0s autopkgtest [15:16:19]: starting date and time: 2024-03-23 15:16:19+0000 0s autopkgtest [15:16:19]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:16:19]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.g5zr3n6y/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 ariba --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-3@bos01-ppc64el-13.secgroup --name adt-noble-ppc64el-ariba-20240323-151618-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 161s autopkgtest [15:19:00]: testbed dpkg architecture: ppc64el 161s autopkgtest [15:19:00]: testbed apt version: 2.7.12 161s autopkgtest [15:19:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 162s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 162s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 163s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 163s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 163s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 163s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 163s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 163s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 163s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 163s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 163s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 163s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 163s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 167s Fetched 9623 kB in 2s (3921 kB/s) 167s Reading package lists... 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s Calculating upgrade... 170s The following packages will be REMOVED: 170s libssl3 170s The following NEW packages will be installed: 170s libssl3t64 170s The following packages have been kept back: 170s curl 170s The following packages will be upgraded: 170s cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales openssl 170s python3-markupsafe 170s 8 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 170s Need to get 12.1 MB of archives. 170s After this operation, 10.2 kB of additional disk space will be used. 170s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 170s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 170s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 170s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 170s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 170s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 171s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 171s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB] 171s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.2-0ubuntu1 [597 kB] 171s Preconfiguring packages ... 171s Fetched 12.1 MB in 1s (11.3 MB/s) 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 ... 70157 files and directories currently installed.) 171s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 171s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 172s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 172s (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.) 172s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 172s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 172s Setting up libc-bin (2.39-0ubuntu6) ... 172s (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.) 172s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 172s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 172s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 172s wget depends on libssl3 (>= 3.0.0). 172s tnftp depends on libssl3 (>= 3.0.0). 172s tcpdump depends on libssl3 (>= 3.0.0). 172s systemd-resolved depends on libssl3 (>= 3.0.0). 172s systemd depends on libssl3 (>= 3.0.0). 172s sudo depends on libssl3 (>= 3.0.0). 172s rsync depends on libssl3 (>= 3.0.0). 172s python3-cryptography depends on libssl3 (>= 3.0.0). 172s openssh-server depends on libssl3 (>= 3.0.10). 172s openssh-client depends on libssl3 (>= 3.0.10). 172s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 172s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 172s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 172s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 172s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 172s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 172s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 172s libnvme1 depends on libssl3 (>= 3.0.0). 172s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 172s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 172s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 172s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 172s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 172s kmod depends on libssl3 (>= 3.0.0). 172s dhcpcd-base depends on libssl3 (>= 3.0.0). 172s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 172s 172s (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.) 172s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 172s Selecting previously unselected package libssl3t64:ppc64el. 172s (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.) 172s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 172s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 172s Preparing to unpack .../1-libbsd0_0.12.1-1_ppc64el.deb ... 172s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 172s Preparing to unpack .../2-locales_2.39-0ubuntu6_all.deb ... 172s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 173s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 173s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 173s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_ppc64el.deb ... 173s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 173s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 173s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 173s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 173s Setting up cloud-init (24.1.2-0ubuntu1) ... 174s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 174s Setting up locales (2.39-0ubuntu6) ... 175s Generating locales (this might take a while)... 176s en_US.UTF-8... done 176s Generation complete. 176s Setting up python3-markupsafe (2.1.5-1build1) ... 176s Setting up openssl (3.0.13-0ubuntu2) ... 176s Setting up libbsd0:ppc64el (0.12.1-1) ... 176s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 176s Processing triggers for man-db (2.12.0-3) ... 178s Processing triggers for libc-bin (2.39-0ubuntu6) ... 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 179s sh: Attempting to set up Debian/Ubuntu apt sources automatically 179s sh: Distribution appears to be Ubuntu 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s eatmydata is already the newest version (131-1). 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s dbus is already the newest version (1.14.10-4ubuntu1). 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s rng-tools-debian is already the newest version (2.4). 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 180s Reading package lists... 