0s autopkgtest [15:23:23]: starting date and time: 2024-03-23 15:23:23+0000 0s autopkgtest [15:23:23]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:23:23]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._lmyrh8m/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:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade optimir --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-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@bos01-ppc64el-20.secgroup --name adt-noble-ppc64el-optimir-20240323-152323-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 107s autopkgtest [15:25:10]: testbed dpkg architecture: ppc64el 107s autopkgtest [15:25:10]: testbed apt version: 2.7.12 107s autopkgtest [15:25:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 108s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 108s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 108s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 108s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 108s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 109s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 109s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 109s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 109s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 109s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 109s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 109s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 109s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 112s Fetched 9623 kB in 2s (4227 kB/s) 112s Reading package lists... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 115s The following packages will be REMOVED: 115s libssl3 115s The following NEW packages will be installed: 115s libssl3t64 115s The following packages have been kept back: 115s curl 115s The following packages will be upgraded: 115s cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales openssl 115s python3-markupsafe 115s 8 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 115s Need to get 12.1 MB of archives. 115s After this operation, 10.2 kB of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 116s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 116s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 116s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 116s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 116s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 116s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 116s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB] 116s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.2-0ubuntu1 [597 kB] 117s Preconfiguring packages ... 117s Fetched 12.1 MB in 1s (12.4 MB/s) 117s (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 ... 70157 files and directories currently installed.) 117s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 117s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 117s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 118s (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 ... 70157 files and directories currently installed.) 118s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 118s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 118s Setting up libc-bin (2.39-0ubuntu6) ... 118s (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 ... 70157 files and directories currently installed.) 118s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 118s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 118s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 118s wget depends on libssl3 (>= 3.0.0). 118s tnftp depends on libssl3 (>= 3.0.0). 118s tcpdump depends on libssl3 (>= 3.0.0). 118s systemd-resolved depends on libssl3 (>= 3.0.0). 118s systemd depends on libssl3 (>= 3.0.0). 118s sudo depends on libssl3 (>= 3.0.0). 118s rsync depends on libssl3 (>= 3.0.0). 118s python3-cryptography depends on libssl3 (>= 3.0.0). 118s openssh-server depends on libssl3 (>= 3.0.10). 118s openssh-client depends on libssl3 (>= 3.0.10). 118s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 118s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 118s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 118s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 118s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 118s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 118s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 118s libnvme1 depends on libssl3 (>= 3.0.0). 118s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 118s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 118s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 118s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 118s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 118s kmod depends on libssl3 (>= 3.0.0). 