0s autopkgtest [09:25:19]: starting date and time: 2024-03-23 09:25:19+0000 0s autopkgtest [09:25:19]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [09:25:19]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l_jecvye/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade berkeley-express --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-24.secgroup --name adt-noble-s390x-berkeley-express-20240323-092519-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 90s autopkgtest [09:26:49]: testbed dpkg architecture: s390x 90s autopkgtest [09:26:49]: testbed apt version: 2.7.12 90s autopkgtest [09:26:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 91s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 91s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 91s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 91s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3972 kB] 92s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 92s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [651 kB] 92s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 92s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 92s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 92s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4148 kB] 92s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 92s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.8 kB] 92s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 94s Fetched 9504 kB in 3s (3633 kB/s) 94s Reading package lists... 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Calculating upgrade... 97s The following packages will be REMOVED: 97s libssl3 97s The following NEW packages will be installed: 97s libssl3t64 97s The following packages have been kept back: 97s curl 97s The following packages will be upgraded: 97s libbsd0 libc-bin libc6 locales openssl 97s 5 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 97s Need to get 10.5 MB of archives. 97s After this operation, 241 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.39-0ubuntu6 [2847 kB] 98s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.39-0ubuntu6 [654 kB] 98s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 98s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 98s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libbsd0 s390x 0.12.1-1 [46.7 kB] 98s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x locales all 2.39-0ubuntu6 [4232 kB] 99s Preconfiguring packages ... 99s Fetched 10.5 MB in 1s (10.1 MB/s) 99s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 99s Preparing to unpack .../libc6_2.39-0ubuntu6_s390x.deb ... 99s Unpacking libc6:s390x (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 99s Setting up libc6:s390x (2.39-0ubuntu6) ... 100s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 100s Preparing to unpack .../libc-bin_2.39-0ubuntu6_s390x.deb ... 100s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 100s Setting up libc-bin (2.39-0ubuntu6) ... 100s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 100s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 100s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 100s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 100s wget depends on libssl3 (>= 3.0.0). 100s tnftp depends on libssl3 (>= 3.0.0). 100s tcpdump depends on libssl3 (>= 3.0.0). 100s systemd-resolved depends on libssl3 (>= 3.0.0). 100s systemd depends on libssl3 (>= 3.0.0). 100s sudo depends on libssl3 (>= 3.0.0). 100s s390-tools depends on libssl3 (>= 3.0.0). 100s rsync depends on libssl3 (>= 3.0.0). 100s python3-cryptography depends on libssl3 (>= 3.0.0). 100s openssh-server depends on libssl3 (>= 3.0.10). 100s openssh-client depends on libssl3 (>= 3.0.10). 100s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 100s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 100s libssh-4:s390x depends on libssl3 (>= 3.0.0). 100s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 100s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 100s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 100s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 100s libnvme1 depends on libssl3 (>= 3.0.0). 