0s autopkgtest [16:44:41]: starting date and time: 2024-03-24 16:44:41+0000 0s autopkgtest [16:44:41]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:44:41]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wjr5i5yf/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@bos03-arm64-6.secgroup --name adt-noble-arm64-ariba-20240324-164441-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 129s autopkgtest [16:46:50]: testbed dpkg architecture: arm64 129s autopkgtest [16:46:50]: testbed apt version: 2.7.12 129s autopkgtest [16:46:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 130s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 130s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 131s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 131s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 131s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 131s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 131s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 131s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 131s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 131s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 131s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 131s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 131s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 133s Fetched 9847 kB in 2s (4800 kB/s) 133s Reading package lists... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Calculating upgrade... 138s The following packages will be REMOVED: 138s libssl3 138s The following NEW packages will be installed: 138s libssl3t64 138s The following packages have been kept back: 138s curl 138s The following packages will be upgraded: 138s openssl 139s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 139s Need to get 2777 kB of archives. 139s After this operation, 139 kB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 139s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 140s Fetched 2777 kB in 1s (3911 kB/s) 140s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74819 files and directories currently installed.) 140s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 140s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 141s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 141s wget depends on libssl3 (>= 3.0.0). 141s u-boot-tools depends on libssl3 (>= 3.0.0). 141s tnftp depends on libssl3 (>= 3.0.0). 141s tcpdump depends on libssl3 (>= 3.0.0). 141s systemd-resolved depends on libssl3 (>= 3.0.0). 141s systemd depends on libssl3 (>= 3.0.0). 141s sudo depends on libssl3 (>= 3.0.0). 141s sbsigntool depends on libssl3 (>= 3.0.0). 141s rsync depends on libssl3 (>= 3.0.0). 141s python3-cryptography depends on libssl3 (>= 3.0.0). 141s openssh-server depends on libssl3 (>= 3.0.10). 141s openssh-client depends on libssl3 (>= 3.0.10). 141s mtd-utils depends on libssl3 (>= 3.0.0). 141s mokutil depends on libssl3 (>= 3.0.0). 141s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 141s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 141s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 141s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 141s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 141s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 141s libnvme1 depends on libssl3 (>= 3.0.0). 141s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 141s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 141s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 141s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 141s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 141s kmod depends on libssl3 (>= 3.0.0). 141s dhcpcd-base depends on libssl3 (>= 3.0.0). 141s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 141s 141s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74819 files and directories currently installed.) 141s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 141s Selecting previously unselected package libssl3t64:arm64. 141s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74808 files and directories currently installed.) 141s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 141s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 141s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 141s Setting up openssl (3.0.13-0ubuntu2) ... 141s Processing triggers for man-db (2.12.0-3) ... 141s Processing triggers for libc-bin (2.39-0ubuntu6) ... 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 143s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 144s sh: Attempting to set up Debian/Ubuntu apt sources automatically 144s sh: Distribution appears to be Ubuntu 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 146s eatmydata is already the newest version (131-1). 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 147s dbus is already the newest version (1.14.10-4ubuntu1). 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s rng-tools-debian is already the newest version (2.4). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s The following packages will be REMOVED: 150s cloud-init* python3-configobj* python3-debconf* 150s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 150s After this operation, 3256 kB disk space will be freed. 150s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74821 files and directories currently installed.) 150s Removing cloud-init (24.1.2-0ubuntu1) ... 151s Removing python3-configobj (5.0.8-3) ... 151s Removing python3-debconf (1.5.86) ... 151s Processing triggers for man-db (2.12.0-3) ... 151s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74432 files and directories currently installed.) 151s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 152s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 152s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 152s invoke-rc.d: policy-rc.d denied execution of try-restart. 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s linux-generic is already the newest version (6.8.0-11.11+1). 153s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 154s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 154s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 156s Reading package lists... 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Calculating upgrade... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s autopkgtest [16:47:20]: rebooting testbed after setup commands that affected boot 186s autopkgtest [16:47:47]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 188s autopkgtest [16:47:49]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 191s Get:1 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (dsc) [2316 B] 191s Get:2 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (tar) [1920 kB] 191s Get:3 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (diff) [10.5 kB] 191s gpgv: Signature made Thu Feb 1 11:28:39 2024 UTC 191s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 191s gpgv: issuer "tille@debian.org" 191s gpgv: Can't check signature: No public key 191s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-2.dsc: no acceptable signature found 191s autopkgtest [16:47:52]: testing package ariba version 2.14.7+ds-2 192s autopkgtest [16:47:53]: build not needed 193s autopkgtest [16:47:54]: test test-example: preparing testbed 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 199s Starting pkgProblemResolver with broken count: 0 199s Starting 2 pkgProblemResolver with broken count: 0 199s Done 200s The following additional packages will be installed: 200s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 200s fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 200s libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 200s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 200s libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 200s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 200s libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 