181s Building dependency tree... 181s Reading state information... 181s The following packages will be REMOVED: 181s cloud-init* python3-configobj* python3-debconf* 181s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 181s After this operation, 3256 kB disk space will be freed. 181s (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.) 181s Removing cloud-init (24.1.2-0ubuntu1) ... 181s Removing python3-configobj (5.0.8-3) ... 181s Removing python3-debconf (1.5.86) ... 182s Processing triggers for man-db (2.12.0-3) ... 182s (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.) 182s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 182s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 182s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 182s invoke-rc.d: policy-rc.d denied execution of try-restart. 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 183s linux-generic is already the newest version (6.8.0-11.11+1). 183s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 183s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 183s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 183s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 186s Reading package lists... 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 186s Calculating upgrade... 186s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 186s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s autopkgtest [15:19:26]: rebooting testbed after setup commands that affected boot 344s autopkgtest [15:22:03]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 347s autopkgtest [15:22:06]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 349s Get:1 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (dsc) [2316 B] 349s Get:2 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (tar) [1920 kB] 349s Get:3 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (diff) [10.5 kB] 349s gpgv: Signature made Thu Feb 1 11:28:39 2024 UTC 349s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 349s gpgv: issuer "tille@debian.org" 349s gpgv: Can't check signature: No public key 349s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-2.dsc: no acceptable signature found 349s autopkgtest [15:22:08]: testing package ariba version 2.14.7+ds-2 350s autopkgtest [15:22:09]: build not needed 352s autopkgtest [15:22:11]: test test-example: preparing testbed 354s Reading package lists... 354s Building dependency tree... 354s Reading state information... 354s Starting pkgProblemResolver with broken count: 0 354s Starting 2 pkgProblemResolver with broken count: 0 354s Done 354s The following additional packages will be installed: 354s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 354s fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 354s libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 354s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 354s libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 354s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 354s libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 354s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 354s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 354s mummer python-matplotlib-data python3-appdirs python3-biopython 354s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 354s python3-dateutil python3-decorator python3-dendropy python3-fonttools 354s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 354s python3-matplotlib python3-mpmath python3-numpy python3-packaging 354s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 354s python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve 354s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 samtools 354s sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 354s xfonts-utils xml-core 354s Suggested packages: 354s spades blt-demo bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf 354s fonts-texgyre gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 354s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 354s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 354s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee 354s wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 354s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 354s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 354s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 354s python3-gmpy2 gcc gfortran python3-dev python3-pytest python-pil-doc 354s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 354s rl-renderpm python-scipy-doc texlive-fonts-extra python-sympy-doc tix 354s python3-tk-dbg cwltool sgml-base-doc debhelper 354s Recommended packages: 354s javascript-common python-biopython-doc ncbi-blast+ python3-cssselect 354s python3-html5lib python3-olefile g++ | c++-compiler isympy-common 354s The following NEW packages will be installed: 354s ariba autopkgtest-satdep blt bowtie2 cd-hit fastaq fontconfig-config 354s fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lyx 354s fonts-urw-base35 libblas3 libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 354s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 354s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 354s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 354s liblcms2-2 liblerc4 libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 354s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 354s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 354s libxslt1.1 libxss1 mash mummer python-matplotlib-data python3-appdirs 354s python3-biopython python3-brotli python3-bs4 python3-cairo python3-contourpy 354s python3-cycler python3-dateutil python3-decorator python3-dendropy 354s python3-fonttools python3-freetype python3-fs python3-kiwisolver 354s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 354s python3-packaging python3-pil python3-pil.imagetk python3-pymummer 354s python3-pysam python3-reportlab python3-rlpycairo python3-scipy 354s python3-soupsieve python3-sympy python3-tk python3-ufolib2 354s python3-unicodedata2 samtools sgml-base tk8.6-blt2.5 unicode-data 354s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 354s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 354s Need to get 101 MB/101 MB of archives. 