0s autopkgtest [17:44:28]: starting date and time: 2024-03-24 17:44:28+0000 0s autopkgtest [17:44:28]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:44:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jvw573km/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 seqsero --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-2@bos03-arm64-1.secgroup --name adt-noble-arm64-seqsero-20240324-174428-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 94s autopkgtest [17:46:02]: testbed dpkg architecture: arm64 95s autopkgtest [17:46:03]: testbed apt version: 2.7.12 95s autopkgtest [17:46:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 95s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 95s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 96s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 96s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 96s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 96s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 96s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 96s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 96s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 96s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 96s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 96s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 97s Fetched 9851 kB in 2s (5812 kB/s) 98s Reading package lists... 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s Calculating upgrade... 101s The following packages will be REMOVED: 101s libssl3 101s The following NEW packages will be installed: 101s libssl3t64 101s The following packages have been kept back: 101s curl 101s The following packages will be upgraded: 101s openssl 101s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 101s Need to get 2777 kB of archives. 101s After this operation, 139 kB of additional disk space will be used. 101s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 102s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 102s Fetched 2777 kB in 1s (3982 kB/s) 102s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74819 files and directories currently installed.) 102s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 102s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 103s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 103s wget depends on libssl3 (>= 3.0.0). 103s u-boot-tools depends on libssl3 (>= 3.0.0). 103s tnftp depends on libssl3 (>= 3.0.0). 103s tcpdump depends on libssl3 (>= 3.0.0). 103s systemd-resolved depends on libssl3 (>= 3.0.0). 103s systemd depends on libssl3 (>= 3.0.0). 103s sudo depends on libssl3 (>= 3.0.0). 103s sbsigntool depends on libssl3 (>= 3.0.0). 103s rsync depends on libssl3 (>= 3.0.0). 103s python3-cryptography depends on libssl3 (>= 3.0.0). 103s openssh-server depends on libssl3 (>= 3.0.10). 103s openssh-client depends on libssl3 (>= 3.0.10). 103s mtd-utils depends on libssl3 (>= 3.0.0). 103s mokutil depends on libssl3 (>= 3.0.0). 103s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 103s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 103s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 103s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 103s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 103s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 103s libnvme1 depends on libssl3 (>= 3.0.0). 103s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 103s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 103s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 103s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 103s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 103s kmod depends on libssl3 (>= 3.0.0). 103s dhcpcd-base depends on libssl3 (>= 3.0.0). 103s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 103s 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74819 files and directories currently installed.) 103s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 103s Selecting previously unselected package libssl3t64:arm64. 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74808 files and directories currently installed.) 103s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 103s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 103s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 103s Setting up openssl (3.0.13-0ubuntu2) ... 103s Processing triggers for man-db (2.12.0-3) ... 103s Processing triggers for libc-bin (2.39-0ubuntu6) ... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 105s sh: Attempting to set up Debian/Ubuntu apt sources automatically 105s sh: Distribution appears to be Ubuntu 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s eatmydata is already the newest version (131-1). 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s dbus is already the newest version (1.14.10-4ubuntu1). 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s rng-tools-debian is already the newest version (2.4). 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s The following packages will be REMOVED: 108s cloud-init* python3-configobj* python3-debconf* 108s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 108s After this operation, 3256 kB disk space will be freed. 108s (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 ... 74821 files and directories currently installed.) 108s Removing cloud-init (24.1.2-0ubuntu1) ... 