118s dhcpcd-base depends on libssl3 (>= 3.0.0). 118s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 118s 118s (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 ... 70157 files and directories currently installed.) 118s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 118s Selecting previously unselected package libssl3t64:ppc64el. 118s (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 ... 70146 files and directories currently installed.) 118s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 118s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 118s Preparing to unpack .../1-libbsd0_0.12.1-1_ppc64el.deb ... 118s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 118s Preparing to unpack .../2-locales_2.39-0ubuntu6_all.deb ... 118s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 118s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 118s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 118s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_ppc64el.deb ... 118s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 118s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 119s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 119s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 119s Setting up cloud-init (24.1.2-0ubuntu1) ... 120s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 120s Setting up locales (2.39-0ubuntu6) ... 120s Generating locales (this might take a while)... 122s en_US.UTF-8... done 122s Generation complete. 122s Setting up python3-markupsafe (2.1.5-1build1) ... 122s Setting up openssl (3.0.13-0ubuntu2) ... 122s Setting up libbsd0:ppc64el (0.12.1-1) ... 122s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 122s Processing triggers for man-db (2.12.0-3) ... 123s Processing triggers for libc-bin (2.39-0ubuntu6) ... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 124s sh: Attempting to set up Debian/Ubuntu apt sources automatically 124s sh: Distribution appears to be Ubuntu 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s eatmydata is already the newest version (131-1). 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s dbus is already the newest version (1.14.10-4ubuntu1). 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s rng-tools-debian is already the newest version (2.4). 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s The following packages will be REMOVED: 126s cloud-init* python3-configobj* python3-debconf* 127s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 127s After this operation, 3256 kB disk space will be freed. 127s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70158 files and directories currently installed.) 127s Removing cloud-init (24.1.2-0ubuntu1) ... 127s Removing python3-configobj (5.0.8-3) ... 127s Removing python3-debconf (1.5.86) ... 127s Processing triggers for man-db (2.12.0-3) ... 128s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69769 files and directories currently installed.) 128s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 128s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 128s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 128s invoke-rc.d: policy-rc.d denied execution of try-restart. 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s linux-generic is already the newest version (6.8.0-11.11+1). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 129s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 129s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 131s Reading package lists... 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Calculating upgrade... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s autopkgtest [15:25:35]: rebooting testbed after setup commands that affected boot 288s autopkgtest [15:28:11]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 291s autopkgtest [15:28:14]: @@@@@@@@@@@@@@@@@@@@ apt-source optimir 293s Get:1 http://ftpmaster.internal/ubuntu noble/universe optimir 1.2-1 (dsc) [1984 B] 293s Get:2 http://ftpmaster.internal/ubuntu noble/universe optimir 1.2-1 (tar) [1748 kB] 293s Get:3 http://ftpmaster.internal/ubuntu noble/universe optimir 1.2-1 (diff) [3476 B] 293s gpgv: Signature made Fri Mar 18 14:54:34 2022 UTC 293s gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 293s gpgv: issuer "daissi@debian.org" 293s gpgv: Can't check signature: No public key 293s dpkg-source: warning: cannot verify inline signature for ./optimir_1.2-1.dsc: no acceptable signature found 293s autopkgtest [15:28:16]: testing package optimir version 1.2-1 293s autopkgtest [15:28:16]: build not needed 294s autopkgtest [15:28:17]: test run-unit-test: preparing testbed 296s Reading package lists... 296s Building dependency tree... 296s Reading state information... 