354s After this operation, 478 MB of additional disk space will be used. 354s Get:1 /tmp/autopkgtest.madvJg/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 354s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-base all 1.31 [11.4 kB] 354s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 355s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 355s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 355s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 355s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el fastaq all 3.17.0-6 [47.9 kB] 355s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 355s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 355s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 355s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 355s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 355s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 355s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 355s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontenc1 ppc64el 1:1.1.8-1 [15.7 kB] 355s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 355s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 355s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-utils ppc64el 1:7.7+6build2 [112 kB] 355s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 355s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 355s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 355s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 355s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 355s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 355s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 355s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7 [778 kB] 355s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el blt ppc64el 2.5.3+dfsg-7 [4832 B] 355s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-tk ppc64el 3.11.5-1 [116 kB] 356s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pil.imagetk ppc64el 10.2.0-1 [10.1 kB] 356s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 356s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libimagequant0 ppc64el 2.18.0-1 [42.5 kB] 356s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 356s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 356s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 356s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libopenjp2-7 ppc64el 2.5.0-2 [233 kB] 356s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 356s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 356s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libraqm0 ppc64el 0.10.1-1 [18.9 kB] 356s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 356s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 356s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 356s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 356s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 356s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpdemux2 ppc64el 1.3.2-0.4 [14.4 kB] 356s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpmux3 ppc64el 1.3.2-0.4 [31.2 kB] 356s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-pil ppc64el 10.2.0-1 [526 kB] 356s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 356s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 356s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 356s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 356s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-cairo ppc64el 1.25.1-2 [162 kB] 356s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-freetype all 2.4.0-1 [83.1 kB] 356s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 356s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-extra all 2.37-8 [1947 kB] 356s Get:55 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-reportlab all 4.1.0-1 [683 kB] 356s Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB] 356s Get:57 http://ftpmaster.internal/ubuntu noble/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 356s Get:58 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-biopython ppc64el 1.81+dfsg-3 [1738 kB] 356s Get:59 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-soupsieve all 2.5-1 [33.0 kB] 356s Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-bs4 all 4.12.3-1 [109 kB] 356s Get:61 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-dendropy all 4.6.1-1 [278 kB] 356s Get:62 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 356s Get:63 http://ftpmaster.internal/ubuntu noble/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 356s Get:64 http://ftpmaster.internal/ubuntu noble/universe ppc64el fonts-lyx all 2.4.0~RC3-1 [170 kB] 356s Get:65 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 356s Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 356s Get:67 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-contourpy ppc64el 1.0.7-1build2 [300 kB] 356s Get:68 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-cycler all 0.11.0-2 [8202 B] 356s Get:69 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-brotli ppc64el 1.1.0-2 [420 kB] 356s Get:70 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 356s Get:71 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 356s Get:72 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 357s Get:73 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 357s Get:74 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-mpmath all 1.2.1-3 [421 kB] 357s Get:75 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-sympy all 1.12-7 [3966 kB] 357s Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 357s Get:77 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-fs all 2.4.16-3 [91.1 kB] 357s Get:78 http://ftpmaster.internal/ubuntu noble/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1 [192 kB] 357s Get:79 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-lxml ppc64el 5.1.0-1 [2191 kB] 357s Get:80 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build2 [28.8 kB] 357s Get:81 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1 [368 kB] 357s Get:82 http://ftpmaster.internal/ubuntu noble/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 357s Get:83 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-fonttools ppc64el 4.46.0-1 [1746 kB] 357s Get:84 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-kiwisolver ppc64el 1.4.4-2 [55.8 kB] 357s Get:85 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB] 357s Get:86 http://ftpmaster.internal/ubuntu noble/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6 [220 kB] 357s Get:87 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-matplotlib ppc64el 3.6.3-1ubuntu3 [7651 kB] 357s Get:88 http://ftpmaster.internal/ubuntu noble/universe ppc64el mummer ppc64el 3.23+dfsg-8 [714 kB] 357s Get:89 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pymummer all 0.11.0-4 [17.1 kB] 357s Get:90 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 357s Get:91 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfml0 ppc64el 0.1+git20190320.b499514-1 [79.9 kB] 357s Get:92 http://ftpmaster.internal/ubuntu noble/universe ppc64el libminimap0 ppc64el 0.2-8 [26.3 kB] 357s Get:93 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie2 ppc64el 2.5.2-1 [1367 kB] 357s Get:94 http://ftpmaster.internal/ubuntu noble/universe ppc64el cd-hit ppc64el 4.8.1-4 [547 kB] 357s Get:95 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcapnp-1.0.1 ppc64el 1.0.1-3 [1544 kB] 357s Get:96 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 357s Get:97 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 357s Get:98 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmurmurhash2 ppc64el 1.6-1 [6626 B] 357s Get:99 http://ftpmaster.internal/ubuntu noble/universe ppc64el mash ppc64el 2.3+dfsg-6 [159 kB] 357s Get:100 http://ftpmaster.internal/ubuntu noble/universe ppc64el ariba ppc64el 2.14.7+ds-2 [2050 kB] 358s Fetched 101 MB in 3s (30.6 MB/s) 358s Selecting previously unselected package sgml-base. 358s (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.) 