100s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 100s libkmod2:s390x depends on libssl3 (>= 3.0.0). 100s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 100s libcurl4:s390x depends on libssl3 (>= 3.0.0). 100s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 100s kmod depends on libssl3 (>= 3.0.0). 100s dhcpcd-base depends on libssl3 (>= 3.0.0). 100s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 100s 100s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 100s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 100s Selecting previously unselected package libssl3t64:s390x. 100s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52159 files and directories currently installed.) 100s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 100s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 100s Preparing to unpack .../libbsd0_0.12.1-1_s390x.deb ... 100s Unpacking libbsd0:s390x (0.12.1-1) over (0.11.8-1) ... 100s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 100s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 100s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 100s Setting up locales (2.39-0ubuntu6) ... 100s Generating locales (this might take a while)... 102s en_US.UTF-8... done 102s Generation complete. 102s Setting up openssl (3.0.13-0ubuntu2) ... 102s Setting up libbsd0:s390x (0.12.1-1) ... 102s Processing triggers for man-db (2.12.0-3) ... 103s Processing triggers for libc-bin (2.39-0ubuntu6) ... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 104s Unknown architecture, assuming PC-style ttyS0 104s sh: Attempting to set up Debian/Ubuntu apt sources automatically 104s sh: Distribution appears to be Ubuntu 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s eatmydata is already the newest version (131-1). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s dbus is already the newest version (1.14.10-4ubuntu1). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s rng-tools-debian is already the newest version (2.4). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s The following packages will be REMOVED: 106s cloud-init* python3-configobj* python3-debconf* 106s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 106s After this operation, 3256 kB disk space will be freed. 106s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52172 files and directories currently installed.) 106s Removing cloud-init (24.1.2-0ubuntu1) ... 106s Removing python3-configobj (5.0.8-3) ... 106s Removing python3-debconf (1.5.86) ... 107s Processing triggers for man-db (2.12.0-3) ... 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51783 files and directories currently installed.) 107s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 107s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 107s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 107s invoke-rc.d: policy-rc.d denied execution of try-restart. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s linux-generic is already the newest version (6.8.0-11.11+1). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 108s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 108s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 110s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s autopkgtest [09:27:10]: rebooting testbed after setup commands that affected boot 129s autopkgtest [09:27:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 131s autopkgtest [09:27:30]: @@@@@@@@@@@@@@@@@@@@ apt-source berkeley-express 133s Get:1 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (dsc) [2571 B] 133s Get:2 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (tar) [366 kB] 133s Get:3 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (diff) [10.9 kB] 133s gpgv: Signature made Tue Dec 19 15:00:44 2023 UTC 133s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 133s gpgv: Can't check signature: No public key 133s dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3build3.dsc: no acceptable signature found 134s autopkgtest [09:27:33]: testing package berkeley-express version 1.5.3+dfsg-3build3 134s