296s Starting pkgProblemResolver with broken count: 0 296s Starting 2 pkgProblemResolver with broken count: 0 296s Done 297s The following additional packages will be installed: 297s bowtie2 cutadapt fontconfig-config fonts-dejavu-core fonts-dejavu-extra 297s fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 libdeflate0 297s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 297s libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 297s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 297s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 297s libxcb-shm0 libxrender1 optimir pigz python3-biopython python3-cairo 297s python3-cutadapt python3-dnaio python3-freetype python3-numpy python3-pil 297s python3-pysam python3-reportlab python3-rlpycairo python3-xopen samtools 297s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 297s Suggested packages: 297s bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 297s liblcms2-utils python3-tk bwa clustalo clustalw dialign dssp emboss fasttree 297s mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib 297s python3-mmtf python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee 297s wise gcc gfortran python3-dev python3-pytest python-pil-doc pdf-viewer 297s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm cwltool 297s sgml-base-doc debhelper 297s Recommended packages: 297s r-cran-gridextra r-cran-ggplot2 python-biopython-doc ncbi-blast+ 297s python3-olefile 297s The following NEW packages will be installed: 297s autopkgtest-satdep bowtie2 cutadapt fontconfig-config fonts-dejavu-core 297s fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 297s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 297s libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 297s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 297s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 297s libxcb-shm0 libxrender1 optimir pigz python3-biopython python3-cairo 297s python3-cutadapt python3-dnaio python3-freetype python3-numpy python3-pil 297s python3-pysam python3-reportlab python3-rlpycairo python3-xopen samtools 297s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 297s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 297s Need to get 41.1 MB/41.1 MB of archives. 297s After this operation, 176 MB of additional disk space will be used. 297s Get:1 /tmp/autopkgtest.Z3qw9d/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 297s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-base all 1.31 [11.4 kB] 297s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el pigz ppc64el 2.8-1 [76.3 kB] 297s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-xopen all 1.7.0-2 [17.0 kB] 297s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-dnaio ppc64el 1.0.1-1build1 [93.5 kB] 297s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-cutadapt ppc64el 4.4-1build1 [362 kB] 297s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el cutadapt all 4.4-1build1 [6776 B] 297s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 297s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 297s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontenc1 ppc64el 1:1.1.8-1 [15.7 kB] 297s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 297s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 297s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-utils ppc64el 1:7.7+6build2 [112 kB] 297s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 298s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 298s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-extra all 2.37-8 [1947 kB] 298s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 298s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 298s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 298s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 298s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 298s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 298s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 298s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 298s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 298s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 298s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 298s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 298s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 298s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 298s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libimagequant0 ppc64el 2.18.0-1 [42.5 kB] 298s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 298s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 298s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 298s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 298s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 