unpack .../43-libdw1_0.190-1_ppc64el.deb ... 390s Unpacking libdw1:ppc64el (0.190-1) ... 390s Selecting previously unselected package debugedit. 390s Preparing to unpack .../44-debugedit_1%3a5.0-5_ppc64el.deb ... 390s Unpacking debugedit (1:5.0-5) ... 390s Selecting previously unselected package dwz. 390s Preparing to unpack .../45-dwz_0.15-1_ppc64el.deb ... 390s Unpacking dwz (0.15-1) ... 390s Selecting previously unselected package gettext. 390s Preparing to unpack .../46-gettext_0.21-14ubuntu1_ppc64el.deb ... 390s Unpacking gettext (0.21-14ubuntu1) ... 390s Selecting previously unselected package intltool-debian. 390s Preparing to unpack .../47-intltool-debian_0.35.0+20060710.6_all.deb ... 390s Unpacking intltool-debian (0.35.0+20060710.6) ... 390s Selecting previously unselected package po-debconf. 390s Preparing to unpack .../48-po-debconf_1.0.21+nmu1_all.deb ... 390s Unpacking po-debconf (1.0.21+nmu1) ... 390s Selecting previously unselected package debhelper. 390s Preparing to unpack .../49-debhelper_13.14.1ubuntu1_all.deb ... 390s Unpacking debhelper (13.14.1ubuntu1) ... 390s Selecting previously unselected package htslib-test. 390s Preparing to unpack .../50-htslib-test_1.18+ds-1_all.deb ... 390s Unpacking htslib-test (1.18+ds-1) ... 390s Selecting previously unselected package libbz2-dev:ppc64el. 390s Preparing to unpack .../51-libbz2-dev_1.0.8-5ubuntu1_ppc64el.deb ... 390s Unpacking libbz2-dev:ppc64el (1.0.8-5ubuntu1) ... 390s Selecting previously unselected package libcurl4-gnutls-dev:ppc64el. 390s Preparing to unpack .../52-libcurl4-gnutls-dev_8.5.0-2ubuntu2_ppc64el.deb ... 390s Unpacking libcurl4-gnutls-dev:ppc64el (8.5.0-2ubuntu2) ... 391s Selecting previously unselected package libdeflate0:ppc64el. 391s Preparing to unpack .../53-libdeflate0_1.19-1_ppc64el.deb ... 391s Unpacking libdeflate0:ppc64el (1.19-1) ... 391s Selecting previously unselected package libdeflate-dev:ppc64el. 391s Preparing to unpack .../54-libdeflate-dev_1.19-1_ppc64el.deb ... 391s Unpacking libdeflate-dev:ppc64el (1.19-1) ... 391s Selecting previously unselected package libhtscodecs2:ppc64el. 391s Preparing to unpack .../55-libhtscodecs2_1.6.0-1_ppc64el.deb ... 391s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 391s Selecting previously unselected package libhts3:ppc64el. 391s Preparing to unpack .../56-libhts3_1.18+ds-1_ppc64el.deb ... 391s Unpacking libhts3:ppc64el (1.18+ds-1) ... 391s Selecting previously unselected package liblzma-dev:ppc64el. 391s Preparing to unpack .../57-liblzma-dev_5.4.5-0.3_ppc64el.deb ... 391s Unpacking liblzma-dev:ppc64el (5.4.5-0.3) ... 391s Selecting previously unselected package zlib1g-dev:ppc64el. 391s Preparing to unpack .../58-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_ppc64el.deb ... 391s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 391s Selecting previously unselected package libhts-dev:ppc64el. 391s Preparing to unpack .../59-libhts-dev_1.18+ds-1_ppc64el.deb ... 391s Unpacking libhts-dev:ppc64el (1.18+ds-1) ... 391s Selecting previously unselected package libhtscodecs-dev:ppc64el. 391s Preparing to unpack .../60-libhtscodecs-dev_1.6.0-1_ppc64el.deb ... 391s Unpacking libhtscodecs-dev:ppc64el (1.6.0-1) ... 391s Selecting previously unselected package libssl-dev:ppc64el. 391s Preparing to unpack .../61-libssl-dev_3.0.10-1ubuntu4_ppc64el.deb ... 391s Unpacking libssl-dev:ppc64el (3.0.10-1ubuntu4) ... 391s Selecting previously unselected package tabix. 391s Preparing to unpack .../62-tabix_1.18+ds-1_ppc64el.deb ... 391s Unpacking tabix (1.18+ds-1) ... 391s Selecting previously unselected package autopkgtest-satdep. 391s Preparing to unpack .../63-1-autopkgtest-satdep.deb ... 391s Unpacking autopkgtest-satdep (0) ... 391s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 391s Setting up libdw1:ppc64el (0.190-1) ... 391s Setting up libarchive-zip-perl (1.68-1) ... 391s Setting up htslib-test (1.18+ds-1) ... 391s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 391s Setting up libssl3:ppc64el (3.0.10-1ubuntu4) ... 391s Setting up libdeflate0:ppc64el (1.19-1) ... 391s Setting up linux-libc-dev:ppc64el (6.8.0-11.11) ... 391s Setting up m4 (1.4.19-4) ... 391s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up libcurl4-gnutls-dev:ppc64el (8.5.0-2ubuntu2) ... 391s Setting up libhtscodecs-dev:ppc64el (1.6.0-1) ... 391s Setting up autotools-dev (20220109.1) ... 391s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 391s Setting up libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up libssl-dev:ppc64el (3.0.10-1ubuntu4) ... 391s Setting up libmpc3:ppc64el (1.3.1-1) ... 391s Setting up libatomic1:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up autopoint (0.21-14ubuntu1) ... 391s Setting up autoconf (2.71-3) ... 391s Setting up liblzma-dev:ppc64el (5.4.5-0.3) ... 391s Setting up libubsan1:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up dwz (0.15-1) ... 391s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 391s Setting up libasan8:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up debugedit (1:5.0-5) ... 391s Setting up libsub-override-perl (0.10-1) ... 391s Setting up libtsan2:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up libisl23:ppc64el (0.26-3) ... 391s Setting up libc-dev-bin (2.39-0ubuntu6) ... 391s Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 391s Setting up libdeflate-dev:ppc64el (1.19-1) ... 391s Setting up tabix (1.18+ds-1) ... 391s Setting up libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up liblsan0:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up libitm1:ppc64el (14-20240303-1ubuntu1) ... 391s Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 391s Setting up automake (1:1.16.5-1.3ubuntu1) ... 391s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 391s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 391s Setting up libhts3:ppc64el (1.18+ds-1) ... 391s Setting up gettext (0.21-14ubuntu1) ... 391s Setting up cpp-13 (13.2.0-17ubuntu2) ... 391s Setting up intltool-debian (0.35.0+20060710.6) ... 391s Setting up dh-strip-nondeterminism (1.13.1-1) ... 391s Setting up libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 391s Setting up cpp (4:13.2.0-7ubuntu1) ... 391s Setting up libc6-dev:ppc64el (2.39-0ubuntu6) ... 391s Setting up libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 391s Setting up libbz2-dev:ppc64el (1.0.8-5ubuntu1) ... 391s Setting up po-debconf (1.0.21+nmu1) ... 391s Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 391s Setting up gcc-13 (13.2.0-17ubuntu2) ... 391s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 391s Setting up libtool (2.4.7-7) ... 391s Setting up libhts-dev:ppc64el (1.18+ds-1) ... 391s Setting up g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 391s Setting up dh-autoreconf (20) ... 391s Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 391s Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 391s Setting up g++-13 (13.2.0-17ubuntu2) ... 391s Setting up debhelper (13.14.1ubuntu1) ... 391s Setting up gcc (4:13.2.0-7ubuntu1) ... 391s Setting up g++ (4:13.2.0-7ubuntu1) ... 391s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 391s Setting up build-essential (12.10ubuntu1) ... 391s Setting up autopkgtest-satdep (0) ... 391s Processing triggers for man-db (2.12.0-3) ... 392s Processing triggers for install-info (7.1-3) ... 392s Processing triggers for libc-bin (2.39-0ubuntu6) ... 396s (Reading database ... 73821 files and directories currently installed.) 396s Removing autopkgtest-satdep (0) ... 396s autopkgtest [06:37:15]: test run-unit-test: [----------------------- 396s + pkg=htslib 396s + '[' /tmp/autopkgtest.VEmnT6/autopkgtest_tmp = '' ']' 396s + 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.VEmnT6/autopkgtest_tmp 396s + cp -aL htslib.pc.in /tmp/autopkgtest.VEmnT6/autopkgtest_tmp 396s + cp -aL htslib.map /tmp/autopkgtest.VEmnT6/autopkgtest_tmp 396s + cd /tmp/autopkgtest.VEmnT6/autopkgtest_tmp 396s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 396s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 396s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 396s + grep sse /proc/cpuinfo 396s + export CFLAGS 396s + make -e check 396s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c 396s : warning: "_FORTIFY_SOURCE" redefined 396s : note: this is the location of the previous definition 397s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c 397s : warning: "_FORTIFY_SOURCE" redefined 397s : note: this is the location of the previous definition 397s 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 397s : warning: "_FORTIFY_SOURCE" redefined 397s : note: this is the location of the previous definition 398s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c 398s : warning: "_FORTIFY_SOURCE" redefined 398s : note: this is the location of the previous definition 399s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c 399s : warning: "_FORTIFY_SOURCE" redefined 399s : note: this is the location of the previous definition 399s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c 399s : warning: "_FORTIFY_SOURCE" redefined 399s : note: this is the location of the previous definition 400s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c 400s : warning: "_FORTIFY_SOURCE" redefined 400s : note: this is the location of the previous definition 401s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c 401s : warning: "_FORTIFY_SOURCE" redefined 401s : note: this is the location of the previous definition 402s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c 402s : warning: "_FORTIFY_SOURCE" redefined 402s : note: this is the location of the previous definition 404s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c 404s : warning: "_FORTIFY_SOURCE" redefined 404s : note: this is the location of the previous definition 405s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c 405s : warning: "_FORTIFY_SOURCE" redefined 405s : note: this is the location of the previous definition 405s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c 405s : warning: "_FORTIFY_SOURCE" redefined 405s : note: this is the location of the previous definition 405s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c 405s : warning: "_FORTIFY_SOURCE" redefined 405s : note: this is the location of the previous definition 405s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c 405s : warning: "_FORTIFY_SOURCE" redefined 405s : note: this is the location of the previous definition 406s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c 406s : warning: "_FORTIFY_SOURCE" redefined 406s : note: this is the location of the previous definition 406s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c 406s : warning: "_FORTIFY_SOURCE" redefined 406s : note: this is the location of the previous definition 406s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c 406s : warning: "_FORTIFY_SOURCE" redefined 406s : note: this is the location of the previous definition 407s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c 407s : warning: "_FORTIFY_SOURCE" redefined 407s : note: this is the location of the previous definition 411s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c 411s : warning: "_FORTIFY_SOURCE" redefined 411s : note: this is the location of the previous definition 411s 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 411s : warning: "_FORTIFY_SOURCE" redefined 411s : note: this is the location of the previous definition 412s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c 412s : warning: "_FORTIFY_SOURCE" redefined 412s : note: this is the location of the previous definition 412s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c 412s : warning: "_FORTIFY_SOURCE" redefined 412s : note: this is the location of the previous definition 412s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c 412s : warning: "_FORTIFY_SOURCE" redefined 412s : note: this is the location of the previous definition 412s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c 412s : warning: "_FORTIFY_SOURCE" redefined 412s : note: this is the location of the previous definition 413s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c 413s : warning: "_FORTIFY_SOURCE" redefined 413s : note: this is the location of the previous definition 418s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c 418s : warning: "_FORTIFY_SOURCE" redefined 418s : note: this is the location of the previous definition 419s 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 419s : warning: "_FORTIFY_SOURCE" redefined 419s : note: this is the location of the previous definition 420s 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 420s : warning: "_FORTIFY_SOURCE" redefined 420s : 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 cram/cram_encode.o cram/cram_encode.c 422s : warning: "_FORTIFY_SOURCE" redefined 422s : note: this is the location of the previous definition 425s 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 425s : warning: "_FORTIFY_SOURCE" redefined 425s : note: this is the location of the previous definition 425s 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 425s : warning: "_FORTIFY_SOURCE" redefined 425s : note: this is the location of the previous definition 425s 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 425s : warning: "_FORTIFY_SOURCE" redefined 425s : note: this is the location of the previous definition 428s 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 428s : warning: "_FORTIFY_SOURCE" redefined 428s : note: this is the location of the previous definition 428s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c 428s : warning: "_FORTIFY_SOURCE" redefined 428s : note: this is the location of the previous definition 428s 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 428s : warning: "_FORTIFY_SOURCE" redefined 428s : note: this is the location of the previous definition 428s 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 428s : warning: "_FORTIFY_SOURCE" redefined 428s : note: this is the location of the previous definition 428s : warning: "_FORTIFY_SOURCE" redefined 428s : note: this is the location of the previous definition 428s 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 429s 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 429s : warning: "_FORTIFY_SOURCE" redefined 429s : note: this is the location of the previous definition 429s 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 429s ranlib libhts.a 429s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.