0s autopkgtest [15:56:48]: starting date and time: 2024-03-24 15:56:48+0000 0s autopkgtest [15:56:48]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:56:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ee2bhut5/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:sra-sdk,src:curl,src:file,src:hdf5,src:libpsl,src:openssl,src:orthanc-python --apt-upgrade seqsero --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=sra-sdk/3.0.3+dfsg-6ubuntu4 curl/8.5.0-2ubuntu7 file/1:5.45-3 hdf5/1.10.10+repack-3.1ubuntu3 libpsl/0.21.2-1.1 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@bos01-arm64-45.secgroup --name adt-noble-arm64-seqsero-20240324-154338-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 102s autopkgtest [15:58:30]: testbed dpkg architecture: arm64 102s autopkgtest [15:58:30]: testbed apt version: 2.7.12 102s autopkgtest [15:58:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 104s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 104s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [538 kB] 104s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 105s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 105s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [736 kB] 105s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 105s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 105s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 105s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4365 kB] 107s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 107s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 107s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 112s Fetched 9919 kB in 3s (3505 kB/s) 112s Reading package lists... 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 119s Calculating upgrade... 119s The following packages will be REMOVED: 119s libmagic1 libssl3 119s The following NEW packages will be installed: 119s libmagic1t64 libssl3t64 119s The following packages have been kept back: 119s curl 119s The following packages will be upgraded: 119s file libmagic-mgc openssl 119s 3 upgraded, 2 newly installed, 2 to remove and 1 not upgraded. 119s Need to get 3192 kB of archives. 119s After this operation, 145 kB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 file arm64 1:5.45-3 [22.0 kB] 119s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmagic-mgc arm64 1:5.45-3 [307 kB] 119s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmagic1t64 arm64 1:5.45-3 [85.7 kB] 119s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 119s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 119s Fetched 3192 kB in 1s (4092 kB/s) 119s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75911 files and directories currently installed.) 119s Preparing to unpack .../file_1%3a5.45-3_arm64.deb ... 119s Unpacking file (1:5.45-3) over (1:5.45-2) ... 119s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75911 files and directories currently installed.) 119s Removing libmagic1:arm64 (1:5.45-2) ... 120s (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 ... 75901 files and directories currently installed.) 120s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_arm64.deb ... 120s Unpacking libmagic-mgc (1:5.45-3) over (1:5.45-2) ... 120s Selecting previously unselected package libmagic1t64:arm64. 120s Preparing to unpack .../libmagic1t64_1%3a5.45-3_arm64.deb ... 120s Unpacking libmagic1t64:arm64 (1:5.45-3) ... 120s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 120s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 120s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 120s wget depends on libssl3 (>= 3.0.0). 120s u-boot-tools depends on libssl3 (>= 3.0.0). 120s tnftp depends on libssl3 (>= 3.0.0). 120s tcpdump depends on libssl3 (>= 3.0.0). 120s systemd-resolved depends on libssl3 (>= 3.0.0). 120s systemd depends on libssl3 (>= 3.0.0). 120s sudo depends on libssl3 (>= 3.0.0). 120s sbsigntool depends on libssl3 (>= 3.0.0). 120s rsync depends on libssl3 (>= 3.0.0). 120s python3-cryptography depends on libssl3 (>= 3.0.0). 120s openssh-server depends on libssl3 (>= 3.0.10). 120s openssh-client depends on libssl3 (>= 3.0.10). 120s mtd-utils depends on libssl3 (>= 3.0.0). 120s mokutil depends on libssl3 (>= 3.0.0). 120s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 120s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 120s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 120s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 120s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 120s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 120s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 120s libnvme1 depends on libssl3 (>= 3.0.0). 