libpython3.11-minimal 200s libpython3.11-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 200s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 200s libxft2 libxrender1 libxslt1.1 libxss1 mash mummer python-matplotlib-data 200s python3-appdirs python3-biopython python3-brotli python3-bs4 python3-cairo 200s python3-contourpy python3-cycler python3-dateutil python3-decorator 200s python3-dendropy python3-fonttools python3-freetype python3-fs 200s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 200s python3-mpmath python3-numpy python3-packaging python3-pil 200s python3-pil.imagetk python3-pymummer python3-pysam python3-reportlab 200s python3-rlpycairo python3-scipy python3-soupsieve python3-sympy python3-tk 200s python3-ufolib2 python3-unicodedata2 python3.11 python3.11-minimal samtools 200s sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 200s xfonts-utils xml-core 200s Suggested packages: 200s spades blt-demo bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf 200s fonts-texgyre gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 200s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 200s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 200s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee 200s wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 200s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 200s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 200s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 200s python3-gmpy2 gcc gfortran python3-dev python3-pytest python-pil-doc 200s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 200s rl-renderpm python-scipy-doc texlive-fonts-extra python-sympy-doc tix 200s python3-tk-dbg python3.11-venv python3.11-doc binfmt-support cwltool 200s sgml-base-doc debhelper 200s Recommended packages: 200s javascript-common python-biopython-doc ncbi-blast+ python3-cssselect 200s python3-html5lib python3-olefile g++ | c++-compiler isympy-common 200s The following NEW packages will be installed: 200s ariba autopkgtest-satdep blt bowtie2 cd-hit fastaq fontconfig-config 200s fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lyx 200s fonts-urw-base35 libblas3 libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 200s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 200s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 200s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 200s liblcms2-2 liblerc4 libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 200s libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 200s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 200s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 200s mummer python-matplotlib-data python3-appdirs python3-biopython 200s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 200s python3-dateutil python3-decorator python3-dendropy python3-fonttools 200s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 200s python3-matplotlib python3-mpmath python3-numpy python3-packaging 200s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 200s python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve 200s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 python3.11 200s python3.11-minimal samtools sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib 200s x11-common xfonts-encodings xfonts-utils xml-core 200s 0 upgraded, 104 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 97.8 MB/97.8 MB of archives. 200s After this operation, 446 MB of additional disk space will be used. 200s Get:1 /tmp/autopkgtest.U8YIpQ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [696 B] 200s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 201s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 201s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 201s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 201s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 201s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 201s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 201s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 201s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 201s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 fastaq all 3.17.0-6 [47.9 kB] 201s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 201s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 201s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 201s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 201s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 201s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 201s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 201s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 201s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 201s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 201s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 201s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 201s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 201s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 201s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 201s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 201s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 201s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.14-1 [767 kB] 201s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] 201s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] 201s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB] 201s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] 201s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 201s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 201s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 201s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 201s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 201s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 201s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 201s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 201s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 201s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 201s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 201s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 201s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 201s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 201s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 201s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 201s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 201s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 201s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 201s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 201s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 201s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 201s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 201s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 201s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 201s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 201s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 202s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 202s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 202s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 python3-soupsieve all 2.5-1 [33.0 kB] 202s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 python3-bs4 all 4.12.3-1 [109 kB] 202s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-dendropy all 4.6.1-1 [278 kB] 202s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 202s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 202s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB] 202s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 202s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 202s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB] 202s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B] 202s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB] 