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 -fPIC -c -o kstring.pico kstring.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 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.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 -fPIC -c -o bgzf.pico bgzf.c 430s : warning: "_FORTIFY_SOURCE" redefined 430s : note: this is the location of the previous definition 431s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c 431s : warning: "_FORTIFY_SOURCE" redefined 431s : note: this is the location of the previous definition 431s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c 431s : warning: "_FORTIFY_SOURCE" redefined 431s : note: this is the location of the previous definition 432s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c 432s : warning: "_FORTIFY_SOURCE" redefined 432s : note: this is the location of the previous definition 433s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c 433s : warning: "_FORTIFY_SOURCE" redefined 433s : note: this is the location of the previous definition 434s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c 434s : warning: "_FORTIFY_SOURCE" redefined 434s : note: this is the location of the previous definition 437s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c 437s : warning: "_FORTIFY_SOURCE" redefined 437s : note: this is the location of the previous definition 437s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c 437s : warning: "_FORTIFY_SOURCE" redefined 437s : note: this is the location of the previous definition 437s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c 437s : warning: "_FORTIFY_SOURCE" redefined 437s : note: this is the location of the previous definition 437s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c 437s : warning: "_FORTIFY_SOURCE" redefined 437s : note: this is the location of the previous definition 437s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c 438s : warning: "_FORTIFY_SOURCE" redefined 438s : note: this is the location of the previous definition 438s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c 438s : warning: "_FORTIFY_SOURCE" redefined 438s : note: this is the location of the previous definition 438s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c 438s : warning: "_FORTIFY_SOURCE" redefined 438s : note: this is the location of the previous definition 438s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c 438s : warning: "_FORTIFY_SOURCE" redefined 438s : note: this is the location of the previous definition 439s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c 439s : warning: "_FORTIFY_SOURCE" redefined 439s : 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 -fPIC -c -o sam_mods.pico sam_mods.c 442s : warning: "_FORTIFY_SOURCE" redefined 442s : note: this is the location of the previous definition 443s 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 443s : warning: "_FORTIFY_SOURCE" redefined 443s : note: this is the location of the previous definition 444s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 444s : warning: "_FORTIFY_SOURCE" redefined 444s : note: this is the location of the previous definition 444s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c 444s : warning: "_FORTIFY_SOURCE" redefined 444s : note: this is the location of the previous definition 444s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c 444s : warning: "_FORTIFY_SOURCE" redefined 444s : note: this is the location of the previous definition 444s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c 444s : warning: "_FORTIFY_SOURCE" redefined 444s : note: this is the location of the previous definition 444s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c 444s : warning: "_FORTIFY_SOURCE" redefined 444s : note: this is the location of the previous definition 449s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c 449s : warning: "_FORTIFY_SOURCE" redefined 449s : 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 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c 450s : warning: "_FORTIFY_SOURCE" redefined 450s : 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 cram/cram_decode.pico cram/cram_decode.c 452s : warning: "_FORTIFY_SOURCE" redefined 452s : note: this is the location of the previous definition 454s 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 454s : warning: "_FORTIFY_SOURCE" redefined 454s : note: this is the location of the previous definition 456s 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 456s : warning: "_FORTIFY_SOURCE" redefined 456s : note: this is the location of the previous definition 456s 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 456s : warning: "_FORTIFY_SOURCE" redefined 456s : note: this is the location of the previous definition 457s 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 457s : warning: "_FORTIFY_SOURCE" redefined 457s : 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 cram/cram_stats.pico cram/cram_stats.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 cram/mFILE.pico cram/mFILE.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 cram/open_trace_file.pico cram/open_trace_file.c 460s : warning: "_FORTIFY_SOURCE" redefined 460s : 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 cram/pooled_alloc.pico cram/pooled_alloc.c 460s : warning: "_FORTIFY_SOURCE" redefined 460s : 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 cram/string_alloc.pico cram/string_alloc.c 460s : warning: "_FORTIFY_SOURCE" redefined 460s : 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 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c 460s : warning: "_FORTIFY_SOURCE" redefined 460s : note: this is the location of the previous definition 460s 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 460s ln -sf libhts.so libhts.so.3 460s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c 460s : warning: "_FORTIFY_SOURCE" redefined 460s : note: this is the location of the previous definition 460s 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 460s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c 460s : warning: "_FORTIFY_SOURCE" redefined 460s : note: this is the location of the previous definition 461s 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 461s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c 461s : warning: "_FORTIFY_SOURCE" redefined 461s : note: this is the location of the previous definition 461s 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 461s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 461s : warning: "_FORTIFY_SOURCE" redefined 461s : note: this is the location of the previous definition 462s 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 462s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 462s : warning: "_FORTIFY_SOURCE" redefined 462s : note: this is the location of the previous definition 462s 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 462s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c 462s : warning: "_FORTIFY_SOURCE" redefined 462s : note: this is the location of the previous definition 463s 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 463s 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 463s : warning: "_FORTIFY_SOURCE" redefined 463s : note: this is the location of the previous definition 463s 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 463s 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 463s : warning: "_FORTIFY_SOURCE" redefined 463s : note: this is the location of the previous definition 464s 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 464s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c 464s : warning: "_FORTIFY_SOURCE" redefined 464s : note: this is the location of the previous definition 464s 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 464s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c 464s : warning: "_FORTIFY_SOURCE" redefined 464s : note: this is the location of the previous definition 464s 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 464s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c 464s : warning: "_FORTIFY_SOURCE" redefined 464s : note: this is the location of the previous definition 464s 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 464s 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 464s : warning: "_FORTIFY_SOURCE" redefined 464s : note: this is the location of the previous definition 464s 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 464s 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 464s : warning: "_FORTIFY_SOURCE" redefined 464s : note: this is the location of the previous definition 464s 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 464s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c 464s : warning: "_FORTIFY_SOURCE" redefined 464s : note: this is the location of the previous definition 465s 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 466s 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 466s : warning: "_FORTIFY_SOURCE" redefined 466s : note: this is the location of the previous definition 466s 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 466s 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 466s : warning: "_FORTIFY_SOURCE" redefined 466s : note: this is the location of the previous definition 466s 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 466s 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 466s : warning: "_FORTIFY_SOURCE" redefined 466s : note: this is the location of the previous definition 466s 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 466s 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 466s : warning: "_FORTIFY_SOURCE" redefined 466s : note: this is the location of the previous definition 467s 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 467s 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 467s : warning: "_FORTIFY_SOURCE" redefined 467s : note: this is the location of the previous definition 467s 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 467s 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 467s : warning: "_FORTIFY_SOURCE" redefined 467s : note: this is the location of the previous definition 467s 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 467s 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 467s : warning: "_FORTIFY_SOURCE" redefined 467s : note: this is the location of the previous definition 467s 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 467s 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 467s : warning: "_FORTIFY_SOURCE" redefined 467s : note: this is the location of the previous definition 467s 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 467s 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 467s : warning: "_FORTIFY_SOURCE" redefined 467s : note: this is the location of the previous definition 468s 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 468s 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 468s : warning: "_FORTIFY_SOURCE" redefined 468s : note: this is the location of the previous definition 468s 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 468s 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 468s : warning: "_FORTIFY_SOURCE" redefined 468s : note: this is the location of the previous definition 468s 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 468s 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 468s : warning: "_FORTIFY_SOURCE" redefined 468s : note: this is the location of the previous definition 468s 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 468s 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 468s : warning: "_FORTIFY_SOURCE" redefined 468s : note: this is the location of the previous definition 469s 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 469s 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 469s : warning: "_FORTIFY_SOURCE" redefined 469s : note: this is the location of the previous definition 469s 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 469s 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 469s : warning: "_FORTIFY_SOURCE" redefined 469s : note: this is the location of the previous definition 469s 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 469s 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 469s : warning: "_FORTIFY_SOURCE" redefined 469s : 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 -c -o test/test-bcf-translate.o test/test-bcf-translate.c 469s : warning: "_FORTIFY_SOURCE" redefined 469s : note: this is the location of the previous definition 469s 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 469s 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 469s : warning: "_FORTIFY_SOURCE" redefined 469s : note: this is the location of the previous definition 469s 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 469s 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 469s : warning: "_FORTIFY_SOURCE" redefined 469s : note: this is the location of the previous definition 469s 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 469s 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 469s : warning: "_FORTIFY_SOURCE" redefined 469s : note: this is the location of the previous definition 474s 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 474s sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 474s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 474s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 474s test/hts_endian 474s test/test_expr 474s test/test_kfunc 474s test/test_kstring 474s test/test_str2int 474s test/test_time_funcs 475s test/fieldarith test/fieldarith.sam 475s test/hfile 475s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 475s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 475s fi 475s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 475s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 475s fi 475s test/test_bgzf test/bgziptest.txt 476s test/test-parse-reg -t test/colons.bam 476s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 476s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 476s Expected error: cd test/faidx && ./test-faidx.sh faidx.tst 476s Testing faidx... 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 476s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 476s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 476s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 476s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 476s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 476s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 476s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 476s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 476s [E::hts_parse_region] Mismatching braces in "{chr1" 476s Expected error: [E::hts_parse_region] Unexpected string "x" after region 476s Expected error: [E::hts_parse_region] Unexpected string "y" after region 476s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 476s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 476s 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 476s 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 476s 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 476s 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 476s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 476s 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 476s 476s Expected passes: 25 476s Unexpected passes: 0 476s Expected failures: 0 476s Unexpected failures: 0 476s cd test/sam_filter && ./filter.sh filter.tst 476s Testing sam_filter... 476s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 476s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 476s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 476s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 476s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 476s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 476s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 476s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 476s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 476s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 476s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 476s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 476s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 476s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 476s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 476s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 476s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 476s 476s Expected passes: 17 476s Unexpected passes: 0 476s Expected failures: 0 476s Unexpected failures: 0 476s cd test/tabix && ./test-tabix.sh tabix.tst 476s Testing tabix... 476s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 476s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 476s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 476s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 476s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 476s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 476s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 476s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 476s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 476s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 476s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 476s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 476s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 476s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 476s 476s Expected passes: 14 476s Unexpected passes: 0 476s Expected failures: 0 476s Unexpected failures: 0 476s cd test/mpileup && ./test-pileup.sh mpileup.tst 476s Testing (m)pileup... 476s PASS : $pileup mp_D.sam 476s PASS : $pileup -m mp_D.sam 476s PASS : $pileup mp_DI.sam 476s PASS : $pileup -m mp_DI.sam 476s PASS : $pileup mp_I.sam 476s PASS : $pileup -m mp_I.sam 476s PASS : $pileup mp_P.sam 476s PASS : $pileup -m mp_P.sam 476s PASS : $pileup mp_ID.sam 476s PASS : $pileup -m mp_ID.sam 476s PASS : $pileup mp_N.sam 476s PASS : $pileup -m mp_N.sam 476s PASS : $pileup mp_N2.sam 476s PASS : $pileup -m mp_N2.sam 476s PASS : $pileup c1#pad1.sam 476s PASS : $pileup -m c1#pad1.sam 476s PASS : $pileup c1#pad2.sam 476s PASS : $pileup -m c1#pad2.sam 476s PASS : $pileup c1#pad3.sam 476s PASS : $pileup -m c1#pad3.sam 476s PASS : $pileup -m small.bam 476s 476s Expected passes: 21 476s Unexpected passes: 0 476s Expected failures: 0 476s Unexpected failures: 0 476s cd test/fastq && ./test-fastq.sh 476s Testing fastq support 476s PASS : $tview minimal.fq 476s PASS : $tview minimal.fa 476s PASS : $tview multiline.fq 476s PASS : $tview multiline.fa 476s PASS : $tview -i fastq_aux longline.fq 476s PASS : $tview single.fq 476s PASS : $tview single.fa 476s PASS : $tview -i fastq_aux single.fq 476s PASS : $tview -i fastq_aux single.fa 476s PASS : $tview interleaved.fq 476s PASS : $tview interleaved.fa 476s PASS : $tview -i fastq_aux interleaved.fq 476s PASS : $tview -i fastq_aux interleaved.fa 476s PASS : $tview -i fastq_casava interleaved_casava.fq 476s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 476s PASS : $tview -i fastq_casava interleaved_casava.fa 476s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 476s PASS : $tview -i fastq_casava filter_casava.fq 476s PASS : $tview -i fastq_casava filter_casava.fa 476s PASS : $tview -i fastq_aux r1.fq 476s PASS : $tview -i fastq_aux r2.fq 476s PASS : $tview -i fastq_aux r1.fa 476s PASS : $tview -i fastq_aux r2.fa 476s PASS : $tview -i fastq_name2 name2.fq 476s PASS : $tview -i fastq_name2 name2.fa 476s PASS : $tview -f minimal.sam 476s PASS : $tview -F minimal.sam 476s PASS : $tview -f -o fastq_aux single_aux.sam 476s PASS : $tview -F -o fastq_aux single_aux.sam 477s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 477s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 477s PASS : $tview -f -o fastq_casava inter_casava.sam 477s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 477s PASS : $tview -F -o fastq_casava inter_casava.sam 477s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 477s PASS : $tview -f -o fastq_casava filter_casava.sam 477s PASS : $tview -F -o fastq_casava filter_casava.sam 477s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 477s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 477s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 477s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 477s 477s Expected passes: 41 477s Unexpected passes: 0 477s Expected failures: 0 477s Unexpected failures: 0 477s cd test/base_mods && ./base-mods.sh base-mods.tst 477s Testing base-modifications... 477s PASS : $test_mod MM-chebi.sam 477s PASS : $test_mod MM-double.sam 477s PASS : $test_mod MM-multi.sam 477s PASS : $test_mod MM-explicit.sam 477s PASS : $test_mod -x MM-explicit.sam 477s PASS : $test_mod -f 1 MM-explicit.sam 477s PASS : $test_mod MM-not-all-modded.sam 477s PASS : $pileup_mod < MM-pileup.sam 477s PASS : $pileup_mod < MM-pileup2.sam 477s PASS : $pileup_mod < MM-MNp.sam 477s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 477s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 477s 477s Expected passes: 12 477s Unexpected passes: 0 477s Expected failures: 0 477s Unexpected failures: 0 477s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 477s (Expect trailing 'x' message for " -1,001x") 477s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 477s (Expect trailing 'k' message for "1.5e+3k") 477s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 477s (Expect dropped fraction message for "12.3456k") 477s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 477s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 477s (Expect invalid numeric message for "A") 477s [W::hts_parse_decimal] Invalid numeric value A[truncated] 477s (Expect invalid numeric message for "G") 477s [W::hts_parse_decimal] Invalid numeric value G[truncated] 477s (Expect invalid numeric message for " +/-") 477s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 477s (Expect invalid numeric message for " -.e+9999") 477s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 477s test/test-regidx 477s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 477s bgzip round-trip no threads: .. ok 477s 477s bgzip text mode round-trip no threads: .. ok 477s 477s bgzip -b no threads: .. ok 477s 477s bgzip -b -I no threads: .. ok 477s 477s bgzip round-trip 4 threads: .. ok 477s 478s bgzip text mode round-trip 4 threads: .. ok 478s 478s bgzip -b 4 threads: .. ok 478s 478s bgzip -b -I 4 threads: .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/VpwdgTVjiM/index.bam.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.bam 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.bam 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/VpwdgTVjiM/index.bam.bai /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.bam 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -b /tmp/VpwdgTVjiM/index.bam 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/VpwdgTVjiM/index.sam.gz.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/VpwdgTVjiM/index.sam.gz.bai /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -b /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/VpwdgTVjiM/index.sam.gz.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index_dos.sam > /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/VpwdgTVjiM/index.sam.gz.bai /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index_dos.sam > /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -b /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/VpwdgTVjiM/index.cram.crai /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.cram 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index /tmp/VpwdgTVjiM/index.cram 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/VpwdgTVjiM/index.bcf.