120s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 120s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 120s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 120s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 120s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 120s kmod depends on libssl3 (>= 3.0.0). 120s dhcpcd-base depends on libssl3 (>= 3.0.0). 120s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 120s 120s (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 ... 75912 files and directories currently installed.) 120s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 120s Selecting previously unselected package libssl3t64:arm64. 120s (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 ... 75901 files and directories currently installed.) 120s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 120s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 120s Setting up libmagic-mgc (1:5.45-3) ... 120s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 120s Setting up libmagic1t64:arm64 (1:5.45-3) ... 120s Setting up file (1:5.45-3) ... 120s Setting up openssl (3.0.13-0ubuntu2) ... 120s Processing triggers for man-db (2.12.0-3) ... 121s Processing triggers for libc-bin (2.39-0ubuntu6) ... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 125s sh: Attempting to set up Debian/Ubuntu apt sources automatically 125s sh: Distribution appears to be Ubuntu 127s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s eatmydata is already the newest version (131-1). 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s dbus is already the newest version (1.14.10-4ubuntu1). 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 133s rng-tools-debian is already the newest version (2.4). 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s The following packages will be REMOVED: 134s cloud-init* python3-configobj* python3-debconf* 135s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 135s After this operation, 3256 kB disk space will be freed. 135s (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 ... 75914 files and directories currently installed.) 135s Removing cloud-init (24.1.2-0ubuntu1) ... 139s Removing python3-configobj (5.0.8-3) ... 139s Removing python3-debconf (1.5.86) ... 139s Processing triggers for man-db (2.12.0-3) ... 139s (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 ... 75525 files and directories currently installed.) 139s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 139s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 139s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 139s invoke-rc.d: policy-rc.d denied execution of try-restart. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 141s linux-generic is already the newest version (6.8.0-11.11+1). 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 141s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 146s Reading package lists... 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 151s Calculating upgrade... 151s autopkgtest [15:59:19]: rebooting testbed after setup commands that affected boot 151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 309s autopkgtest [16:01:57]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 312s autopkgtest [16:02:00]: @@@@@@@@@@@@@@@@@@@@ apt-source seqsero 314s Get:1 http://ftpmaster.internal/ubuntu noble/universe seqsero 1.0.1+dfsg-6 (dsc) [2024 B] 314s Get:2 http://ftpmaster.internal/ubuntu noble/universe seqsero 1.0.1+dfsg-6 (tar) [356 kB] 314s Get:3 http://ftpmaster.internal/ubuntu noble/universe seqsero 1.0.1+dfsg-6 (diff) [43.1 kB] 314s gpgv: Signature made Thu Sep 29 13:38:36 2022 UTC 314s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 314s gpgv: issuer "tille@debian.org" 314s gpgv: Can't check signature: No public key 314s dpkg-source: warning: cannot verify inline signature for ./seqsero_1.0.1+dfsg-6.dsc: no acceptable signature found 315s autopkgtest [16:02:03]: testing package seqsero version 1.0.1+dfsg-6 315s autopkgtest [16:02:03]: build not needed 316s autopkgtest [16:02:04]: test run-unit-test: preparing testbed 319s Reading package lists... 320s Building dependency tree... 320s Reading state information... 320s Starting pkgProblemResolver with broken count: 0 321s Starting 2 pkgProblemResolver with broken count: 0 321s Done 322s The following additional packages will be installed: 322s bwa fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 322s fonts-urw-base35 libaec0 libblas3 libcairo2 libdeflate0 libfontconfig1 322s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1 322s libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 322s liblapack3 liblcms2-2 liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 322s libncbi-vdb3 libncbi-wvdb3 libopenjp2-7 libpixman-1-0 libraqm0 libre2-10 322s libsharpyuv0 libsz2 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 322s libxcb-render0 libxcb-shm0 libxrender1 ncbi-vdb-data