autopkgtest [09:27:33]: build not needed 134s autopkgtest [09:27:33]: test run-tests: preparing testbed 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s Starting pkgProblemResolver with broken count: 0 143s Starting 2 pkgProblemResolver with broken count: 0 143s Done 143s The following additional packages will be installed: 143s berkeley-express berkeley-express-doc bowtie libbamtools2.5.2 143s libboost-filesystem1.83.0 libboost-program-options1.83.0 143s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 143s samtools 143s Suggested packages: 143s bowtie-examples cwltool 143s Recommended packages: 143s med-config 143s The following NEW packages will be installed: 143s autopkgtest-satdep berkeley-express berkeley-express-doc bowtie 143s libbamtools2.5.2 libboost-filesystem1.83.0 libboost-program-options1.83.0 143s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 143s samtools 143s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 6076 kB/6076 kB of archives. 143s After this operation, 23.5 MB of additional disk space will be used. 143s Get:1 /tmp/autopkgtest.biJZiS/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [740 B] 143s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-4 [134 kB] 144s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libboost-filesystem1.83.0 s390x 1.83.0-2ubuntu1 [372 kB] 144s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2ubuntu1 [418 kB] 145s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libboost-thread1.83.0 s390x 1.83.0-2ubuntu1 [362 kB] 146s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libprotobuf32 s390x 3.21.12-8ubuntu5 [954 kB] 147s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x berkeley-express s390x 1.5.3+dfsg-3build3 [232 kB] 147s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x berkeley-express-doc all 1.5.3+dfsg-3build3 [724 kB] 148s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 148s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 148s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 148s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x samtools s390x 1.19.2-1 [613 kB] 149s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x bowtie s390x 1.3.1-3 [1671 kB] 151s Fetched 6076 kB in 7s (812 kB/s) 151s Selecting previously unselected package libbamtools2.5.2:s390x. 151s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51728 files and directories currently installed.) 151s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_s390x.deb ... 151s Unpacking libbamtools2.5.2:s390x (2.5.2+dfsg-4) ... 151s Selecting previously unselected package libboost-filesystem1.83.0:s390x. 151s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_s390x.deb ... 151s Unpacking libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 151s Selecting previously unselected package libboost-program-options1.83.0:s390x. 151s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_s390x.deb ... 151s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 151s Selecting previously unselected package libboost-thread1.83.0:s390x. 151s Preparing to unpack .../03-libboost-thread1.83.0_1.83.0-2ubuntu1_s390x.deb ... 151s Unpacking libboost-thread1.83.0:s390x (1.83.0-2ubuntu1) ... 151s Selecting previously unselected package libprotobuf32:s390x. 151s Preparing to unpack .../04-libprotobuf32_3.21.12-8ubuntu5_s390x.deb ... 151s Unpacking libprotobuf32:s390x (3.21.12-8ubuntu5) ... 151s Selecting previously unselected package berkeley-express. 151s Preparing to unpack .../05-berkeley-express_1.5.3+dfsg-3build3_s390x.deb ... 151s Unpacking berkeley-express (1.5.3+dfsg-3build3) ... 151s Selecting previously unselected package berkeley-express-doc. 151s Preparing to unpack .../06-berkeley-express-doc_1.5.3+dfsg-3build3_all.deb ... 151s Unpacking berkeley-express-doc (1.5.3+dfsg-3build3) ... 151s Selecting previously unselected package libdeflate0:s390x. 151s Preparing to unpack .../07-libdeflate0_1.19-1_s390x.deb ... 151s Unpacking libdeflate0:s390x (1.19-1) ... 151s Selecting previously unselected package libhtscodecs2:s390x. 151s Preparing to unpack .../08-libhtscodecs2_1.6.0-1_s390x.deb ... 