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.vcf > /tmp/VpwdgTVjiM/index.bcf 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.bcf 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/VpwdgTVjiM/index.vcf.gz.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.vcf > /tmp/VpwdgTVjiM/index.vcf.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.vcf.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/VpwdgTVjiM/index.vcf.gz.tbi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.vcf > /tmp/VpwdgTVjiM/index.vcf.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -t /tmp/VpwdgTVjiM/index.vcf.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/tabix /tmp/VpwdgTVjiM/index.vcf.gz##idx##/tmp/VpwdgTVjiM/index.vcf.gz.tbi 1:10000060-10000060 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/VpwdgTVjiM/index2.bam 1:1000000-1000000 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/VpwdgTVjiM/index2.bam 1:2000000-2000000 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/VpwdgTVjiM/index2.bam 2:1000000-1000000 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/VpwdgTVjiM/index2.bam 2:2000000-2000000 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/VpwdgTVjiM/index.bam.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.bam 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.bam 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/VpwdgTVjiM/index.bam.bai /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.bam 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -b /tmp/VpwdgTVjiM/index.bam 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/VpwdgTVjiM/index.sam.gz.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/VpwdgTVjiM/index.sam.gz.bai /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -b /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/VpwdgTVjiM/index.sam.gz.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index_dos.sam > /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/VpwdgTVjiM/index.sam.gz.bai /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index_dos.sam > /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -b /tmp/VpwdgTVjiM/index.sam.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/VpwdgTVjiM/index.cram.crai /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.sam > /tmp/VpwdgTVjiM/index.cram 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index /tmp/VpwdgTVjiM/index.cram 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/VpwdgTVjiM/index.bcf.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.vcf > /tmp/VpwdgTVjiM/index.bcf 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.bcf 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/VpwdgTVjiM/index.vcf.gz.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.vcf > /tmp/VpwdgTVjiM/index.vcf.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c /tmp/VpwdgTVjiM/index.vcf.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/VpwdgTVjiM/index.vcf.gz.tbi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/index.vcf > /tmp/VpwdgTVjiM/index.vcf.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -t /tmp/VpwdgTVjiM/index.vcf.gz 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/tabix /tmp/VpwdgTVjiM/index.vcf.gz##idx##/tmp/VpwdgTVjiM/index.vcf.gz.tbi 1:10000060-10000060 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/VpwdgTVjiM/index2.bam 1:1000000-1000000 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/VpwdgTVjiM/index2.bam 1:2000000-2000000 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/VpwdgTVjiM/index2.bam 2:1000000-1000000 478s .. ok 478s 478s test_index: 478s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/VpwdgTVjiM/index2.bam 2:2000000-2000000 478s .. ok 478s 478s test_view testing multi-ref CRAM modes: 478s ./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 478s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 478s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 478s ./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 478s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 478s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 478s ./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 478s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 478s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 478s .. ok 478s 478s test_view testing multi-ref CRAM modes: 478s ./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 478s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 478s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 478s ./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 479s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 479s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 479s ./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 479s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 479s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 479s .. ok 479s 479s test_view testing auxf#values.sam, ref auxf.fa: 479s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 479s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 479s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 479s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 479s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 479s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 479s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 479s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 479s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 479s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 479s .. ok 479s 479s test_view testing c1#bounds.sam, ref c1.fa: 479s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 479s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 479s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 479s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 479s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 479s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 479s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 479s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 479s .. ok 479s 479s test_view testing c1#clip.sam, ref c1.fa: 479s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 479s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 479s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 479s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 479s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 479s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 479s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 479s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 479s .. ok 479s 479s test_view testing c1#noseq.sam, ref c1.fa: 479s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 479s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 479s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 479s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 479s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 479s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 479s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 479s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 479s .. ok 479s 479s test_view testing c1#pad1.sam, ref c1.fa: 479s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 479s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 479s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 479s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 479s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 479s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 479s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 479s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 479s .. ok 479s 479s test_view testing c1#pad2.sam, ref c1.fa: 479s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 479s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 479s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 479s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 479s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 479s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 479s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 479s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 479s .. ok 479s 479s test_view testing c1#pad3.sam, ref c1.fa: 479s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 479s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 479s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 479s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 479s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 479s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 479s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 479s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 479s .. ok 479s 479s test_view testing c1#unknown.sam, ref c1.fa: 479s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 479s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 479s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 479s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 479s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 479s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 479s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 479s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 479s .. ok 479s 479s test_view testing c2#pad.sam, ref c2.fa: 479s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 479s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 479s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 479s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 479s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 479s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 479s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 479s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 479s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 479s .. ok 479s 479s test_view testing ce#1.sam, ref ce.fa: 479s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 479s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 480s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 480s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 480s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 480s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 480s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 480s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 480s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 480s .. ok 480s 480s test_view testing ce#1000.sam, ref ce.fa: 480s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 480s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 480s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 480s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 480s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 480s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 480s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 480s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 480s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 480s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 480s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 480s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 480s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 480s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 480s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 480s .. ok 480s 480s test_view testing ce#2.sam, ref ce.fa: 480s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 480s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 480s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 480s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 480s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 480s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 480s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 480s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 480s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 480s .. ok 480s 480s test_view testing ce#5.sam, ref ce.fa: 480s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 480s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 480s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 480s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 480s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 480s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 480s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 480s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 480s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 480s .. ok 480s 480s test_view testing ce#5b.sam, ref ce.fa: 480s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 480s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 480s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 