python3-biopython 322s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 322s python3-rlpycairo samtools seqsero sgml-base sra-toolkit w3c-sgml-lib 322s x11-common xfonts-encodings xfonts-utils xml-core 322s Suggested packages: 322s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 322s python3-tk clustalo clustalw dialign dssp emboss fasttree mafft muscle3 322s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 322s python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee wise gcc 322s gfortran python3-dev python3-pytest python-pil-doc pdf-viewer 322s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm cwltool 322s ispcr sgml-base-doc debhelper 322s Recommended packages: 322s python-biopython-doc ncbi-blast+ python3-olefile med-config 322s The following NEW packages will be installed: 322s autopkgtest-satdep bwa fontconfig-config fonts-dejavu-core 322s fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 libaec0 libblas3 322s libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 322s libgraphite2-3 libharfbuzz0b libhdf5-103-1 libhts3 libhtscodecs2 322s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 322s liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncbi-vdb3 322s libncbi-wvdb3 libopenjp2-7 libpixman-1-0 libraqm0 libre2-10 libsharpyuv0 322s libsz2 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 322s libxcb-shm0 libxrender1 ncbi-vdb-data python3-biopython python3-cairo 322s python3-freetype python3-numpy python3-pil python3-reportlab 322s python3-rlpycairo samtools seqsero sgml-base sra-toolkit w3c-sgml-lib 322s x11-common xfonts-encodings xfonts-utils xml-core 322s 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. 322s Need to get 41.3 MB/41.3 MB of archives. 322s After this operation, 134 MB of additional disk space will be used. 322s Get:1 /tmp/autopkgtest.8VgKT3/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 322s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 322s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 bwa arm64 0.7.17-7 [192 kB] 322s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 323s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 323s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 323s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 323s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 323s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 323s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 323s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 323s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 323s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 323s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 323s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 323s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 323s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 324s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 324s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 324s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 324s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 324s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 324s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 324s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 324s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 324s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 324s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 324s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 324s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 324s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 324s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 324s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 324s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 324s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 324s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 324s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 324s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 324s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 324s Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [65.8 kB] 324s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [1130 kB] 324s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-wvdb3 arm64 3.0.2+dfsg-2 [1153 kB] 324s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 324s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libre2-10 arm64 20230301-3 [159 kB] 324s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 324s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 324s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 324s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 324s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 324s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 