358s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 358s Unpacking sgml-base (1.31) ... 358s Selecting previously unselected package libdeflate0:ppc64el. 358s Preparing to unpack .../01-libdeflate0_1.19-1_ppc64el.deb ... 358s Unpacking libdeflate0:ppc64el (1.19-1) ... 358s Selecting previously unselected package libhtscodecs2:ppc64el. 358s Preparing to unpack .../02-libhtscodecs2_1.6.0-1_ppc64el.deb ... 358s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 358s Selecting previously unselected package libhts3:ppc64el. 358s Preparing to unpack .../03-libhts3_1.18+ds-1_ppc64el.deb ... 358s Unpacking libhts3:ppc64el (1.18+ds-1) ... 358s Selecting previously unselected package samtools. 358s Preparing to unpack .../04-samtools_1.19.2-1_ppc64el.deb ... 358s Unpacking samtools (1.19.2-1) ... 358s Selecting previously unselected package fastaq. 358s Preparing to unpack .../05-fastaq_3.17.0-6_all.deb ... 358s Unpacking fastaq (3.17.0-6) ... 358s Selecting previously unselected package libblas3:ppc64el. 358s Preparing to unpack .../06-libblas3_3.12.0-3_ppc64el.deb ... 358s Unpacking libblas3:ppc64el (3.12.0-3) ... 358s Selecting previously unselected package libgfortran5:ppc64el. 358s Preparing to unpack .../07-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 358s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 358s Selecting previously unselected package liblapack3:ppc64el. 358s Preparing to unpack .../08-liblapack3_3.12.0-3_ppc64el.deb ... 358s Unpacking liblapack3:ppc64el (3.12.0-3) ... 358s Selecting previously unselected package python3-numpy. 358s Preparing to unpack .../09-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 358s Unpacking python3-numpy (1:1.24.2-2) ... 359s Selecting previously unselected package libtcl8.6:ppc64el. 359s Preparing to unpack .../10-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 359s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 359s Selecting previously unselected package fonts-dejavu-mono. 359s Preparing to unpack .../11-fonts-dejavu-mono_2.37-8_all.deb ... 359s Unpacking fonts-dejavu-mono (2.37-8) ... 359s Selecting previously unselected package fonts-dejavu-core. 359s Preparing to unpack .../12-fonts-dejavu-core_2.37-8_all.deb ... 359s Unpacking fonts-dejavu-core (2.37-8) ... 359s Selecting previously unselected package libfontenc1:ppc64el. 359s Preparing to unpack .../13-libfontenc1_1%3a1.1.8-1_ppc64el.deb ... 359s Unpacking libfontenc1:ppc64el (1:1.1.8-1) ... 359s Selecting previously unselected package x11-common. 359s Preparing to unpack .../14-x11-common_1%3a7.7+23ubuntu2_all.deb ... 359s Unpacking x11-common (1:7.7+23ubuntu2) ... 359s Selecting previously unselected package xfonts-encodings. 359s Preparing to unpack .../15-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 359s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 359s Selecting previously unselected package xfonts-utils. 359s Preparing to unpack .../16-xfonts-utils_1%3a7.7+6build2_ppc64el.deb ... 359s Unpacking xfonts-utils (1:7.7+6build2) ... 359s Selecting previously unselected package fonts-urw-base35. 359s Preparing to unpack .../17-fonts-urw-base35_20200910-8_all.deb ... 359s Unpacking fonts-urw-base35 (20200910-8) ... 359s Selecting previously unselected package fontconfig-config. 359s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 359s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 359s Selecting previously unselected package libfontconfig1:ppc64el. 359s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 359s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 359s Selecting previously unselected package libxrender1:ppc64el. 359s Preparing to unpack .../20-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 359s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 359s Selecting previously unselected package libxft2:ppc64el. 359s Preparing to unpack .../21-libxft2_2.3.6-1_ppc64el.deb ... 359s Unpacking libxft2:ppc64el (2.3.6-1) ... 359s Selecting previously unselected package libxss1:ppc64el. 359s Preparing to unpack .../22-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 359s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 359s Selecting previously unselected package libtk8.6:ppc64el. 359s Preparing to unpack .../23-libtk8.6_8.6.14-1_ppc64el.deb ... 359s Unpacking libtk8.6:ppc64el (8.6.14-1) ... 359s Selecting previously unselected package tk8.6-blt2.5. 359s Preparing to unpack .../24-tk8.6-blt2.5_2.5.3+dfsg-7_ppc64el.deb ... 359s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... 359s Selecting previously unselected package blt. 359s Preparing to unpack .../25-blt_2.5.3+dfsg-7_ppc64el.deb ... 359s Unpacking blt (2.5.3+dfsg-7) ... 359s Selecting previously unselected package python3-tk:ppc64el. 359s Preparing to unpack .../26-python3-tk_3.11.5-1_ppc64el.deb ... 359s Unpacking python3-tk:ppc64el (3.11.5-1) ... 359s Selecting previously unselected package python3-pil.imagetk:ppc64el. 359s Preparing to unpack .../27-python3-pil.imagetk_10.2.0-1_ppc64el.deb ... 359s Unpacking python3-pil.imagetk:ppc64el (10.2.0-1) ... 359s Selecting previously unselected package libgomp1:ppc64el. 359s Preparing to unpack .../28-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 359s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 359s Selecting previously unselected package libimagequant0:ppc64el. 359s Preparing to unpack .../29-libimagequant0_2.18.0-1_ppc64el.deb ... 359s Unpacking libimagequant0:ppc64el (2.18.0-1) ... 359s Selecting previously unselected package libjpeg-turbo8:ppc64el. 359s Preparing to unpack .../30-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 359s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 359s Selecting previously unselected package libjpeg8:ppc64el. 359s Preparing to unpack .../31-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 359s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 359s Selecting previously unselected package liblcms2-2:ppc64el. 359s Preparing to unpack .../32-liblcms2-2_2.14-2_ppc64el.deb ... 359s Unpacking liblcms2-2:ppc64el (2.14-2) ... 359s Selecting previously unselected package libopenjp2-7:ppc64el. 359s Preparing to unpack .../33-libopenjp2-7_2.5.0-2_ppc64el.deb ... 359s Unpacking libopenjp2-7:ppc64el (2.5.0-2) ... 359s Selecting previously unselected package libgraphite2-3:ppc64el. 359s Preparing to unpack .../34-libgraphite2-3_1.3.14-2_ppc64el.deb ... 