151s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 151s Selecting previously unselected package libhts3:s390x. 151s Preparing to unpack .../09-libhts3_1.18+ds-1_s390x.deb ... 151s Unpacking libhts3:s390x (1.18+ds-1) ... 151s Selecting previously unselected package samtools. 151s Preparing to unpack .../10-samtools_1.19.2-1_s390x.deb ... 151s Unpacking samtools (1.19.2-1) ... 151s Selecting previously unselected package bowtie. 151s Preparing to unpack .../11-bowtie_1.3.1-3_s390x.deb ... 151s Unpacking bowtie (1.3.1-3) ... 151s Selecting previously unselected package autopkgtest-satdep. 151s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 151s Unpacking autopkgtest-satdep (0) ... 151s Setting up libhtscodecs2:s390x (1.6.0-1) ... 151s Setting up libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 151s Setting up bowtie (1.3.1-3) ... 151s Setting up berkeley-express-doc (1.5.3+dfsg-3build3) ... 151s Setting up libdeflate0:s390x (1.19-1) ... 151s Setting up libboost-thread1.83.0:s390x (1.83.0-2ubuntu1) ... 151s Setting up libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 151s Setting up libbamtools2.5.2:s390x (2.5.2+dfsg-4) ... 151s Setting up libprotobuf32:s390x (3.21.12-8ubuntu5) ... 151s Setting up libhts3:s390x (1.18+ds-1) ... 151s Setting up samtools (1.19.2-1) ... 151s Setting up berkeley-express (1.5.3+dfsg-3build3) ... 151s Setting up autopkgtest-satdep (0) ... 151s Processing triggers for man-db (2.12.0-3) ... 152s Processing triggers for libc-bin (2.39-0ubuntu6) ... 154s (Reading database ... 51962 files and directories currently installed.) 154s Removing autopkgtest-satdep (0) ... 154s autopkgtest [09:27:53]: test run-tests: [----------------------- 155s + pkg=berkeley-express 155s + [ /tmp/autopkgtest.biJZiS/autopkgtest_tmp = ] 155s + cd /tmp/autopkgtest.biJZiS/autopkgtest_tmp 155s + cp /usr/share/doc/berkeley-express/sample_data/reads_1.fastq.gz /usr/share/doc/berkeley-express/sample_data/reads_2.fastq.gz /usr/share/doc/berkeley-express/sample_data/transcripts.fasta.gz . 155s + gunzip reads_1.fastq.gz reads_2.fastq.gz transcripts.fasta.gz 155s + bowtie-build --offrate 1 transcripts.fasta transcripts 155s Settings: 155s Output files: "transcripts.*.ebwt" 155s Line rate: 6 (line is 64 bytes) 155s Lines per side: 1 (side is 64 bytes) 155s Offset rate: 1 (one in 2) 155s FTable chars: 10 155s Strings: unpacked 155s Max bucket size: default 155s Max bucket size, sqrt multiplier: default 155s Max bucket size, len divisor: 4 155s Difference-cover sample period: 1024 155s Endianness: little 155s Actual local endianness: big 155s Sanity checking: disabled 155s Assertions: disabled 155s Random seed: 0 155s Sizeofs: void*:8, int:4, long:8, size_t:8 155s Input files DNA, FASTA: 155s transcripts.fasta 155s Reading reference sizes 155s Time reading reference sizes: 00:00:00 155s Calculating joined length 155s Writing header 155s Reserving space for joined string 155s Joining reference sequences 155s Time to join reference sequences: 00:00:00 155s bmax according to bmaxDivN setting: 7140 155s Using parameters --bmax 5355 --dcv 1024 155s Doing ahead-of-time memory usage test 155s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 155s Constructing suffix-array element generator 155s Building DifferenceCoverSample 155s Building sPrime 155s Building sPrimeOrder 155s V-Sorting samples 155s V-Sorting samples time: 00:00:00 155s Allocating rank array 155s Ranking v-sort output 155s Ranking v-sort output time: 00:00:00 155s Invoking Larsson-Sadakane on ranks 155s Invoking Larsson-Sadakane on ranks time: 00:00:00 155s Sanity-checking and returning 155s Building samples 155s Reserving space for 12 sample suffixes 155s Generating random suffixes 155s QSorting 12 sample offsets, eliminating duplicates 155s Multikey QSorting 12 samples 155s (Using difference cover) 155s Multikey QSorting samples time: 00:00:00 155s QSorting sample offsets, eliminating duplicates time: 00:00:00 155s Calculating bucket sizes 155s Splitting and merging 155s Splitting and merging time: 00:00:00 155s Split 2, merged 6; iterating... 