324s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 324s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 324s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 324s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 324s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 324s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 324s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 324s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 324s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 324s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 324s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 324s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 sra-toolkit arm64 3.0.3+dfsg-6ubuntu1 [6998 kB] 325s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 seqsero arm64 1.0.1+dfsg-6 [369 kB] 325s Fetched 41.3 MB in 3s (15.5 MB/s) 326s Selecting previously unselected package sgml-base. 326s (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 ... 75470 files and directories currently installed.) 326s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 326s Unpacking sgml-base (1.31) ... 326s Selecting previously unselected package bwa. 326s Preparing to unpack .../01-bwa_0.7.17-7_arm64.deb ... 326s Unpacking bwa (0.7.17-7) ... 326s Selecting previously unselected package fonts-dejavu-mono. 326s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 326s Unpacking fonts-dejavu-mono (2.37-8) ... 326s Selecting previously unselected package fonts-dejavu-core. 326s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 326s Unpacking fonts-dejavu-core (2.37-8) ... 326s Selecting previously unselected package libfontenc1:arm64. 326s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1_arm64.deb ... 326s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 326s Selecting previously unselected package x11-common. 326s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu2_all.deb ... 326s Unpacking x11-common (1:7.7+23ubuntu2) ... 326s Selecting previously unselected package xfonts-encodings. 326s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 326s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 326s Selecting previously unselected package xfonts-utils. 326s Preparing to unpack .../07-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 326s Unpacking xfonts-utils (1:7.7+6build2) ... 326s Selecting previously unselected package fonts-urw-base35. 326s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 326s Unpacking fonts-urw-base35 (20200910-8) ... 327s Selecting previously unselected package fontconfig-config. 327s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 327s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 327s Selecting previously unselected package fonts-dejavu-extra. 327s Preparing to unpack .../10-fonts-dejavu-extra_2.37-8_all.deb ... 327s Unpacking fonts-dejavu-extra (2.37-8) ... 327s Selecting previously unselected package libaec0:arm64. 327s Preparing to unpack .../11-libaec0_1.1.2-1_arm64.deb ... 327s Unpacking libaec0:arm64 (1.1.2-1) ... 327s Selecting previously unselected package libblas3:arm64. 327s Preparing to unpack .../12-libblas3_3.12.0-3_arm64.deb ... 327s Unpacking libblas3:arm64 (3.12.0-3) ... 327s Selecting previously unselected package libfontconfig1:arm64. 327s Preparing to unpack .../13-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 327s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 327s Selecting previously unselected package libpixman-1-0:arm64. 327s Preparing to unpack .../14-libpixman-1-0_0.42.2-1_arm64.deb ... 327s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 327s Selecting previously unselected package libxcb-render0:arm64. 327s Preparing to unpack .../15-libxcb-render0_1.15-1_arm64.deb ... 327s Unpacking libxcb-render0:arm64 (1.15-1) ... 327s Selecting previously unselected package libxcb-shm0:arm64. 327s Preparing to unpack .../16-libxcb-shm0_1.15-1_arm64.deb ... 327s Unpacking libxcb-shm0:arm64 (1.15-1) ... 327s Selecting previously unselected package libxrender1:arm64. 327s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 327s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 327s Selecting previously unselected package libcairo2:arm64. 327s Preparing to unpack .../18-libcairo2_1.18.0-1_arm64.deb ... 327s Unpacking libcairo2:arm64 (1.18.0-1) ... 328s Selecting previously unselected package libdeflate0:arm64. 328s Preparing to unpack .../19-libdeflate0_1.19-1_arm64.deb ... 328s Unpacking libdeflate0:arm64 (1.19-1) ... 328s Selecting previously unselected package libgfortran5:arm64. 328s Preparing to unpack .../20-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 328s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 328s Selecting previously unselected package libgomp1:arm64. 