480s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 480s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 480s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 480s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 480s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 480s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 480s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 480s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 480s .. ok 480s 480s test_view testing ce#large_seq.sam, ref ce.fa: 480s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 480s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 480s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 480s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 480s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 480s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 480s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 480s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 480s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing ce#supp.sam, ref ce.fa: 481s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 481s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 481s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 481s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 481s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 481s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 481s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 481s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing ce#tag_depadded.sam, ref ce.fa: 481s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 481s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 481s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 481s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 481s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 481s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 481s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 481s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing ce#tag_padded.sam, ref ce.fa: 481s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 481s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 481s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 481s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 481s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 481s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 481s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 481s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing ce#unmap.sam, ref ce.fa: 481s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 481s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 481s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 481s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 481s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 481s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 481s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 481s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing ce#unmap1.sam, ref ce.fa: 481s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 481s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 481s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 481s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 481s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 481s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 481s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 481s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing ce#unmap2.sam, ref ce.fa: 481s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 481s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 481s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 481s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 481s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 481s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 481s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 481s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing md#1.sam, ref md.fa: 481s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 481s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 481s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 481s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 481s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 481s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 481s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 481s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing xx#blank.sam, ref xx.fa: 481s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 481s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 481s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 481s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 481s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 481s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 481s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 481s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing xx#large_aux.sam, ref xx.fa: 481s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 481s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 481s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 481s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 481s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 481s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 481s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 481s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 481s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 481s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 481s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 481s .. ok 481s 481s test_view testing xx#large_aux2.sam, ref xx.fa: 481s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 481s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 481s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 481s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 481s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 481s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 481s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 481s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 481s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 481s .. ok 481s 481s test_view testing xx#MD.sam, ref xx.fa: 481s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 481s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 481s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 481s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 481s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 481s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 482s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#MD2.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 482s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 482s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 482s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 482s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#minimal.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 482s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 482s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 482s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 482s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#pair.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 482s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 482s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 482s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 482s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#repeated.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 482s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 482s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 482s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 482s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#rg.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 482s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 482s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 482s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 482s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#tlen.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 482s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 482s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 482s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 482s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#tlen2.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 482s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 482s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 482s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 482s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#triplet.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 482s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 482s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 482s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 482s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing xx#unsorted.sam, ref xx.fa: 482s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 482s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 482s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 482s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 482s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 482s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 482s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 482s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 482s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 482s .. ok 482s 482s test_view testing embed_ref=2: 482s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 482s [W::cram_get_ref] Failed to populate reference for id 0 482s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 482s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 482s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 482s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 482s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 482s .. ok 482s 482s test_view testing region queries: 482s ./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 482s ./compare_sam.pl range.tmp range.out 482s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 482s ./compare_sam.pl range.tmp range.out 482s .. ok 482s 482s test_view testing BAM files with absent @SQ lines: 482s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 482s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 482s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 482s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 482s .. ok 482s 482s test_view testing large (> 2Gbases) positions: 482s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 482s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 482s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 482s test_view: 482s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 482s .. ok 482s 482s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 482s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 482s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 482s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 482s .. ok 482s 482s test_view testing auxf#values.sam, ref auxf.fa: 482s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 483s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 483s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 483s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 483s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 483s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 483s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 483s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 483s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 483s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 483s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 483s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 483s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 483s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 483s This is a technology demonstration that should not be used for archival data. 483s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 483s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 483s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 483s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 483s .. ok 483s 483s test_view testing c1#bounds.sam, ref c1.fa: 483s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 483s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 483s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 483s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 483s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 