155s Splitting and merging 155s Splitting and merging time: 00:00:00 155s Split 1, merged 2; iterating... 155s Splitting and merging 155s Splitting and merging time: 00:00:00 155s Avg bucket size: 3569.38 (target: 5354) 155s Converting suffix-array elements to index image 155s Allocating ftab, absorbFtab 155s Entering Ebwt loop 155s Getting block 1 of 8 155s Reserving size (5355) for bucket 1 155s Calculating Z arrays for bucket 1 155s Entering block accumulator loop for bucket 1: 155s bucket 1: 10% 155s bucket 1: 20% 155s bucket 1: 30% 155s bucket 1: 40% 155s bucket 1: 50% 155s bucket 1: 60% 155s bucket 1: 70% 155s bucket 1: 80% 155s bucket 1: 90% 155s bucket 1: 100% 155s Sorting block of length 3445 for bucket 1 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 3446 for bucket 1 155s Getting block 2 of 8 155s Reserving size (5355) for bucket 2 155s Calculating Z arrays for bucket 2 155s Entering block accumulator loop for bucket 2: 155s bucket 2: 10% 155s bucket 2: 20% 155s bucket 2: 30% 155s bucket 2: 40% 155s bucket 2: 50% 155s bucket 2: 60% 155s bucket 2: 70% 155s bucket 2: 80% 155s bucket 2: 90% 155s bucket 2: 100% 155s Sorting block of length 5081 for bucket 2 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 5082 for bucket 2 155s Getting block 3 of 8 155s Reserving size (5355) for bucket 3 155s Calculating Z arrays for bucket 3 155s Entering block accumulator loop for bucket 3: 155s bucket 3: 10% 155s bucket 3: 20% 155s bucket 3: 30% 155s bucket 3: 40% 155s bucket 3: 50% 155s bucket 3: 60% 155s bucket 3: 70% 155s bucket 3: 80% 155s bucket 3: 90% 155s bucket 3: 100% 155s Sorting block of length 2382 for bucket 3 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 2383 for bucket 3 155s Getting block 4 of 8 155s Reserving size (5355) for bucket 4 155s Calculating Z arrays for bucket 4 155s Entering block accumulator loop for bucket 4: 155s bucket 4: 10% 155s bucket 4: 20% 155s bucket 4: 30% 155s bucket 4: 40% 155s bucket 4: 50% 155s bucket 4: 60% 155s bucket 4: 70% 155s bucket 4: 80% 155s bucket 4: 90% 155s bucket 4: 100% 155s Sorting block of length 5217 for bucket 4 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 5218 for bucket 4 155s Getting block 5 of 8 155s Reserving size (5355) for bucket 5 155s Calculating Z arrays for bucket 5 155s Entering block accumulator loop for bucket 5: 155s bucket 5: 10% 155s bucket 5: 20% 155s bucket 5: 30% 155s bucket 5: 40% 155s bucket 5: 50% 155s bucket 5: 60% 155s bucket 5: 70% 155s bucket 5: 80% 155s bucket 5: 90% 155s bucket 5: 100% 155s Sorting block of length 3095 for bucket 5 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 3096 for bucket 5 155s Getting block 6 of 8 155s Reserving size (5355) for bucket 6 155s Calculating Z arrays for bucket 6 155s Entering block accumulator loop for bucket 6: 155s bucket 6: 10% 155s bucket 6: 20% 155s bucket 6: 30% 155s bucket 6: 40% 155s bucket 6: 50% 155s bucket 6: 60% 155s bucket 6: 70% 155s bucket 6: 80% 155s bucket 6: 90% 155s bucket 6: 100% 155s Sorting block of length 3727 for bucket 6 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 3728 for bucket 6 155s Getting block 7 of 8 155s Reserving size (5355) for bucket 7 155s Calculating Z arrays for bucket 7 155s Entering block accumulator loop for bucket 7: 155s bucket 7: 10% 155s bucket 7: 20% 155s bucket 7: 30% 155s bucket 7: 40% 155s bucket 7: 50% 155s bucket 7: 60% 155s bucket 7: 70% 155s bucket 7: 80% 155s bucket 7: 90% 155s bucket 7: 100% 155s Sorting block of length 5329 for bucket 7 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 5330 for bucket 7 155s Getting block 8 of 8 155s Reserving size (5355) for bucket 8 155s Calculating Z arrays for bucket 8 155s Entering block accumulator loop for bucket 8: 155s bucket 8: 10% 155s bucket 8: 20% 155s bucket 8: 30% 155s bucket 8: 40% 155s bucket 8: 50% 155s bucket 8: 60% 155s bucket 8: 70% 155s bucket 8: 80% 155s bucket 8: 90% 155s bucket 8: 100% 155s Sorting block of length 279 for bucket 8 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 280 for bucket 8 155s Exited Ebwt loop 155s fchr[A]: 0 155s fchr[C]: 7097 155s fchr[G]: 15029 155s fchr[T]: 22254 155s