109s Removing python3-configobj (5.0.8-3) ... 109s Removing python3-debconf (1.5.86) ... 109s Processing triggers for man-db (2.12.0-3) ... 109s (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 ... 74432 files and directories currently installed.) 109s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 110s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 110s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 110s invoke-rc.d: policy-rc.d denied execution of try-restart. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s linux-generic is already the newest version (6.8.0-11.11+1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 111s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 111s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 113s Reading package lists... 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s Calculating upgrade... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s autopkgtest [17:46:24]: rebooting testbed after setup commands that affected boot 144s autopkgtest [17:46:52]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 156s autopkgtest [17:47:04]: @@@@@@@@@@@@@@@@@@@@ apt-source seqsero 159s Get:1 http://ftpmaster.internal/ubuntu noble/universe seqsero 1.0.1+dfsg-6 (dsc) [2024 B] 159s Get:2 http://ftpmaster.internal/ubuntu noble/universe seqsero 1.0.1+dfsg-6 (tar) [356 kB] 159s Get:3 http://ftpmaster.internal/ubuntu noble/universe seqsero 1.0.1+dfsg-6 (diff) [43.1 kB] 159s gpgv: Signature made Thu Sep 29 13:38:36 2022 UTC 159s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 159s gpgv: issuer "tille@debian.org" 159s gpgv: Can't check signature: No public key 159s dpkg-source: warning: cannot verify inline signature for ./seqsero_1.0.1+dfsg-6.dsc: no acceptable signature found 159s autopkgtest [17:47:07]: testing package seqsero version 1.0.1+dfsg-6 160s autopkgtest [17:47:08]: build not needed 160s autopkgtest [17:47:08]: test run-unit-test: preparing testbed 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 168s Starting pkgProblemResolver with broken count: 0 168s Starting 2 pkgProblemResolver with broken count: 0 168s Done 168s The following additional packages will be installed: 168s bwa fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 168s fonts-urw-base35 libaec0 libblas3 libcairo2 libdeflate0 libfontconfig1 168s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1 168s libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 168s liblapack3 liblcms2-2 liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 168s libncbi-vdb3 libncbi-wvdb3 libopenjp2-7 libpixman-1-0 libpython3.11-minimal 168s libpython3.11-stdlib libraqm0 libre2-10 libsharpyuv0 libsz2 libtiff6 168s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 168s ncbi-vdb-data python3-biopython python3-cairo python3-freetype python3-numpy 168s python3-pil python3-reportlab python3-rlpycairo python3.11 168s python3.11-minimal samtools seqsero sgml-base sra-toolkit w3c-sgml-lib 168s x11-common xfonts-encodings xfonts-utils xml-core 168s Suggested packages: 168s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 168s python3-tk clustalo clustalw dialign dssp emboss fasttree mafft muscle3 168s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 168s python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee wise gcc 168s gfortran python3-dev python3-pytest python-pil-doc pdf-viewer 168s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 168s python3.11-venv python3.11-doc binfmt-support cwltool ispcr sgml-base-doc 168s debhelper 168s Recommended packages: 168s python-biopython-doc ncbi-blast+ python3-olefile med-config 168s The following NEW packages will be installed: 168s autopkgtest-satdep bwa fontconfig-config fonts-dejavu-core 168s fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 libaec0 libblas3 168s libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 168s libgraphite2-3 libharfbuzz0b libhdf5-103-1 libhts3 libhtscodecs2 168s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 168s liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncbi-vdb3 168s libncbi-wvdb3 libopenjp2-7 libpixman-1-0 libpython3.11-minimal 168s libpython3.11-stdlib libraqm0 libre2-10 libsharpyuv0 libsz2 libtiff6 168s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 168s ncbi-vdb-data python3-biopython python3-cairo python3-freetype python3-numpy 168s python3-pil python3-reportlab python3-rlpycairo python3.11 168s python3.11-minimal samtools seqsero sgml-base sra-toolkit w3c-sgml-lib 168s x11-common xfonts-encodings xfonts-utils xml-core 168s 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. 168s Need to get 46.8 MB/46.8 MB of archives. 