359s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 359s Selecting previously unselected package libharfbuzz0b:ppc64el. 359s Preparing to unpack .../35-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 359s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 359s Selecting previously unselected package libraqm0:ppc64el. 359s Preparing to unpack .../36-libraqm0_0.10.1-1_ppc64el.deb ... 359s Unpacking libraqm0:ppc64el (0.10.1-1) ... 360s Selecting previously unselected package libjbig0:ppc64el. 360s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 360s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 360s Selecting previously unselected package liblerc4:ppc64el. 360s Preparing to unpack .../38-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 360s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 360s Selecting previously unselected package libsharpyuv0:ppc64el. 360s Preparing to unpack .../39-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 360s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 360s Selecting previously unselected package libwebp7:ppc64el. 360s Preparing to unpack .../40-libwebp7_1.3.2-0.4_ppc64el.deb ... 360s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 360s Selecting previously unselected package libtiff6:ppc64el. 360s Preparing to unpack .../41-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 360s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 360s Selecting previously unselected package libwebpdemux2:ppc64el. 360s Preparing to unpack .../42-libwebpdemux2_1.3.2-0.4_ppc64el.deb ... 360s Unpacking libwebpdemux2:ppc64el (1.3.2-0.4) ... 360s Selecting previously unselected package libwebpmux3:ppc64el. 360s Preparing to unpack .../43-libwebpmux3_1.3.2-0.4_ppc64el.deb ... 360s Unpacking libwebpmux3:ppc64el (1.3.2-0.4) ... 360s Selecting previously unselected package python3-pil:ppc64el. 360s Preparing to unpack .../44-python3-pil_10.2.0-1_ppc64el.deb ... 360s Unpacking python3-pil:ppc64el (10.2.0-1) ... 360s Selecting previously unselected package libpixman-1-0:ppc64el. 360s Preparing to unpack .../45-libpixman-1-0_0.42.2-1_ppc64el.deb ... 360s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 360s Selecting previously unselected package libxcb-render0:ppc64el. 360s Preparing to unpack .../46-libxcb-render0_1.15-1_ppc64el.deb ... 360s Unpacking libxcb-render0:ppc64el (1.15-1) ... 360s Selecting previously unselected package libxcb-shm0:ppc64el. 360s Preparing to unpack .../47-libxcb-shm0_1.15-1_ppc64el.deb ... 360s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 360s Selecting previously unselected package libcairo2:ppc64el. 360s Preparing to unpack .../48-libcairo2_1.18.0-1_ppc64el.deb ... 360s Unpacking libcairo2:ppc64el (1.18.0-1) ... 360s Selecting previously unselected package python3-cairo. 360s Preparing to unpack .../49-python3-cairo_1.25.1-2_ppc64el.deb ... 360s Unpacking python3-cairo (1.25.1-2) ... 360s Selecting previously unselected package python3-freetype. 360s Preparing to unpack .../50-python3-freetype_2.4.0-1_all.deb ... 360s Unpacking python3-freetype (2.4.0-1) ... 360s Selecting previously unselected package python3-rlpycairo. 360s Preparing to unpack .../51-python3-rlpycairo_0.3.0-3_all.deb ... 360s Unpacking python3-rlpycairo (0.3.0-3) ... 360s Selecting previously unselected package fonts-dejavu-extra. 360s Preparing to unpack .../52-fonts-dejavu-extra_2.37-8_all.deb ... 360s Unpacking fonts-dejavu-extra (2.37-8) ... 360s Selecting previously unselected package python3-reportlab. 360s Preparing to unpack .../53-python3-reportlab_4.1.0-1_all.deb ... 360s Unpacking python3-reportlab (4.1.0-1) ... 360s Selecting previously unselected package xml-core. 360s Preparing to unpack .../54-xml-core_0.19_all.deb ... 360s Unpacking xml-core (0.19) ... 360s Selecting previously unselected package w3c-sgml-lib. 360s Preparing to unpack .../55-w3c-sgml-lib_1.3-3_all.deb ... 360s Unpacking w3c-sgml-lib (1.3-3) ... 360s Selecting previously unselected package python3-biopython. 360s Preparing to unpack .../56-python3-biopython_1.81+dfsg-3_ppc64el.deb ... 360s Unpacking python3-biopython (1.81+dfsg-3) ... 360s Selecting previously unselected package python3-soupsieve. 360s Preparing to unpack .../57-python3-soupsieve_2.5-1_all.deb ... 360s Unpacking python3-soupsieve (2.5-1) ... 360s Selecting previously unselected package python3-bs4. 360s Preparing to unpack .../58-python3-bs4_4.12.3-1_all.deb ... 360s Unpacking python3-bs4 (4.12.3-1) ... 360s Selecting previously unselected package python3-dendropy. 360s Preparing to unpack .../59-python3-dendropy_4.6.1-1_all.deb ... 360s Unpacking python3-dendropy (4.6.1-1) ... 360s Selecting previously unselected package libjs-jquery. 360s Preparing to unpack .../60-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 360s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 360s Selecting previously unselected package libjs-jquery-ui. 360s Preparing to unpack .../61-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 360s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 360s Selecting previously unselected package fonts-lyx. 360s Preparing to unpack .../62-fonts-lyx_2.4.0~RC3-1_all.deb ... 360s Unpacking fonts-lyx (2.4.0~RC3-1) ... 360s Selecting previously unselected package python-matplotlib-data. 360s Preparing to unpack .../63-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ... 360s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ... 361s Selecting previously unselected package python3-dateutil. 361s Preparing to unpack .../64-python3-dateutil_2.8.2-3_all.deb ... 361s Unpacking python3-dateutil (2.8.2-3) ... 361s Selecting previously unselected package python3-contourpy. 361s Preparing to unpack .../65-python3-contourpy_1.0.7-1build2_ppc64el.deb ... 361s Unpacking python3-contourpy (1.0.7-1build2) ... 361s Selecting previously unselected package python3-cycler. 361s Preparing to unpack .../66-python3-cycler_0.11.0-2_all.deb ... 361s Unpacking python3-cycler (0.11.0-2) ... 361s Selecting previously unselected package python3-brotli. 361s Preparing to unpack .../67-python3-brotli_1.1.0-2_ppc64el.deb ... 361s Unpacking python3-brotli (1.1.0-2) ... 361s Selecting previously unselected package python3-decorator. 361s Preparing to unpack .../68-python3-decorator_5.1.1-5_all.deb ... 361s Unpacking python3-decorator (5.1.1-5) ... 361s Selecting previously unselected package liblbfgsb0:ppc64el. 361s Preparing to unpack .../69-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 361s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 361s Selecting previously unselected package python3-scipy. 361s Preparing to unpack .../70-python3-scipy_1.11.4-6_ppc64el.deb ... 361s Unpacking python3-scipy (1.11.4-6) ... 361s Selecting previously unselected package python3-ufolib2. 361s Preparing to unpack .../71-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 361s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 362s Selecting previously unselected package python3-mpmath. 