483s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 483s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 483s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 483s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 483s .. ok 483s 483s test_view testing c1#clip.sam, ref c1.fa: 483s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 483s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 483s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 483s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 483s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 483s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 483s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 483s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 483s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 483s .. ok 483s 483s test_view testing c1#noseq.sam, ref c1.fa: 483s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 483s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 483s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 483s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 483s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 483s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 483s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 483s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 483s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 483s .. ok 483s 483s test_view testing c1#pad1.sam, ref c1.fa: 483s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 483s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 483s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 483s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 483s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 483s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 483s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 483s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 483s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 483s .. ok 483s 483s test_view testing c1#pad2.sam, ref c1.fa: 483s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 483s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 483s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 483s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 483s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 483s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 483s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 483s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 483s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 483s .. ok 483s 483s test_view testing c1#pad3.sam, ref c1.fa: 483s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 483s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 483s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 483s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 483s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 483s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 483s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 483s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 483s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 483s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 484s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 484s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 484s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 484s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 484s This is a technology demonstration that should not be used for archival data. 484s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 484s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 484s .. ok 484s 484s test_view testing c1#unknown.sam, ref c1.fa: 484s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 484s ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 484s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 484s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 484s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 484s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 484s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 484s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 484s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 484s .. ok 484s 484s test_view testing c2#pad.sam, ref c2.fa: 484s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 484s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 484s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 484s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 484s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 484s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 484s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 484s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 484s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 484s .. ok 484s 484s test_view testing ce#1.sam, ref ce.fa: 484s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 484s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 484s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 484s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 484s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 484s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 484s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 484s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 484s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 484s .. ok 484s 484s test_view testing ce#1000.sam, ref ce.fa: 484s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 484s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 484s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 484s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 484s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 484s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 484s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 484s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 484s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 484s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 484s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 484s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 484s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 484s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 484s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 484s ./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 484s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 484s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 484s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 485s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 485s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 485s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 485s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 485s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 485s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 485s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 485s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 485s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 485s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 485s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 485s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 485s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 485s This is a technology demonstration that should not be used for archival data. 485s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 485s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 485s .. ok 485s 485s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 485s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 485s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 485s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 485s ./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 485s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 485s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 485s ./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 485s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 485s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 485s .. ok 485s 485s test_view testing ce#2.sam, ref ce.fa: 485s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 485s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 485s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 485s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 486s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 486s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 486s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 486s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 486s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 486s .. ok 486s 486s test_view testing ce#5.sam, ref ce.fa: 486s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 486s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 486s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 486s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 486s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 486s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 486s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 486s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 486s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 486s ./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 486s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 486s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 486s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 486s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 486s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 486s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 486s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 486s This is a technology demonstration that should not be used for archival data. 486s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 486s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 486s .. ok 486s 486s test_view testing ce#5b.sam, ref ce.fa: 486s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 486s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 486s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 486s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 486s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 486s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 486s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 486s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 486s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 486s ./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 486s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 486s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 486s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 486s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 486s .. ok 486s 486s test_view testing ce#large_seq.sam, ref ce.fa: 486s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 486s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 486s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 486s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 486s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 486s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 487s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 487s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 487s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 487s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 487s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 487s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 487s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 487s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 487s This is a technology demonstration that should not be used for archival data. 487s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 487s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 487s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 487s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 487s This is a technology demonstration that should not be used for archival data. 488s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 488s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 488s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 488s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 488s This is a technology demonstration that should not be used for archival data. 488s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 488s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 488s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 488s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 488s This is a technology demonstration that should not be used for archival data. 488s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 