298s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libraqm0 ppc64el 0.10.1-1 [18.9 kB] 298s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 298s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 298s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 298s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 298s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpdemux2 ppc64el 1.3.2-0.4 [14.4 kB] 298s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpmux3 ppc64el 1.3.2-0.4 [31.2 kB] 298s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 299s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libopenjp2-7 ppc64el 2.5.0-2 [233 kB] 299s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-pil ppc64el 10.2.0-1 [526 kB] 299s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-cairo ppc64el 1.25.1-2 [162 kB] 299s Get:48 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-freetype all 2.4.0-1 [83.1 kB] 299s Get:49 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 299s Get:50 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-reportlab all 4.1.0-1 [683 kB] 299s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB] 299s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 299s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-biopython ppc64el 1.81+dfsg-3 [1738 kB] 299s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 299s Get:55 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie2 ppc64el 2.5.2-1 [1367 kB] 299s Get:56 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 299s Get:57 http://ftpmaster.internal/ubuntu noble/universe ppc64el optimir all 1.2-1 [1128 kB] 299s Fetched 41.1 MB in 2s (17.0 MB/s) 300s Selecting previously unselected package sgml-base. 300s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69714 files and directories currently installed.) 300s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 300s Unpacking sgml-base (1.31) ... 300s Selecting previously unselected package pigz. 300s Preparing to unpack .../01-pigz_2.8-1_ppc64el.deb ... 300s Unpacking pigz (2.8-1) ... 300s Selecting previously unselected package python3-xopen. 300s Preparing to unpack .../02-python3-xopen_1.7.0-2_all.deb ... 300s Unpacking python3-xopen (1.7.0-2) ... 300s Selecting previously unselected package python3-dnaio. 300s Preparing to unpack .../03-python3-dnaio_1.0.1-1build1_ppc64el.deb ... 300s Unpacking python3-dnaio (1.0.1-1build1) ... 300s Selecting previously unselected package python3-cutadapt. 300s Preparing to unpack .../04-python3-cutadapt_4.4-1build1_ppc64el.deb ... 300s Unpacking python3-cutadapt (4.4-1build1) ... 300s Selecting previously unselected package cutadapt. 300s Preparing to unpack .../05-cutadapt_4.4-1build1_all.deb ... 300s Unpacking cutadapt (4.4-1build1) ... 300s Selecting previously unselected package fonts-dejavu-mono. 300s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 300s Unpacking fonts-dejavu-mono (2.37-8) ... 300s Selecting previously unselected package fonts-dejavu-core. 300s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 300s Unpacking fonts-dejavu-core (2.37-8) ... 300s Selecting previously unselected package libfontenc1:ppc64el. 300s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1_ppc64el.deb ... 300s Unpacking libfontenc1:ppc64el (1:1.1.8-1) ... 300s Selecting previously unselected package x11-common. 300s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu2_all.deb ... 300s Unpacking x11-common (1:7.7+23ubuntu2) ... 300s Selecting previously unselected package xfonts-encodings. 300s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 300s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 300s Selecting previously unselected package xfonts-utils. 300s Preparing to unpack .../11-xfonts-utils_1%3a7.7+6build2_ppc64el.deb ... 300s Unpacking xfonts-utils (1:7.7+6build2) ... 300s Selecting previously unselected package fonts-urw-base35. 300s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 300s Unpacking fonts-urw-base35 (20200910-8) ... 300s Selecting previously unselected package fontconfig-config. 300s Preparing to unpack .../13-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 300s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 300s Selecting previously unselected package fonts-dejavu-extra. 300s Preparing to unpack .../14-fonts-dejavu-extra_2.37-8_all.deb ... 300s Unpacking fonts-dejavu-extra (2.37-8) ... 300s Selecting previously unselected package libblas3:ppc64el. 300s Preparing to unpack .../15-libblas3_3.12.0-3_ppc64el.deb ... 300s Unpacking libblas3:ppc64el (3.12.0-3) ... 300s Selecting previously unselected package libfontconfig1:ppc64el. 300s Preparing to unpack .../16-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 300s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 300s Selecting previously unselected package libpixman-1-0:ppc64el. 300s Preparing to unpack .../17-libpixman-1-0_0.42.2-1_ppc64el.deb ... 