362s Preparing to unpack .../72-python3-mpmath_1.2.1-3_all.deb ... 362s Unpacking python3-mpmath (1.2.1-3) ... 362s Selecting previously unselected package python3-sympy. 362s Preparing to unpack .../73-python3-sympy_1.12-7_all.deb ... 362s Unpacking python3-sympy (1.12-7) ... 362s Selecting previously unselected package python3-appdirs. 362s Preparing to unpack .../74-python3-appdirs_1.4.4-4_all.deb ... 362s Unpacking python3-appdirs (1.4.4-4) ... 362s Selecting previously unselected package python3-fs. 362s Preparing to unpack .../75-python3-fs_2.4.16-3_all.deb ... 362s Unpacking python3-fs (2.4.16-3) ... 362s Selecting previously unselected package libxslt1.1:ppc64el. 362s Preparing to unpack .../76-libxslt1.1_1.1.39-0exp1_ppc64el.deb ... 362s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1) ... 362s Selecting previously unselected package python3-lxml:ppc64el. 362s Preparing to unpack .../77-python3-lxml_5.1.0-1_ppc64el.deb ... 362s Unpacking python3-lxml:ppc64el (5.1.0-1) ... 362s Selecting previously unselected package python3-lz4. 362s Preparing to unpack .../78-python3-lz4_4.0.2+dfsg-1build2_ppc64el.deb ... 362s Unpacking python3-lz4 (4.0.2+dfsg-1build2) ... 362s Selecting previously unselected package python3-unicodedata2. 362s Preparing to unpack .../79-python3-unicodedata2_15.1.0+ds-1_ppc64el.deb ... 362s Unpacking python3-unicodedata2 (15.1.0+ds-1) ... 362s Selecting previously unselected package unicode-data. 362s Preparing to unpack .../80-unicode-data_15.1.0-1_all.deb ... 362s Unpacking unicode-data (15.1.0-1) ... 362s Selecting previously unselected package python3-fonttools. 362s Preparing to unpack .../81-python3-fonttools_4.46.0-1_ppc64el.deb ... 362s Unpacking python3-fonttools (4.46.0-1) ... 362s Selecting previously unselected package python3-kiwisolver. 362s Preparing to unpack .../82-python3-kiwisolver_1.4.4-2_ppc64el.deb ... 362s Unpacking python3-kiwisolver (1.4.4-2) ... 363s Selecting previously unselected package python3-packaging. 363s Preparing to unpack .../83-python3-packaging_23.2-1_all.deb ... 363s Unpacking python3-packaging (23.2-1) ... 363s Selecting previously unselected package libqhull-r8.0:ppc64el. 363s Preparing to unpack .../84-libqhull-r8.0_2020.2-6_ppc64el.deb ... 363s Unpacking libqhull-r8.0:ppc64el (2020.2-6) ... 363s Selecting previously unselected package python3-matplotlib. 363s Preparing to unpack .../85-python3-matplotlib_3.6.3-1ubuntu3_ppc64el.deb ... 363s Unpacking python3-matplotlib (3.6.3-1ubuntu3) ... 363s Selecting previously unselected package mummer. 363s Preparing to unpack .../86-mummer_3.23+dfsg-8_ppc64el.deb ... 363s Unpacking mummer (3.23+dfsg-8) ... 363s Selecting previously unselected package python3-pymummer. 363s Preparing to unpack .../87-python3-pymummer_0.11.0-4_all.deb ... 363s Unpacking python3-pymummer (0.11.0-4) ... 363s Selecting previously unselected package python3-pysam. 363s Preparing to unpack .../88-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 363s Unpacking python3-pysam (0.22.0+ds-1) ... 363s Selecting previously unselected package libfml0:ppc64el. 363s Preparing to unpack .../89-libfml0_0.1+git20190320.b499514-1_ppc64el.deb ... 363s Unpacking libfml0:ppc64el (0.1+git20190320.b499514-1) ... 363s Selecting previously unselected package libminimap0:ppc64el. 363s Preparing to unpack .../90-libminimap0_0.2-8_ppc64el.deb ... 363s Unpacking libminimap0:ppc64el (0.2-8) ... 363s Selecting previously unselected package bowtie2. 363s Preparing to unpack .../91-bowtie2_2.5.2-1_ppc64el.deb ... 363s Unpacking bowtie2 (2.5.2-1) ... 363s Selecting previously unselected package cd-hit. 363s Preparing to unpack .../92-cd-hit_4.8.1-4_ppc64el.deb ... 363s Unpacking cd-hit (4.8.1-4) ... 363s Selecting previously unselected package libcapnp-1.0.1:ppc64el. 363s Preparing to unpack .../93-libcapnp-1.0.1_1.0.1-3_ppc64el.deb ... 363s Unpacking libcapnp-1.0.1:ppc64el (1.0.1-3) ... 363s Selecting previously unselected package libgslcblas0:ppc64el. 363s Preparing to unpack .../94-libgslcblas0_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 363s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 363s Selecting previously unselected package libgsl27:ppc64el. 363s Preparing to unpack .../95-libgsl27_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 363s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 363s Selecting previously unselected package libmurmurhash2:ppc64el. 363s Preparing to unpack .../96-libmurmurhash2_1.6-1_ppc64el.deb ... 363s Unpacking libmurmurhash2:ppc64el (1.6-1) ... 363s Selecting previously unselected package mash. 363s Preparing to unpack .../97-mash_2.3+dfsg-6_ppc64el.deb ... 363s Unpacking mash (2.3+dfsg-6) ... 363s Selecting previously unselected package ariba. 363s Preparing to unpack .../98-ariba_2.14.7+ds-2_ppc64el.deb ... 363s Unpacking ariba (2.14.7+ds-2) ... 364s Selecting previously unselected package autopkgtest-satdep. 364s Preparing to unpack .../99-1-autopkgtest-satdep.deb ... 364s Unpacking autopkgtest-satdep (0) ... 364s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 364s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 364s Setting up liblcms2-2:ppc64el (2.14-2) ... 364s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 364s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 364s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 364s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 364s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 364s Setting up libmurmurhash2:ppc64el (1.6-1) ... 364s Setting up libcapnp-1.0.1:ppc64el (1.0.1-3) ... 364s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 364s Setting up libxcb-render0:ppc64el (1.15-1) ... 364s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 364s Setting up fonts-lyx (2.4.0~RC3-1) ... 364s Setting up x11-common (1:7.7+23ubuntu2) ... 364s Setting up libdeflate0:ppc64el (1.19-1) ... 364s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 364s Setting up libqhull-r8.0:ppc64el (2020.2-6) ... 364s Setting up libxcb-shm0:ppc64el (1.15-1) ... 364s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 364s Setting up python3-freetype (2.4.0-1) ... 364s Setting up libfml0:ppc64el (0.1+git20190320.b499514-1) ... 364s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 364s Setting up bowtie2 (2.5.2-1) ... 364s Setting up unicode-data (15.1.0-1) ... 364s Setting up python3-decorator (5.1.1-5) ... 365s Setting up libminimap0:ppc64el (0.2-8) ... 365s Setting up libfontenc1:ppc64el (1:1.1.8-1) ... 365s Setting up libblas3:ppc64el (3.12.0-3) ... 365s 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 365s Setting up python3-packaging (23.2-1) ... 365s Setting up python3-brotli (1.1.0-2) ... 365s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 365s Setting up python3-cycler (0.11.0-2) ... 365s Setting up libimagequant0:ppc64el (2.18.0-1) ... 365s Setting up fonts-dejavu-mono (2.37-8) ... 365s Setting up python3-kiwisolver (1.4.4-2) ... 