488s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 488s .. ok 488s 488s test_view testing ce#supp.sam, ref ce.fa: 488s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 488s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 488s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 488s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 488s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 488s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 489s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 489s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 489s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 489s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 489s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 489s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 489s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 489s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 489s This is a technology demonstration that should not be used for archival data. 489s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 489s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 489s .. ok 489s 489s test_view testing ce#tag_depadded.sam, ref ce.fa: 489s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 489s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 489s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 489s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 489s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 489s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 489s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 489s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 489s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 489s .. ok 489s 489s test_view testing ce#tag_padded.sam, ref ce.fa: 489s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 489s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 489s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 489s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 489s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 489s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 489s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 489s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 489s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 489s .. ok 489s 489s test_view testing ce#unmap.sam, ref ce.fa: 489s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 489s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 489s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 489s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 489s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 489s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 489s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 489s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 489s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 489s ./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 489s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 489s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 489s .. ok 489s 489s test_view testing ce#unmap1.sam, ref ce.fa: 489s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 489s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 489s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 489s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 489s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 489s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 489s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 489s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 489s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 489s ./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 489s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 489s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 489s .. ok 489s 489s test_view testing ce#unmap2.sam, ref ce.fa: 489s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 489s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 489s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 489s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 489s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 489s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 489s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 489s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 489s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 489s ./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 489s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 489s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 489s .. ok 489s 489s test_view testing md#1.sam, ref md.fa: 489s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 489s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 489s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 489s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 489s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 489s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 489s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 489s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 490s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 490s .. ok 490s 490s test_view testing xx#blank.sam, ref xx.fa: 490s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 490s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 490s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 490s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 490s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 490s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 490s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 490s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 490s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 490s ./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 490s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 490s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 490s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 490s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 490s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 490s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 490s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 490s This is a technology demonstration that should not be used for archival data. 490s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 490s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 490s .. ok 490s 490s test_view testing xx#large_aux.sam, ref xx.fa: 490s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 490s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 490s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 490s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 490s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 490s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 490s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 490s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 490s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 490s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 490s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 490s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 490s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 490s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 490s This is a technology demonstration that should not be used for archival data. 490s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 490s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 490s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 490s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 490s This is a technology demonstration that should not be used for archival data. 491s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 491s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 491s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 491s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 491s This is a technology demonstration that should not be used for archival data. 491s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 491s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 491s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 491s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 491s This is a technology demonstration that should not be used for archival data. 491s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 491s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 491s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 491s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 491s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 491s .. ok 491s 491s test_view testing xx#large_aux2.sam, ref xx.fa: 491s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 491s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 491s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 491s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 491s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 491s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 491s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 491s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 491s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 491s .. ok 491s 491s test_view testing xx#MD.sam, ref xx.fa: 491s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 491s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 491s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 491s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 491s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 491s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 491s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 491s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 491s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 491s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 491s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 491s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 491s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 491s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 491s This is a technology demonstration that should not be used for archival data. 491s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 491s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 491s .. ok 491s 491s test_view testing xx#MD2.sam, ref xx.fa: 491s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 491s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 492s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 492s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 492s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 492s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 492s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 492s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 492s .. ok 492s 492s test_view testing xx#minimal.sam, ref xx.fa: 492s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 492s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 492s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 492s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 492s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 492s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 492s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 492s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 492s ./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 492s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 492s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 492s .. ok 492s 492s test_view testing xx#pair.sam, ref xx.fa: 492s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 492s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 492s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 492s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 492s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 492s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 492s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 492s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 492s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 492s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 492s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 492s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 492s This is a technology demonstration that should not be used for archival data. 492s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 492s .. ok 492s 492s test_view testing xx#repeated.sam, ref xx.fa: 492s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 492s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 492s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 492s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 492s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 