300s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 300s Selecting previously unselected package libxcb-render0:ppc64el. 300s Preparing to unpack .../18-libxcb-render0_1.15-1_ppc64el.deb ... 300s Unpacking libxcb-render0:ppc64el (1.15-1) ... 300s Selecting previously unselected package libxcb-shm0:ppc64el. 300s Preparing to unpack .../19-libxcb-shm0_1.15-1_ppc64el.deb ... 300s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 300s Selecting previously unselected package libxrender1:ppc64el. 300s Preparing to unpack .../20-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 300s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 300s Selecting previously unselected package libcairo2:ppc64el. 300s Preparing to unpack .../21-libcairo2_1.18.0-1_ppc64el.deb ... 300s Unpacking libcairo2:ppc64el (1.18.0-1) ... 300s Selecting previously unselected package libdeflate0:ppc64el. 300s Preparing to unpack .../22-libdeflate0_1.19-1_ppc64el.deb ... 300s Unpacking libdeflate0:ppc64el (1.19-1) ... 300s Selecting previously unselected package libgfortran5:ppc64el. 300s Preparing to unpack .../23-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 300s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 300s Selecting previously unselected package libgomp1:ppc64el. 300s Preparing to unpack .../24-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 300s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 300s Selecting previously unselected package libgraphite2-3:ppc64el. 300s Preparing to unpack .../25-libgraphite2-3_1.3.14-2_ppc64el.deb ... 300s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 301s Selecting previously unselected package libharfbuzz0b:ppc64el. 301s Preparing to unpack .../26-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 301s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 301s Selecting previously unselected package libhtscodecs2:ppc64el. 301s Preparing to unpack .../27-libhtscodecs2_1.6.0-1_ppc64el.deb ... 301s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 301s Selecting previously unselected package libhts3:ppc64el. 301s Preparing to unpack .../28-libhts3_1.18+ds-1_ppc64el.deb ... 301s Unpacking libhts3:ppc64el (1.18+ds-1) ... 301s Selecting previously unselected package libimagequant0:ppc64el. 301s Preparing to unpack .../29-libimagequant0_2.18.0-1_ppc64el.deb ... 301s Unpacking libimagequant0:ppc64el (2.18.0-1) ... 301s Selecting previously unselected package libjpeg-turbo8:ppc64el. 301s Preparing to unpack .../30-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 301s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 301s Selecting previously unselected package libjpeg8:ppc64el. 301s Preparing to unpack .../31-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 301s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 301s Selecting previously unselected package liblapack3:ppc64el. 301s Preparing to unpack .../32-liblapack3_3.12.0-3_ppc64el.deb ... 301s Unpacking liblapack3:ppc64el (3.12.0-3) ... 301s Selecting previously unselected package liblcms2-2:ppc64el. 301s Preparing to unpack .../33-liblcms2-2_2.14-2_ppc64el.deb ... 301s Unpacking liblcms2-2:ppc64el (2.14-2) ... 301s Selecting previously unselected package liblerc4:ppc64el. 301s Preparing to unpack .../34-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 301s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 301s Selecting previously unselected package libraqm0:ppc64el. 301s Preparing to unpack .../35-libraqm0_0.10.1-1_ppc64el.deb ... 301s Unpacking libraqm0:ppc64el (0.10.1-1) ... 301s Selecting previously unselected package libsharpyuv0:ppc64el. 301s Preparing to unpack .../36-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 301s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 301s Selecting previously unselected package libjbig0:ppc64el. 301s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 301s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 301s Selecting previously unselected package libwebp7:ppc64el. 301s Preparing to unpack .../38-libwebp7_1.3.2-0.4_ppc64el.deb ... 301s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 301s Selecting previously unselected package libtiff6:ppc64el. 301s Preparing to unpack .../39-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 301s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 301s Selecting previously unselected package libwebpdemux2:ppc64el. 301s Preparing to unpack .../40-libwebpdemux2_1.3.2-0.4_ppc64el.deb ... 301s Unpacking libwebpdemux2:ppc64el (1.3.2-0.4) ... 301s Selecting previously unselected package libwebpmux3:ppc64el. 301s Preparing to unpack .../41-libwebpmux3_1.3.2-0.4_ppc64el.deb ... 