328s Preparing to unpack .../21-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 328s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 328s Selecting previously unselected package libgraphite2-3:arm64. 328s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_arm64.deb ... 328s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 328s Selecting previously unselected package libharfbuzz0b:arm64. 328s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_arm64.deb ... 328s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 328s Selecting previously unselected package libsz2:arm64. 328s Preparing to unpack .../24-libsz2_1.1.2-1_arm64.deb ... 328s Unpacking libsz2:arm64 (1.1.2-1) ... 328s Selecting previously unselected package libhdf5-103-1:arm64. 328s Preparing to unpack .../25-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 328s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 328s Selecting previously unselected package libhtscodecs2:arm64. 328s Preparing to unpack .../26-libhtscodecs2_1.6.0-1_arm64.deb ... 328s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 328s Selecting previously unselected package libhts3:arm64. 328s Preparing to unpack .../27-libhts3_1.18+ds-1_arm64.deb ... 328s Unpacking libhts3:arm64 (1.18+ds-1) ... 328s Selecting previously unselected package libimagequant0:arm64. 328s Preparing to unpack .../28-libimagequant0_2.18.0-1_arm64.deb ... 328s Unpacking libimagequant0:arm64 (2.18.0-1) ... 328s Selecting previously unselected package libjpeg-turbo8:arm64. 328s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 328s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 328s Selecting previously unselected package libjpeg8:arm64. 328s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_arm64.deb ... 328s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 328s Selecting previously unselected package liblapack3:arm64. 328s Preparing to unpack .../31-liblapack3_3.12.0-3_arm64.deb ... 328s Unpacking liblapack3:arm64 (3.12.0-3) ... 328s Selecting previously unselected package liblcms2-2:arm64. 328s Preparing to unpack .../32-liblcms2-2_2.14-2_arm64.deb ... 328s Unpacking liblcms2-2:arm64 (2.14-2) ... 328s Selecting previously unselected package liblerc4:arm64. 328s Preparing to unpack .../33-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 328s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 328s Selecting previously unselected package libmbedcrypto7:arm64. 328s Preparing to unpack .../34-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 328s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 329s Selecting previously unselected package libmbedx509-1:arm64. 329s Preparing to unpack .../35-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 329s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 329s Selecting previously unselected package libmbedtls14:arm64. 329s Preparing to unpack .../36-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 329s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 329s Selecting previously unselected package ncbi-vdb-data. 329s Preparing to unpack .../37-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ... 329s Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ... 329s Selecting previously unselected package libncbi-vdb3:arm64. 329s Preparing to unpack .../38-libncbi-vdb3_3.0.2+dfsg-2_arm64.deb ... 329s Unpacking libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 329s Selecting previously unselected package libncbi-wvdb3:arm64. 329s Preparing to unpack .../39-libncbi-wvdb3_3.0.2+dfsg-2_arm64.deb ... 329s Unpacking libncbi-wvdb3:arm64 (3.0.2+dfsg-2) ... 329s Selecting previously unselected package libraqm0:arm64. 329s Preparing to unpack .../40-libraqm0_0.10.1-1_arm64.deb ... 329s Unpacking libraqm0:arm64 (0.10.1-1) ... 329s Selecting previously unselected package libre2-10:arm64. 329s Preparing to unpack .../41-libre2-10_20230301-3_arm64.deb ... 329s Unpacking libre2-10:arm64 (20230301-3) ... 329s Selecting previously unselected package libsharpyuv0:arm64. 329s Preparing to unpack .../42-libsharpyuv0_1.3.2-0.4_arm64.deb ... 329s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 329s Selecting previously unselected package libjbig0:arm64. 329s Preparing to unpack .../43-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 329s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 329s Selecting previously unselected package libwebp7:arm64. 329s Preparing to unpack .../44-libwebp7_1.3.2-0.4_arm64.deb ... 329s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 329s Selecting previously unselected package libtiff6:arm64. 329s Preparing to unpack .../45-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 329s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 329s Selecting previously unselected package libwebpdemux2:arm64. 329s Preparing to unpack .../46-libwebpdemux2_1.3.2-0.4_arm64.deb ... 