492s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 492s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 492s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 492s .. ok 492s 492s test_view testing xx#rg.sam, ref xx.fa: 492s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 492s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 492s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 492s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 492s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 492s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 492s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 492s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 492s .. ok 492s 492s test_view testing xx#tlen.sam, ref xx.fa: 492s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 492s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 492s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 492s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 492s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 492s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 492s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 492s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 492s ./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 492s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 492s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 492s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 492s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 492s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 492s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 492s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 492s This is a technology demonstration that should not be used for archival data. 493s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 493s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 493s .. ok 493s 493s test_view testing xx#tlen2.sam, ref xx.fa: 493s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 493s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 493s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 493s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 493s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 493s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 493s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 493s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 493s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 493s ./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 493s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 493s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 493s .. ok 493s 493s test_view testing xx#triplet.sam, ref xx.fa: 493s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 493s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 493s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 493s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 493s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 493s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 493s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 493s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 493s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 493s ./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 493s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 493s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 493s .. ok 493s 493s test_view testing xx#unsorted.sam, ref xx.fa: 493s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 493s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 493s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 493s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 493s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 493s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 493s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 493s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 493s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 493s .. ok 493s 493s test_view testing embed_ref=2: 493s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 493s [W::cram_get_ref] Failed to populate reference for id 0 493s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 493s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 493s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 493s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 493s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 493s .. ok 493s 493s test_view testing region queries: 493s ./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 493s ./compare_sam.pl range.tmp range.out 493s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 493s ./compare_sam.pl range.tmp range.out 493s .. ok 493s 493s test_view testing BAM files with absent @SQ lines: 493s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 493s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 493s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 493s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 493s .. ok 493s 493s test_view testing large (> 2Gbases) positions: 493s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 493s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 493s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 493s test_view: 493s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 493s .. ok 493s 493s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 493s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 493s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 493s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 493s .. ok 493s 493s 493s test_MD testing xx#MD.sam, ref xx.fa: 493s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 493s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 493s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 493s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 493s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 493s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 493s Checking for MD/NM in xx#MD.sam 493s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 493s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 493s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 493s .. ok 493s 493s 493s test_MD testing xx#MD2.sam, ref xx.fa: 493s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 493s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 493s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 493s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 493s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 493s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 493s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 493s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 493s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 493s .. ok 493s 493s test_vcf_api: 493s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-vcf-api /tmp/VpwdgTVjiM/test-vcf-api.bcf 493s [W::bcf_record_check] Bad BCF record at 1:1: No REF allele 493s [E::bcf_index_build3] TBI indices for BCF files are not supported 493s [E::idx_find_and_load] Could not retrieve index file for '/tmp/VpwdgTVjiM/test-vcf-api.bcf' 493s .. ok 493s 493s test_bcf2vcf: 493s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/tabix/vcf_file.bcf 493s .. ok 493s 493s test_vcf_sweep: 493s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-vcf-sweep /tmp/VpwdgTVjiM/test-vcf-api.bcf 494s .. ok 494s 494s test_vcf_various: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 494s .. ok 494s 494s test_vcf_various: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/formatcols.vcf 494s .. ok 494s 494s test_vcf_various: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/noroundtrip.vcf 494s .. ok 494s 494s test_vcf_various: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/formatmissing.vcf 494s .. ok 494s 494s test_vcf_various: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/vcf_meta_meta.vcf 494s .. ok 494s 494s test_vcf_various: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 494s .. ok 494s 494s test-bcf-sr: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 74452500 494s .. ok 494s 494s test-bcf-sr: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 34270147 494s .. ok 494s 494s test-bcf-sr: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 11108528 494s .. ok 494s 494s test-bcf-sr: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 42233895 494s .. ok 494s 494s test-bcf-sr: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 8111117 494s .. ok 494s 494s test-bcf-sr: 494s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 85644070 495s .. ok 495s 495s test-bcf-sr: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 49879942 495s .. ok 495s 495s test-bcf-sr: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 47881429 495s .. ok 495s 495s test-bcf-sr: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 69081244 495s .. ok 495s 495s test-bcf-sr: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/VpwdgTVjiM -s 83459376 495s .. ok 495s 495s test_bcf_sr_no_index: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/VpwdgTVjiM/no_index_1.err 495s .. ok 495s 495s test_bcf_sr_no_index: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/VpwdgTVjiM/no_index_2.out 2> /tmp/VpwdgTVjiM/no_index_2.err (expected fail) 495s .. ok 495s 495s test_bcf_sr_no_index: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/VpwdgTVjiM/no_index_3.out 2> /tmp/VpwdgTVjiM/no_index_3.err (expected fail) 495s .. ok 495s 495s test_bcf_sr_no_index: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/VpwdgTVjiM/no_index_4.out 2> /tmp/VpwdgTVjiM/no_index_4.err (expected fail) 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -b -p /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf -x /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_1.out.vcf -r '1' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_2.out.vcf -r '1:1-2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_4.out.vcf -r '1:1-1' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_5.out.vcf -r '{1:1}' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf (expected fail) 495s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 495s Failed to set regions 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_14.out.vcf -t '1' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_15.out.vcf -t '1:1-2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_17.out.vcf -t '1:1-1' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_18.out.vcf -t '{1:1}' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 495s Failed to set targets 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf 495s .. ok 495s 495s test_bcf_sr_range: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/VpwdgTVjiM/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/VpwdgTVjiM/weird-chr-names.vcf.bcf (expected fail) 495s .. ok 495s 495s test_command: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf-translate - 495s .. ok 495s 495s test_convert_padded_header: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/VpwdgTVjiM/headernul0.bam 495s .. ok 495s 495s test_convert_padded_header: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/VpwdgTVjiM/headernul1.bam 495s .. ok 495s 495s test_convert_padded_header: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/VpwdgTVjiM/headernul678.bam 495s .. ok 495s 495s test_rebgzip: Alternate zlib/deflate library detected 495s test_rebgzip: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/bgziptest.txt 495s .. ok 495s 495s test-logging: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-logging.pl 495s .. ok 495s 495s test_plugin_loading: 495s HTS_PATH=/tmp/autopkgtest.VEmnT6/autopkgtest_tmp /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn01.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn01.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn01.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02-r.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02_exp.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn02_exp-a.sam -o - 495s .. ok 495s 495s test_realn: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/realn03.sam -o - 495s .. ok 495s 495s test-bcf_set_variant_type: 495s /tmp/autopkgtest.VEmnT6/autopkgtest_tmp/test/test-bcf_set_variant_type 495s .. ok 495s 495s 495s Number of tests: 495s total .. 211 495s passed .. 211 495s failed .. 0 495s 495s + echo PASS 495s PASS 495s autopkgtest [06:38:54]: test run-unit-test: -----------------------] 496s autopkgtest [06:38:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 496s run-unit-test PASS 496s autopkgtest [06:38:55]: @@@@@@@@@@@@@@@@@@@@ summary 496s run-unit-test PASS 509s Creating nova instance adt-noble-ppc64el-htslib-20240324-063039-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...