301s Unpacking libwebpmux3:ppc64el (1.3.2-0.4) ... 301s Selecting previously unselected package python3-numpy. 301s Preparing to unpack .../42-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 301s Unpacking python3-numpy (1:1.24.2-2) ... 301s Selecting previously unselected package libopenjp2-7:ppc64el. 301s Preparing to unpack .../43-libopenjp2-7_2.5.0-2_ppc64el.deb ... 301s Unpacking libopenjp2-7:ppc64el (2.5.0-2) ... 301s Selecting previously unselected package python3-pil:ppc64el. 301s Preparing to unpack .../44-python3-pil_10.2.0-1_ppc64el.deb ... 301s Unpacking python3-pil:ppc64el (10.2.0-1) ... 301s Selecting previously unselected package python3-cairo. 301s Preparing to unpack .../45-python3-cairo_1.25.1-2_ppc64el.deb ... 301s Unpacking python3-cairo (1.25.1-2) ... 301s Selecting previously unselected package python3-freetype. 301s Preparing to unpack .../46-python3-freetype_2.4.0-1_all.deb ... 301s Unpacking python3-freetype (2.4.0-1) ... 301s Selecting previously unselected package python3-rlpycairo. 301s Preparing to unpack .../47-python3-rlpycairo_0.3.0-3_all.deb ... 301s Unpacking python3-rlpycairo (0.3.0-3) ... 301s Selecting previously unselected package python3-reportlab. 301s Preparing to unpack .../48-python3-reportlab_4.1.0-1_all.deb ... 301s Unpacking python3-reportlab (4.1.0-1) ... 301s Selecting previously unselected package xml-core. 301s Preparing to unpack .../49-xml-core_0.19_all.deb ... 301s Unpacking xml-core (0.19) ... 301s Selecting previously unselected package w3c-sgml-lib. 301s Preparing to unpack .../50-w3c-sgml-lib_1.3-3_all.deb ... 301s Unpacking w3c-sgml-lib (1.3-3) ... 302s Selecting previously unselected package python3-biopython. 302s Preparing to unpack .../51-python3-biopython_1.81+dfsg-3_ppc64el.deb ... 302s Unpacking python3-biopython (1.81+dfsg-3) ... 302s Selecting previously unselected package python3-pysam. 302s Preparing to unpack .../52-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 302s Unpacking python3-pysam (0.22.0+ds-1) ... 302s Selecting previously unselected package bowtie2. 302s Preparing to unpack .../53-bowtie2_2.5.2-1_ppc64el.deb ... 302s Unpacking bowtie2 (2.5.2-1) ... 302s Selecting previously unselected package samtools. 302s Preparing to unpack .../54-samtools_1.19.2-1_ppc64el.deb ... 302s Unpacking samtools (1.19.2-1) ... 302s Selecting previously unselected package optimir. 302s Preparing to unpack .../55-optimir_1.2-1_all.deb ... 302s Unpacking optimir (1.2-1) ... 302s Selecting previously unselected package autopkgtest-satdep. 302s Preparing to unpack .../56-1-autopkgtest-satdep.deb ... 302s Unpacking autopkgtest-satdep (0) ... 302s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 302s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 302s Setting up liblcms2-2:ppc64el (2.14-2) ... 302s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 302s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 302s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 302s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 302s Setting up libxcb-render0:ppc64el (1.15-1) ... 302s Setting up x11-common (1:7.7+23ubuntu2) ... 303s Setting up libdeflate0:ppc64el (1.19-1) ... 303s Setting up libxcb-shm0:ppc64el (1.15-1) ... 303s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 303s Setting up python3-freetype (2.4.0-1) ... 303s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 303s Setting up bowtie2 (2.5.2-1) ... 303s Setting up libfontenc1:ppc64el (1:1.1.8-1) ... 303s Setting up libblas3:ppc64el (3.12.0-3) ... 303s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 303s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 303s Setting up libimagequant0:ppc64el (2.18.0-1) ... 303s Setting up fonts-dejavu-mono (2.37-8) ... 303s Setting up fonts-dejavu-core (2.37-8) ... 303s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 303s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 303s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 303s Setting up fonts-dejavu-extra (2.37-8) ... 303s Setting up pigz (2.8-1) ... 303s Setting up libopenjp2-7:ppc64el (2.5.0-2) ... 303s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 303s Setting up sgml-base (1.31) ... 303s Setting up libwebpmux3:ppc64el (1.3.2-0.4) ... 303s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 303s Setting up liblapack3:ppc64el (3.12.0-3) ... 303s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 303s Setting up libhts3:ppc64el (1.18+ds-1) ... 303s Setting up python3-pysam (0.22.0+ds-1) ... 303s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 303s Setting up libwebpdemux2:ppc64el (1.3.2-0.4) ... 303s Setting up xfonts-utils (1:7.7+6build2) ... 303s Setting up samtools (1.19.2-1) ... 303s Setting up python3-xopen (1.7.0-2) ... 