fchr[$]: 28562 155s Exiting Ebwt::buildToDisk() 155s Returning from initFromVector 155s Wrote 4203034 bytes to primary EBWT file: transcripts.1.ebwt 155s Wrote 57132 bytes to secondary EBWT file: transcripts.2.ebwt 155s Re-opening _in1 and _in2 as input streams 155s Returning from Ebwt constructor 155s Headers: 155s len: 28562 155s bwtLen: 28563 155s sz: 7141 155s bwtSz: 7141 155s lineRate: 6 155s linesPerSide: 1 155s offRate: 1 155s offMask: 0xfffffffe 155s isaRate: -1 155s isaMask: 0xffffffff 155s ftabChars: 10 155s eftabLen: 20 155s eftabSz: 80 155s ftabLen: 1048577 155s ftabSz: 4194308 155s offsLen: 14282 155s offsSz: 57128 155s isaLen: 0 155s isaSz: 0 155s lineSz: 64 155s sideSz: 64 155s sideBwtSz: 56 155s sideBwtLen: 224 155s numSidePairs: 64 155s numSides: 128 155s numLines: 128 155s ebwtTotLen: 8192 155s ebwtTotSz: 8192 155s reverse: 0 155s Total time for call to driver() for forward index: 00:00:00 155s Reading reference sizes 155s Time reading reference sizes: 00:00:00 155s Calculating joined length 155s Writing header 155s Reserving space for joined string 155s Joining reference sequences 155s Time to join reference sequences: 00:00:00 155s bmax according to bmaxDivN setting: 7140 155s Using parameters --bmax 5355 --dcv 1024 155s Doing ahead-of-time memory usage test 155s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 155s Constructing suffix-array element generator 155s Building DifferenceCoverSample 155s Building sPrime 155s Building sPrimeOrder 155s V-Sorting samples 155s V-Sorting samples time: 00:00:00 155s Allocating rank array 155s Ranking v-sort output 155s Ranking v-sort output time: 00:00:00 155s Invoking Larsson-Sadakane on ranks 155s Invoking Larsson-Sadakane on ranks time: 00:00:00 155s Sanity-checking and returning 155s Building samples 155s Reserving space for 12 sample suffixes 155s Generating random suffixes 155s QSorting 12 sample offsets, eliminating duplicates 155s Multikey QSorting 12 samples 155s (Using difference cover) 155s Multikey QSorting samples time: 00:00:00 155s QSorting sample offsets, eliminating duplicates time: 00:00:00 155s Calculating bucket sizes 155s Splitting and merging 155s Splitting and merging time: 00:00:00 155s Avg bucket size: 4079.43 (target: 5354) 155s Converting suffix-array elements to index image 155s Allocating ftab, absorbFtab 155s Entering Ebwt loop 155s Getting block 1 of 7 155s Reserving size (5355) for bucket 1 155s Calculating Z arrays for bucket 1 155s Entering block accumulator loop for bucket 1: 155s bucket 1: 10% 155s bucket 1: 20% 155s bucket 1: 30% 155s bucket 1: 40% 155s bucket 1: 50% 155s bucket 1: 60% 155s bucket 1: 70% 155s bucket 1: 80% 155s bucket 1: 90% 155s bucket 1: 100% 155s Sorting block of length 1796 for bucket 1 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 1797 for bucket 1 155s Getting block 2 of 7 155s Reserving size (5355) for bucket 2 155s Calculating Z arrays for bucket 2 155s Entering block accumulator loop for bucket 2: 155s bucket 2: 10% 155s bucket 2: 20% 155s bucket 2: 30% 155s bucket 2: 40% 155s bucket 2: 50% 155s bucket 2: 60% 155s bucket 2: 70% 155s bucket 2: 80% 155s bucket 2: 90% 155s bucket 2: 100% 155s Sorting block of length 4275 for bucket 2 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 4276 for bucket 2 155s Getting block 3 of 7 155s Reserving size (5355) for bucket 3 155s Calculating Z arrays for bucket 3 155s Entering block accumulator loop for bucket 3: 155s bucket 3: 10% 155s bucket 3: 20% 155s bucket 3: 30% 155s bucket 3: 40% 155s bucket 3: 50% 155s bucket 3: 60% 155s bucket 3: 70% 155s bucket 3: 80% 155s bucket 3: 90% 155s bucket 3: 100% 155s Sorting block of length 4010 for bucket 3 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 4011 for bucket 3 155s Getting block 4 of 7 155s Reserving size (5355) for bucket 4 155s Calculating Z arrays for bucket 4 155s Entering block accumulator loop for bucket 4: 155s bucket 4: 10% 155s bucket 4: 20% 155s bucket 4: 30% 155s bucket 4: 40% 155s bucket 4: 50% 155s bucket 4: 60% 155s bucket 4: 70% 155s bucket 4: 80% 155s bucket 4: 90% 155s bucket 4: 100% 155s Sorting block