329s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 329s Selecting previously unselected package libwebpmux3:arm64. 329s Preparing to unpack .../47-libwebpmux3_1.3.2-0.4_arm64.deb ... 329s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 329s Selecting previously unselected package python3-numpy. 329s Preparing to unpack .../48-python3-numpy_1%3a1.24.2-2_arm64.deb ... 329s Unpacking python3-numpy (1:1.24.2-2) ... 330s Selecting previously unselected package libopenjp2-7:arm64. 330s Preparing to unpack .../49-libopenjp2-7_2.5.0-2_arm64.deb ... 330s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 330s Selecting previously unselected package python3-pil:arm64. 330s Preparing to unpack .../50-python3-pil_10.2.0-1_arm64.deb ... 330s Unpacking python3-pil:arm64 (10.2.0-1) ... 330s Selecting previously unselected package python3-cairo. 330s Preparing to unpack .../51-python3-cairo_1.25.1-2_arm64.deb ... 330s Unpacking python3-cairo (1.25.1-2) ... 330s Selecting previously unselected package python3-freetype. 330s Preparing to unpack .../52-python3-freetype_2.4.0-1_all.deb ... 330s Unpacking python3-freetype (2.4.0-1) ... 330s Selecting previously unselected package python3-rlpycairo. 330s Preparing to unpack .../53-python3-rlpycairo_0.3.0-3_all.deb ... 330s Unpacking python3-rlpycairo (0.3.0-3) ... 330s Selecting previously unselected package python3-reportlab. 330s Preparing to unpack .../54-python3-reportlab_4.1.0-1_all.deb ... 330s Unpacking python3-reportlab (4.1.0-1) ... 330s Selecting previously unselected package xml-core. 330s Preparing to unpack .../55-xml-core_0.19_all.deb ... 330s Unpacking xml-core (0.19) ... 330s Selecting previously unselected package w3c-sgml-lib. 330s Preparing to unpack .../56-w3c-sgml-lib_1.3-3_all.deb ... 330s Unpacking w3c-sgml-lib (1.3-3) ... 330s Selecting previously unselected package python3-biopython. 331s Preparing to unpack .../57-python3-biopython_1.81+dfsg-3_arm64.deb ... 331s Unpacking python3-biopython (1.81+dfsg-3) ... 331s Selecting previously unselected package samtools. 331s Preparing to unpack .../58-samtools_1.19.2-1_arm64.deb ... 331s Unpacking samtools (1.19.2-1) ... 331s Selecting previously unselected package sra-toolkit. 331s Preparing to unpack .../59-sra-toolkit_3.0.3+dfsg-6ubuntu1_arm64.deb ... 331s Unpacking sra-toolkit (3.0.3+dfsg-6ubuntu1) ... 331s Selecting previously unselected package seqsero. 331s Preparing to unpack .../60-seqsero_1.0.1+dfsg-6_arm64.deb ... 331s Unpacking seqsero (1.0.1+dfsg-6) ... 331s Selecting previously unselected package autopkgtest-satdep. 331s Preparing to unpack .../61-1-autopkgtest-satdep.deb ... 331s Unpacking autopkgtest-satdep (0) ... 332s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 332s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 332s Setting up liblcms2-2:arm64 (2.14-2) ... 332s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 332s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 332s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 332s Setting up libre2-10:arm64 (20230301-3) ... 332s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 332s Setting up libxcb-render0:arm64 (1.15-1) ... 332s Setting up bwa (0.7.17-7) ... 332s Setting up x11-common (1:7.7+23ubuntu2) ... 332s Setting up libdeflate0:arm64 (1.19-1) ... 332s Setting up libxcb-shm0:arm64 (1.15-1) ... 332s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 332s Setting up python3-freetype (2.4.0-1) ... 333s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 333s Setting up libaec0:arm64 (1.1.2-1) ... 333s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 333s Setting up libblas3:arm64 (3.12.0-3) ... 333s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 333s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 333s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 333s Setting up libimagequant0:arm64 (2.18.0-1) ... 333s Setting up fonts-dejavu-mono (2.37-8) ... 333s Setting up fonts-dejavu-core (2.37-8) ... 333s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 333s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 333s Setting up libwebp7:arm64 (1.3.2-0.4) ... 333s Setting up fonts-dejavu-extra (2.37-8) ... 333s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 333s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 333s Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... 333s Setting up sgml-base (1.31) ... 333s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 333s Setting up libsz2:arm64 (1.1.2-1) ... 333s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 333s Setting up liblapack3:arm64 (3.12.0-3) ... 333s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 333s Setting up libhts3:arm64 (1.18+ds-1) ... 