303s Setting up libraqm0:ppc64el (0.10.1-1) ... 303s Setting up python3-numpy (1:1.24.2-2) ... 305s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 305s Setting up xml-core (0.19) ... 305s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 305s Setting up python3-dnaio (1.0.1-1build1) ... 306s Setting up fonts-urw-base35 (20200910-8) ... 306s Setting up libcairo2:ppc64el (1.18.0-1) ... 306s Setting up python3-pil:ppc64el (10.2.0-1) ... 306s Setting up python3-cutadapt (4.4-1build1) ... 306s Setting up python3-cairo (1.25.1-2) ... 306s Setting up cutadapt (4.4-1build1) ... 306s Setting up python3-rlpycairo (0.3.0-3) ... 306s Setting up python3-reportlab (4.1.0-1) ... 307s Processing triggers for libc-bin (2.39-0ubuntu6) ... 307s Processing triggers for man-db (2.12.0-3) ... 308s Processing triggers for sgml-base (1.31) ... 308s Setting up w3c-sgml-lib (1.3-3) ... 336s Setting up python3-biopython (1.81+dfsg-3) ... 337s Setting up optimir (1.2-1) ... 337s /usr/lib/python3/dist-packages/optimir/libs/get_counts.py:453: SyntaxWarning: "is" with 'str' literal. Did you mean "=="? 337s if prefix is '': 337s Setting up autopkgtest-satdep (0) ... 340s (Reading database ... 73627 files and directories currently installed.) 340s Removing autopkgtest-satdep (0) ... 341s autopkgtest [15:29:04]: test run-unit-test: [----------------------- 342s 342s ######################### 342s ## OPTIMIR ## 342s ######################### 342s 342s Starting workflow for sample S1 342s > Starting Library preparation... 342s Library prepared! VCF available : True; Geno available : True; Elapsed time: 0.3s 342s > Starting trimming reads... (can take several minutes) 342s Trimming done! Elapsed time: 0.12s 342s > Starting collapsing reads... (can take several minutes) 342s Collapsing done! Elapsed time: 0.01s 342s > Starting mapping reads.... 342s Mapping done! Elapsed time: 0.13s 342s > Starting post-processing.... 342s - Computing Alignment score 342s - Checking genotype consistency 342s - Resolving ambigous alignments 342s - Generating outputs 342s Post-process done! Elapsed time: 0.04s 342s 342s OptimiR Run Completed. 342s Results are available in ./OptimiR_Results_Dir/OptimiR_Results/ 342s Total time: 0.6s 342s 342s 343s 343s ################################## 343s # OPTIMIR: Library Preparation # 343s ################################## 343s Library preparation : 343s Start process... Depending on the number of variants provided, the preparation can take a few seconds to several minutes... 343s Library built! 343s 343s ######################### 343s ## OPTIMIR ## 343s ######################### 343s 343s Starting workflow for sample S1 343s > Starting Library preparation... 343s Library prepared! VCF available : True; Geno available : True; Elapsed time: 0.01s 343s > Starting trimming reads... (can take several minutes) 343s Trimming done! Elapsed time: 0.11s 343s > Starting collapsing reads... (can take several minutes) 343s Collapsing done! Elapsed time: 0.01s 343s > Starting mapping reads.... 343s Mapping done! Elapsed time: 0.12s 343s > Starting post-processing.... 343s - Computing Alignment score 343s - Checking genotype consistency 343s - Resolving ambigous alignments 343s - Generating outputs 343s Post-process done! Elapsed time: 0.05s 343s 343s OptimiR Run Completed. 343s Results are available in results/OptimiR_Results/ 343s Total time: 0.3s 343s 343s 344s 344s ######################### 344s ## OPTIMIR ## 344s ######################### 344s 344s Starting workflow for sample S2 344s > Starting Library preparation... 344s Library prepared! VCF available : True; Geno available : True; Elapsed time: 0.01s 344s > Starting trimming reads... (can take several minutes) 344s Trimming done! Elapsed time: 0.1s 344s > Starting collapsing reads... (can take several minutes) 344s Collapsing done! Elapsed time: 0.01s 344s > Starting mapping reads.... 344s Mapping done! Elapsed time: 0.13s 344s > Starting post-processing.... 344s - Computing Alignment score 344s - Checking genotype consistency 344s - Resolving ambigous alignments 344s - Generating outputs 344s Post-process done! Elapsed time: 0.04s 344s 344s OptimiR Run Completed. 344s Results are available in results/OptimiR_Results/ 344s Total time: 0.28s 344s 344s 344s 344s ############################# 344s # OPTIMIR: Summary tables # 344s ############################# 344s OptimiR summary tables are available. 344s autopkgtest [15:29:07]: test run-unit-test: -----------------------] 345s autopkgtest [15:29:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 345s run-unit-test PASS 345s autopkgtest [15:29:08]: @@@@@@@@@@@@@@@@@@@@ summary 345s run-unit-test PASS 360s Creating nova instance adt-noble-ppc64el-optimir-20240323-152323-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...