168s After this operation, 158 MB of additional disk space will be used. 168s Get:1 /tmp/autopkgtest.y3mo3E/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 168s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 169s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 169s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 169s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 169s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 169s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 bwa arm64 0.7.17-7 [192 kB] 169s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 169s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 169s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 169s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 169s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 169s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 169s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 169s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 169s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 169s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 169s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 169s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 169s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 169s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 169s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 169s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 169s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 170s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 170s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 170s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 170s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 170s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 170s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 170s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 170s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 170s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 170s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 170s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 170s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 170s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 170s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 170s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 170s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 170s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 170s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 170s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [65.8 kB] 170s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [1130 kB] 170s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi-wvdb3 arm64 3.0.2+dfsg-2 [1153 kB] 170s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 170s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libre2-10 arm64 20230301-3 [159 kB] 170s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 170s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 170s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 170s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 170s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 170s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 170s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 170s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 170s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 170s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 170s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 170s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 170s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 170s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 170s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 170s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 170s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 170s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 sra-toolkit arm64 3.0.3+dfsg-6ubuntu1 [6998 kB] 170s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 seqsero arm64 1.0.1+dfsg-6 [369 kB] 171s Fetched 46.8 MB in 2s (24.6 MB/s) 171s Selecting previously unselected package libpython3.11-minimal:arm64. 171s (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 ... 74377 files and directories currently installed.) 171s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 171s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 171s Selecting previously unselected package python3.11-minimal. 171s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 171s Unpacking python3.11-minimal (3.11.8-1) ... 171s Selecting previously unselected package sgml-base. 171s Preparing to unpack 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... 174s Setting up libxcb-render0:arm64 (1.15-1) ... 174s Setting up bwa (0.7.17-7) ... 174s Setting up x11-common (1:7.7+23ubuntu2) ... 174s Setting up libdeflate0:arm64 (1.19-1) ... 174s Setting up libxcb-shm0:arm64 (1.15-1) ... 174s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 174s Setting up python3-freetype (2.4.0-1) ... 174s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 174s Setting up libaec0:arm64 (1.1.2-1) ... 174s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 174s Setting up libblas3:arm64 (3.12.0-3) ... 175s 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 175s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 175s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 175s Setting up libimagequant0:arm64 (2.18.0-1) ... 175s Setting up fonts-dejavu-mono (2.37-8) ... 175s Setting up fonts-dejavu-core (2.37-8) ... 175s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 175s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 175s Setting up libwebp7:arm64 (1.3.2-0.4) ... 175s Setting up fonts-dejavu-extra (2.37-8) ... 175s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 175s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 175s Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... 175s Setting up sgml-base (1.31) ... 