365s Setting up mash (2.3+dfsg-6) ... 365s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 365s Setting up fonts-dejavu-core (2.37-8) ... 365s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 365s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 365s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 365s Setting up fonts-dejavu-extra (2.37-8) ... 365s Setting up libxslt1.1:ppc64el (1.1.39-0exp1) ... 365s Setting up mummer (3.23+dfsg-8) ... 365s Setting up libopenjp2-7:ppc64el (2.5.0-2) ... 365s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 365s Setting up python3-dateutil (2.8.2-3) ... 365s Setting up sgml-base (1.31) ... 365s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 365s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 365s Setting up python3-mpmath (1.2.1-3) ... 366s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 366s Setting up libwebpmux3:ppc64el (1.3.2-0.4) ... 366s Setting up python3-dendropy (4.6.1-1) ... 366s Setting up python3-appdirs (1.4.4-4) ... 366s Setting up python3-soupsieve (2.5-1) ... 366s Setting up cd-hit (4.8.1-4) ... 366s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 366s Setting up python3-sympy (1.12-7) ... 372s Setting up liblapack3:ppc64el (3.12.0-3) ... 372s 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 372s Setting up libhts3:ppc64el (1.18+ds-1) ... 372s Setting up python3-pysam (0.22.0+ds-1) ... 372s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 372s Setting up libwebpdemux2:ppc64el (1.3.2-0.4) ... 372s Setting up xfonts-utils (1:7.7+6build2) ... 372s Setting up python3-bs4 (4.12.3-1) ... 373s Setting up samtools (1.19.2-1) ... 373s Setting up python3-fs (2.4.16-3) ... 373s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 373s Setting up libraqm0:ppc64el (0.10.1-1) ... 373s Setting up python3-numpy (1:1.24.2-2) ... 375s Setting up python3-lxml:ppc64el (5.1.0-1) ... 375s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 375s Setting up xml-core (0.19) ... 375s Setting up python3-contourpy (1.0.7-1build2) ... 375s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 375s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 375s Setting up libxft2:ppc64el (2.3.6-1) ... 375s Setting up python3-scipy (1.11.4-6) ... 379s Setting up libtk8.6:ppc64el (8.6.14-1) ... 379s Setting up fastaq (3.17.0-6) ... 379s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 379s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 379s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 379s gbk_regex = re.compile('^LOCUS\s+\S') 379s Setting up fonts-urw-base35 (20200910-8) ... 379s Setting up libcairo2:ppc64el (1.18.0-1) ... 379s Setting up python3-pymummer (0.11.0-4) ... 379s Setting up python3-pil:ppc64el (10.2.0-1) ... 379s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 379s Setting up python3-cairo (1.25.1-2) ... 379s Setting up blt (2.5.3+dfsg-7) ... 379s Setting up python3-tk:ppc64el (3.11.5-1) ... 380s Setting up python3-pil.imagetk:ppc64el (10.2.0-1) ... 380s Setting up python3-rlpycairo (0.3.0-3) ... 380s Setting up python3-reportlab (4.1.0-1) ... 381s Setting up python3-fonttools (4.46.0-1) ... 382s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 382s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 383s Processing triggers for libc-bin (2.39-0ubuntu6) ... 383s Processing triggers for man-db (2.12.0-3) ... 384s Processing triggers for sgml-base (1.31) ... 384s Setting up w3c-sgml-lib (1.3-3) ... 411s Setting up python3-biopython (1.81+dfsg-3) ... 413s Setting up ariba (2.14.7+ds-2) ... 413s /usr/lib/python3/dist-packages/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.' 413s 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), 413s /usr/lib/python3/dist-packages/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.' 413s 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), 413s /usr/lib/python3/dist-packages/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.' 413s 'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)')) 413s Setting up autopkgtest-satdep (0) ... 416s (Reading database ... 80399 files and directories currently installed.) 416s Removing autopkgtest-satdep (0) ... 417s autopkgtest [15:23:16]: test test-example: [----------------------- 419s ARIBA version: 2.14.6 419s 419s External dependencies: 419s bowtie2 2.5.2 /usr/bin/bowtie2 419s cdhit 4.8.1 /usr/bin/cd-hit-est 419s nucmer 3.1 /usr/bin/nucmer 419s 419s External dependencies OK: True 419s 419s Python version: 419s 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 419s 419s Python packages: 419s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 419s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 419s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 419s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 419s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 419s pysam 0.22.0 /usr/lib/python3/dist-packages/pysam/__init__.py 419s 419s Python packages OK: True 419s 419s Everything looks OK: True 419s 419s Loading and checking input data 419s 419s Running cdhit 420s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.0F0XctEldr/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.0F0XctEldr/foo/tmp.run_cd-hit.249szmah/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 420s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.0F0XctEldr/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.0F0XctEldr/foo/tmp.run_cd-hit.k6zdjiha/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 420s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.0F0XctEldr/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.0F0XctEldr/foo/tmp.run_cd-hit.o4d1b3xn/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 420s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.0F0XctEldr/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.0F0XctEldr/foo/tmp.run_cd-hit.mksnb19g/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 420s 420s Writing clusters to file. 10 in total 421s Found reads file: reads_1.fq 421s Found reads file: reads_2.fq 421s ARIBA version: 2.14.6 421s 421s External dependencies: 421s bowtie2 2.5.2 /usr/bin/bowtie2 421s cdhit 4.8.1 /usr/bin/cd-hit-est 421s nucmer 3.1 /usr/bin/nucmer 421s 421s External dependencies OK: True 421s 421s Python version: 421s 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 421s 421s Python packages: 421s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 421s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 421s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 421s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 421s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 421s pysam 0.22.0 /usr/lib/python3/dist-packages/pysam/__init__.py 421s 421s Python packages OK: True 421s 421s Everything looks OK: True 421s Temporary directory: /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_ 421s ______________________ Mapping reads to clustered genes _______________________ 