333s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 333s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 333s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 333s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 333s Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 333s Setting up xfonts-utils (1:7.7+6build2) ... 333s Setting up samtools (1.19.2-1) ... 333s Setting up libraqm0:arm64 (0.10.1-1) ... 333s Setting up libncbi-wvdb3:arm64 (3.0.2+dfsg-2) ... 333s Setting up python3-numpy (1:1.24.2-2) ... 337s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 337s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 337s Setting up xml-core (0.19) ... 338s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 338s Setting up sra-toolkit (3.0.3+dfsg-6ubuntu1) ... 338s Setting up fonts-urw-base35 (20200910-8) ... 338s Setting up libcairo2:arm64 (1.18.0-1) ... 338s Setting up python3-pil:arm64 (10.2.0-1) ... 339s Setting up python3-cairo (1.25.1-2) ... 339s Setting up python3-rlpycairo (0.3.0-3) ... 340s Setting up python3-reportlab (4.1.0-1) ... 342s Processing triggers for libc-bin (2.39-0ubuntu6) ... 342s Processing triggers for man-db (2.12.0-3) ... 342s Processing triggers for sgml-base (1.31) ... 342s Setting up w3c-sgml-lib (1.3-3) ... 409s Setting up python3-biopython (1.81+dfsg-3) ... 411s Setting up seqsero (1.0.1+dfsg-6) ... 412s Setting up autopkgtest-satdep (0) ... 425s (Reading database ... 79128 files and directories currently installed.) 425s Removing autopkgtest-satdep (0) ... 425s autopkgtest [16:03:53]: test run-unit-test: [----------------------- 426s Test for checking functionality 427s gzip: sra_data.fastq: unknown suffix -- ignored 427s [bwa_index] Pack FASTA... 0.00 sec 427s [bwa_index] Construct BWT for the packed sequence... 427s [bwa_index] 0.02 seconds elapse. 427s [bwa_index] Update BWT... 0.00 sec 427s [bwa_index] Pack forward-only FASTA... 0.00 sec 427s [bwa_index] Construct SA from BWT and Occ... 0.01 sec 427s [main] Version: 0.7.17-r1188 427s [main] CMD: bwa index database/special_new_O_genes.fasta 427s [main] Real time: 0.038 sec; CPU: 0.028 sec 427s [bwa_aln] 17bp reads: max_diff = 2 427s [bwa_aln] 38bp reads: max_diff = 3 427s [bwa_aln] 64bp reads: max_diff = 4 427s [bwa_aln] 93bp reads: max_diff = 5 427s [bwa_aln] 124bp reads: max_diff = 6 427s [bwa_aln] 157bp reads: max_diff = 7 427s [bwa_aln] 190bp reads: max_diff = 8 427s [bwa_aln] 225bp reads: max_diff = 9 427s [main] Version: 0.7.17-r1188 427s [main] CMD: bwa aln database/special_new_O_genes.fasta sra_data.fastq 427s [main] Real time: 0.002 sec; CPU: 0.002 sec 427s [main] Version: 0.7.17-r1188 427s [main] CMD: bwa samse database/special_new_O_genes.fasta sra_data_1.sai sra_data.fastq 427s [main] Real time: 0.002 sec; CPU: 0.002 sec 427s [bwa_index] Pack FASTA... 0.01 sec 427s [bwa_index] Construct BWT for the packed sequence... 428s [bwa_index] 0.33 seconds elapse. 428s [bwa_index] Update BWT... 0.01 sec 428s [bwa_index] Pack forward-only FASTA... 0.01 sec 428s [bwa_index] Construct SA from BWT and Occ... 0.11 sec 428s [main] Version: 0.7.17-r1188 428s [main] CMD: bwa index database/H_combine_update_9_03_2014_new.fasta 428s [main] Real time: 0.489 sec; CPU: 0.474 sec 428s [bwa_aln] 17bp reads: max_diff = 2 428s [bwa_aln] 38bp reads: max_diff = 3 428s [bwa_aln] 64bp reads: max_diff = 4 428s [bwa_aln] 93bp reads: max_diff = 5 428s [bwa_aln] 124bp reads: max_diff = 6 428s [bwa_aln] 157bp reads: max_diff = 7 428s [bwa_aln] 190bp reads: max_diff = 8 428s [bwa_aln] 225bp reads: max_diff = 9 428s [main] Version: 0.7.17-r1188 428s [main] CMD: bwa aln database/H_combine_update_9_03_2014_new.fasta sra_data.fastq 428s [main] Real time: 0.003 sec; CPU: 0.003 sec 428s [main] Version: 0.7.17-r1188 428s [main] CMD: bwa samse database/H_combine_update_9_03_2014_new.fasta sra_data_1.sai sra_data.fastq 428s [main] Real time: 0.003 sec; CPU: 0.003 sec 428s 428s 428s 428s Input files: sra_data.fastq 428s O antigen prediction: O-- 428s H1 antigen prediction(fliC): - 428s H2 antigen prediction(fljB): - 428s Predicted antigenic profile: -:-:- 428s Predicted serotype(s): N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme) 428s 428s 428s 428s 428s Result: 428s 428s Input files: sra_data.fastq 428s O antigen prediction: O-- 428s H1 antigen prediction(fliC): - 428s H2 antigen prediction(fljB): - 428s Predicted antigenic profile: -:-:- 428s Predicted serotype(s): N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme) 428s 428s PASS 428s autopkgtest [16:03:56]: test run-unit-test: -----------------------] 429s autopkgtest [16:03:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 429s run-unit-test PASS 429s autopkgtest [16:03:57]: @@@@@@@@@@@@@@@@@@@@ summary 429s run-unit-test PASS 447s Creating nova instance adt-noble-arm64-seqsero-20240324-154338-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...