175s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 175s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 175s Setting up libsz2:arm64 (1.1.2-1) ... 175s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 175s Setting up python3.11-minimal (3.11.8-1) ... 175s Setting up liblapack3:arm64 (3.12.0-3) ... 175s 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 175s Setting up libhts3:arm64 (1.18+ds-1) ... 175s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 175s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 175s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 176s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 176s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 176s Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... 176s Setting up xfonts-utils (1:7.7+6build2) ... 176s Setting up samtools (1.19.2-1) ... 176s Setting up libraqm0:arm64 (0.10.1-1) ... 176s Setting up libncbi-wvdb3:arm64 (3.0.2+dfsg-2) ... 176s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 176s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 176s Setting up xml-core (0.19) ... 176s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 176s Setting up sra-toolkit (3.0.3+dfsg-6ubuntu1) ... 176s Setting up python3.11 (3.11.8-1) ... 177s Setting up fonts-urw-base35 (20200910-8) ... 177s Setting up libcairo2:arm64 (1.18.0-1) ... 177s Setting up python3-pil:arm64 (10.2.0-1) ... 177s Setting up python3-numpy (1:1.24.2-2) ... 179s Setting up python3-cairo (1.25.1-2) ... 179s Setting up python3-rlpycairo (0.3.0-3) ... 179s Setting up python3-reportlab (4.1.0-1) ... 182s Processing triggers for libc-bin (2.39-0ubuntu6) ... 182s Processing triggers for systemd (255.2-3ubuntu2) ... 182s Processing triggers for man-db (2.12.0-3) ... 182s Processing triggers for sgml-base (1.31) ... 182s Setting up w3c-sgml-lib (1.3-3) ... 207s Setting up python3-biopython (1.81+dfsg-3) ... 208s Setting up seqsero (1.0.1+dfsg-6) ... 208s Setting up autopkgtest-satdep (0) ... 213s (Reading database ... 78731 files and directories currently installed.) 213s Removing autopkgtest-satdep (0) ... 214s autopkgtest [17:48:02]: test run-unit-test: [----------------------- 214s Test for checking functionality 215s gzip: sra_data.fastq: unknown suffix -- ignored 215s [bwa_index] Pack FASTA... 0.00 sec 215s [bwa_index] Construct BWT for the packed sequence... 215s [bwa_index] 0.01 seconds elapse. 215s [bwa_index] Update BWT... 0.00 sec 215s [bwa_index] Pack forward-only FASTA... 0.00 sec 215s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 215s [main] Version: 0.7.17-r1188 215s [main] CMD: bwa index database/special_new_O_genes.fasta 215s [main] Real time: 0.041 sec; CPU: 0.027 sec 215s [bwa_aln] 17bp reads: max_diff = 2 215s [bwa_aln] 38bp reads: max_diff = 3 215s [bwa_aln] 64bp reads: max_diff = 4 215s [bwa_aln] 93bp reads: max_diff = 5 215s [bwa_aln] 124bp reads: max_diff = 6 215s [bwa_aln] 157bp reads: max_diff = 7 215s [bwa_aln] 190bp reads: max_diff = 8 215s [bwa_aln] 225bp reads: max_diff = 9 215s [main] Version: 0.7.17-r1188 215s [main] CMD: bwa aln database/special_new_O_genes.fasta sra_data.fastq 215s [main] Real time: 0.001 sec; CPU: 0.001 sec 215s [main] Version: 0.7.17-r1188 215s [main] CMD: bwa samse database/special_new_O_genes.fasta sra_data_1.sai sra_data.fastq 215s [main] Real time: 0.010 sec; CPU: 0.008 sec 215s [bwa_index] Pack FASTA... 0.01 sec 215s [bwa_index] Construct BWT for the packed sequence... 216s [bwa_index] 0.12 seconds elapse. 216s [bwa_index] Update BWT... 0.00 sec 216s [bwa_index] Pack forward-only FASTA... 0.00 sec 216s [bwa_index] Construct SA from BWT and Occ... 0.06 sec 216s [main] Version: 0.7.17-r1188 216s [main] CMD: bwa index database/H_combine_update_9_03_2014_new.fasta 216s [main] Real time: 0.307 sec; CPU: 0.197 sec 216s [bwa_aln] 17bp reads: max_diff = 2 216s [bwa_aln] 38bp reads: max_diff = 3 216s [bwa_aln] 64bp reads: max_diff = 4 216s [bwa_aln] 93bp reads: max_diff = 5 216s [bwa_aln] 124bp reads: max_diff = 6 216s [bwa_aln] 157bp reads: max_diff = 7 216s [bwa_aln] 190bp reads: max_diff = 8 216s [bwa_aln] 225bp reads: max_diff = 9 216s [main] Version: 0.7.17-r1188 216s [main] CMD: bwa aln database/H_combine_update_9_03_2014_new.fasta sra_data.fastq 216s [main] Real time: 0.003 sec; CPU: 0.001 sec 216s [main] Version: 0.7.17-r1188 216s [main] CMD: bwa samse database/H_combine_update_9_03_2014_new.fasta sra_data_1.sai sra_data.fastq 216s [main] Real time: 0.003 sec; CPU: 0.001 sec 216s 216s 216s 216s Input files: sra_data.fastq 216s O antigen prediction: O-- 216s H1 antigen prediction(fliC): - 216s H2 antigen prediction(fljB): - 216s Predicted antigenic profile: -:-:- 216s Predicted serotype(s): N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme) 216s 216s 216s 216s 216s Result: 216s 216s Input files: sra_data.fastq 216s O antigen prediction: O-- 216s H1 antigen prediction(fliC): - 216s H2 antigen prediction(fljB): - 216s Predicted antigenic profile: -:-:- 216s Predicted serotype(s): N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme) 216s 216s PASS 216s autopkgtest [17:48:04]: test run-unit-test: -----------------------] 217s autopkgtest [17:48:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 217s run-unit-test PASS 217s autopkgtest [17:48:05]: @@@@@@@@@@@@@@@@@@@@ summary 217s run-unit-test PASS 229s Creating nova instance adt-noble-arm64-seqsero-20240324-174428-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...