421s Finished mapping 421s 421s _____________________________ Generating clusters _____________________________ 421s syscall: sort -k1,1 -k 2,2n /tmp/tmp.0F0XctEldr/foo/OUT/minimap.reads > /tmp/tmp.0F0XctEldr/foo/OUT/read_store 421s Compressing file /tmp/tmp.0F0XctEldr/foo/OUT/read_store 421s Found 51 proper read pairs from minimap 421s Total clusters to perform local assemblies: 9 421s 421s Insert size information from reads mapped to reference genes: 421s Insert size: 185.0 421s Insert sspace sd: 0.27 421s Max insert: 220.55 421s 421s ___________________________ Assembling each cluster ___________________________ 421s Will run 1 cluster(s) in parallel 421s Not constructing cluster cluster because it only has 2 reads (1 of 9) 421s Constructing cluster cluster_1 (2 of 9) 421s Constructing cluster cluster_2 (3 of 9) 421s Constructing cluster cluster_3 (4 of 9) 421s Constructing cluster cluster_4 (5 of 9) 421s Constructing cluster gene (6 of 9) 421s Constructing cluster gene_1 (7 of 9) 421s Constructing cluster noncoding (8 of 9) 421s Constructing cluster noncoding_1 (9 of 9) 421s Start running cluster cluster_1 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_1 423s cluster_1 detected 1 threads available to it 423s cluster_1 reported completion 423s Finished running cluster cluster_1 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_1 423s Deleting cluster dir /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_1 423s Start running cluster cluster_2 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_2 425s cluster_2 detected 1 threads available to it 425s cluster_2 reported completion 425s Finished running cluster cluster_2 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_2 425s Deleting cluster dir /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_2 425s Start running cluster cluster_3 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_3 428s cluster_3 detected 1 threads available to it 428s cluster_3 reported completion 428s Finished running cluster cluster_3 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_3 428s Deleting cluster dir /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_3 428s Start running cluster cluster_4 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_4 430s cluster_4 detected 1 threads available to it 430s cluster_4 reported completion 430s Finished running cluster cluster_4 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_4 430s Deleting cluster dir /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/cluster_4 430s Start running cluster gene in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/gene 432s gene detected 1 threads available to it 432s gene reported completion 432s Finished running cluster gene in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/gene 432s Deleting cluster dir /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/gene 432s Start running cluster gene_1 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/gene_1 435s gene_1 detected 1 threads available to it 435s gene_1 reported completion 435s Finished running cluster gene_1 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/gene_1 435s Deleting cluster dir /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/gene_1 435s Start running cluster noncoding in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/noncoding 437s noncoding detected 1 threads available to it 437s noncoding reported completion 437s Finished running cluster noncoding in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/noncoding 437s Deleting cluster dir /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/noncoding 437s Start running cluster noncoding_1 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/noncoding_1 439s noncoding_1 detected 1 threads available to it 439s noncoding_1 reported completion 439s Finished running cluster noncoding_1 in directory /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/noncoding_1 439s Deleting cluster dir /tmp/tmp.0F0XctEldr/foo/OUT/ariba.tmp.2u79mib_/noncoding_1 439s Final value of remaining_clusters counter: Value('l', 0) 439s Finished assembling clusters 439s 439s _______________________________ Writing reports _______________________________ 439s Making /tmp/tmp.0F0XctEldr/foo/OUT/debug.report.tsv 439s Making /tmp/tmp.0F0XctEldr/foo/OUT/report.tsv 439s 439s ____________________ Writing fasta of assembled sequences _____________________ 439s /tmp/tmp.0F0XctEldr/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.0F0XctEldr/foo/OUT/assembled_genes.fa.gz 439s 439s __________________________ Catting cluster log files __________________________ 439s Writing file /tmp/tmp.0F0XctEldr/foo/OUT/log.clusters.gz 439s 439s _______________________________ Cleaning files ________________________________ 439s Deleting Logs directory /tmp/tmp.0F0XctEldr/foo/OUT/Logs 439s Deleting reads store files /tmp/tmp.0F0XctEldr/foo/OUT/read_store.gz[.tbi] 439s 439s All done! 439s 439s Running ARIBA on test data... 439s ------------------------------------------------------------------------------- 439s |=============================================================================| 439s | Preparing input data | 439s |=============================================================================| 439s ------------------------------------------------------------------------------- 439s Made output directory ./foo. Copying test data files into it: 439s copied ref_seqs.fa 439s copied metadata.tsv 439s copied reads_1.fq 439s copied reads_2.fq 439s ------------------------------------------------------------------------------- 439s |=============================================================================| 439s | Try running ariba prepareref | 439s |=============================================================================| 439s ------------------------------------------------------------------------------- 439s 439s Running ariba prepareref with: 439s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 439s 439s 439s ariba prepareref finished OK 439s ------------------------------------------------------------------------------- 439s |=============================================================================| 439s | Try running ariba run | 439s |=============================================================================| 439s ------------------------------------------------------------------------------- 439s 439s Running ARIBA with: 439s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 439s 439s 439s ariba run finished OK 439s Finished run on test data OK 440s autopkgtest [15:23:39]: test test-example: -----------------------] 440s autopkgtest [15:23:39]: test test-example: - - - - - - - - - - results - - - - - - - - - - 440s test-example PASS 441s autopkgtest [15:23:40]: @@@@@@@@@@@@@@@@@@@@ summary 441s test-example PASS 455s Creating nova instance adt-noble-ppc64el-ariba-20240323-151618-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...