of length 3860 for bucket 4 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 3861 for bucket 4 155s Getting block 5 of 7 155s Reserving size (5355) for bucket 5 155s Calculating Z arrays for bucket 5 155s Entering block accumulator loop for bucket 5: 155s bucket 5: 10% 155s bucket 5: 20% 155s bucket 5: 30% 155s bucket 5: 40% 155s bucket 5: 50% 155s bucket 5: 60% 155s bucket 5: 70% 155s bucket 5: 80% 155s bucket 5: 90% 155s bucket 5: 100% 155s Sorting block of length 4188 for bucket 5 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 4189 for bucket 5 155s Getting block 6 of 7 155s Reserving size (5355) for bucket 6 155s Calculating Z arrays for bucket 6 155s Entering block accumulator loop for bucket 6: 155s bucket 6: 10% 155s bucket 6: 20% 155s bucket 6: 30% 155s bucket 6: 40% 155s bucket 6: 50% 155s bucket 6: 60% 155s bucket 6: 70% 155s bucket 6: 80% 155s bucket 6: 90% 155s bucket 6: 100% 155s Sorting block of length 5102 for bucket 6 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 5103 for bucket 6 155s Getting block 7 of 7 155s Reserving size (5355) for bucket 7 155s Calculating Z arrays for bucket 7 155s Entering block accumulator loop for bucket 7: 155s bucket 7: 10% 155s bucket 7: 20% 155s bucket 7: 30% 155s bucket 7: 40% 155s bucket 7: 50% 155s bucket 7: 60% 155s bucket 7: 70% 155s bucket 7: 80% 155s bucket 7: 90% 155s bucket 7: 100% 155s Sorting block of length 5325 for bucket 7 155s (Using difference cover) 155s Sorting block time: 00:00:00 155s Returning block of 5326 for bucket 7 155s Exited Ebwt loop 155s fchr[A]: 0 155s fchr[C]: 7097 155s fchr[G]: 15029 155s fchr[T]: 22254 155s fchr[$]: 28562 155s Exiting Ebwt::buildToDisk() 155s + bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq 155s + samtools view -Sb - 155s Returning from initFromVector 155s Wrote 4203034 bytes to primary EBWT file: transcripts.rev.1.ebwt 155s Wrote 57132 bytes to secondary EBWT file: transcripts.rev.2.ebwt 155s Re-opening _in1 and _in2 as input streams 155s Returning from Ebwt constructor 155s Headers: 155s len: 28562 155s bwtLen: 28563 155s sz: 7141 155s bwtSz: 7141 155s lineRate: 6 155s linesPerSide: 1 155s offRate: 1 155s offMask: 0xfffffffe 155s isaRate: -1 155s isaMask: 0xffffffff 155s ftabChars: 10 155s eftabLen: 20 155s eftabSz: 80 155s ftabLen: 1048577 155s ftabSz: 4194308 155s offsLen: 14282 155s offsSz: 57128 155s isaLen: 0 155s isaSz: 0 155s lineSz: 64 155s sideSz: 64 155s sideBwtSz: 56 155s sideBwtLen: 224 155s numSidePairs: 64 155s numSides: 128 155s numLines: 128 155s ebwtTotLen: 8192 155s ebwtTotSz: 8192 155s reverse: 0 155s Total time for backward call to driver() for mirror index: 00:00:00 155s Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. 156s # reads processed: 10000 156s # reads with at least one alignment: 10000 (100.00%) 156s # reads that failed to align: 0 (0.00%) 156s Reported 14270 paired-end alignments 156s + berkeley-express transcripts.fasta hits.bam 156s 2024-Mar-23 09:27:55 - Attempting to read 'hits.bam' in BAM format... 156s 2024-Mar-23 09:27:55 - Parsing BAM header... 156s 2024-Mar-23 09:27:55 - Loading target sequences and measuring bias background... 156s 2024-Mar-23 09:27:55 - Initialized 15 targets. 156s 2024-Mar-23 09:27:55 - Processing input fragment alignments... 157s 2024-Mar-23 09:27:55 - COMPLETED: Processed 10000 mapped fragments, targets are in 8 bundles. 157s 2024-Mar-23 09:27:55 - WARNING: Not enough fragments observed to accurately learn bias parameters. Either disable bias correction (--no-bias-correct) or provide a file containing auxiliary parameters (--aux-param-file). 157s 2024-Mar-23 09:27:55 - Writing results to file... 157s 2024-Mar-23 09:27:56 - Done. 157s autopkgtest [09:27:56]: test run-tests: -----------------------] 157s autopkgtest [09:27:56]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 157s run-tests PASS 158s autopkgtest [09:27:57]: @@@@@@@@@@@@@@@@@@@@ summary 158s run-tests PASS 171s Creating nova instance adt-noble-s390x-berkeley-express-20240323-092519-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240322.img (UUID c8671f9a-0e89-48e3-af4f-3c79b89294e8)...