202s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 202s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 202s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 202s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 202s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 202s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB] 202s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 202s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] 202s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.39-0exp1 [166 kB] 202s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] 202s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB] 202s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1 [362 kB] 202s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 202s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB] 202s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-2 [48.5 kB] 202s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 202s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] 202s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] 203s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 203s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pymummer all 0.11.0-4 [17.1 kB] 203s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 203s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 libfml0 arm64 0.1+git20190320.b499514-1 [64.7 kB] 203s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 libminimap0 arm64 0.2-8 [22.6 kB] 203s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie2 arm64 2.5.2-1 [1261 kB] 203s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 cd-hit arm64 4.8.1-4 [522 kB] 203s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 libcapnp-1.0.1 arm64 1.0.1-3 [1326 kB] 203s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 203s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 203s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 libmurmurhash2 arm64 1.6-1 [6098 B] 203s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 mash arm64 2.3+dfsg-6 [145 kB] 203s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 ariba arm64 2.14.7+ds-2 [2042 kB] 204s Fetched 97.8 MB in 3s (28.2 MB/s) 204s Selecting previously unselected package libpython3.11-minimal:arm64. 204s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74377 files and directories currently installed.) 204s Preparing to unpack .../000-libpython3.11-minimal_3.11.8-1_arm64.deb ... 204s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 204s Selecting previously unselected package python3.11-minimal. 204s Preparing to unpack .../001-python3.11-minimal_3.11.8-1_arm64.deb ... 204s Unpacking python3.11-minimal (3.11.8-1) ... 205s Selecting previously unselected package sgml-base. 205s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 205s Unpacking sgml-base (1.31) ... 205s Selecting previously unselected package libpython3.11-stdlib:arm64. 205s Preparing to unpack .../003-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 205s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 205s Selecting previously unselected package python3.11. 205s Preparing to unpack .../004-python3.11_3.11.8-1_arm64.deb ... 205s Unpacking python3.11 (3.11.8-1) ... 205s Selecting previously unselected package libdeflate0:arm64. 205s Preparing to unpack .../005-libdeflate0_1.19-1_arm64.deb ... 205s Unpacking libdeflate0:arm64 (1.19-1) ... 205s Selecting previously unselected package libhtscodecs2:arm64. 205s Preparing to unpack .../006-libhtscodecs2_1.6.0-1_arm64.deb ... 205s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 205s Selecting previously unselected package libhts3:arm64. 205s Preparing to unpack .../007-libhts3_1.18+ds-1_arm64.deb ... 205s Unpacking libhts3:arm64 (1.18+ds-1) ... 205s Selecting previously unselected package samtools. 205s Preparing to unpack .../008-samtools_1.19.2-1_arm64.deb ... 205s Unpacking samtools (1.19.2-1) ... 205s Selecting previously unselected package fastaq. 205s Preparing to unpack .../009-fastaq_3.17.0-6_all.deb ... 205s Unpacking fastaq (3.17.0-6) ... 205s Selecting previously unselected package libblas3:arm64. 205s Preparing to unpack .../010-libblas3_3.12.0-3_arm64.deb ... 205s Unpacking libblas3:arm64 (3.12.0-3) ... 205s Selecting previously unselected package libgfortran5:arm64. 205s Preparing to unpack .../011-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 205s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 205s Selecting previously unselected package liblapack3:arm64. 205s Preparing to unpack .../012-liblapack3_3.12.0-3_arm64.deb ... 205s Unpacking liblapack3:arm64 (3.12.0-3) ... 205s Selecting previously unselected package python3-numpy. 205s Preparing to unpack .../013-python3-numpy_1%3a1.24.2-2_arm64.deb ... 205s Unpacking python3-numpy (1:1.24.2-2) ... 205s Selecting previously unselected package libtcl8.6:arm64. 205s Preparing to unpack .../014-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 205s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 205s Selecting previously unselected package fonts-dejavu-mono. 205s Preparing to unpack .../015-fonts-dejavu-mono_2.37-8_all.deb ... 205s Unpacking fonts-dejavu-mono (2.37-8) ... 205s Selecting previously unselected package fonts-dejavu-core. 205s Preparing to unpack .../016-fonts-dejavu-core_2.37-8_all.deb ... 205s Unpacking fonts-dejavu-core (2.37-8) ... 205s Selecting previously unselected package libfontenc1:arm64. 205s Preparing to unpack .../017-libfontenc1_1%3a1.1.8-1_arm64.deb ... 205s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 205s Selecting previously unselected package x11-common. 205s Preparing to unpack .../018-x11-common_1%3a7.7+23ubuntu2_all.deb ... 205s Unpacking x11-common (1:7.7+23ubuntu2) ... 205s Selecting previously unselected package xfonts-encodings. 205s Preparing to unpack .../019-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 205s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 205s Selecting previously unselected package xfonts-utils. 205s Preparing to unpack .../020-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 205s Unpacking xfonts-utils (1:7.7+6build2) ... 205s Selecting previously unselected package fonts-urw-base35. 205s Preparing to unpack .../021-fonts-urw-base35_20200910-8_all.deb ... 206s Unpacking fonts-urw-base35 (20200910-8) ... 206s Selecting previously unselected package fontconfig-config. 206s Preparing to unpack .../022-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 206s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 206s Selecting previously unselected package libfontconfig1:arm64. 206s Preparing to unpack .../023-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 206s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 206s Selecting previously unselected package libxrender1:arm64. 206s Preparing to unpack .../024-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 206s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 206s Selecting previously unselected package libxft2:arm64. 206s Preparing to unpack .../025-libxft2_2.3.6-1_arm64.deb ... 206s Unpacking libxft2:arm64 (2.3.6-1) ... 206s Selecting previously unselected package libxss1:arm64. 206s Preparing to unpack .../026-libxss1_1%3a1.2.3-1build2_arm64.deb ... 206s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 206s Selecting previously unselected package libtk8.6:arm64. 206s Preparing to unpack .../027-libtk8.6_8.6.14-1_arm64.deb ... 206s Unpacking libtk8.6:arm64 (8.6.14-1) ... 206s Selecting previously unselected package tk8.6-blt2.5. 206s Preparing to unpack .../028-tk8.6-blt2.5_2.5.3+dfsg-7_arm64.deb ... 206s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... 206s Selecting previously unselected package blt. 206s Preparing to unpack .../029-blt_2.5.3+dfsg-7_arm64.deb ... 206s Unpacking blt (2.5.3+dfsg-7) ... 206s Selecting previously unselected package python3-tk:arm64. 206s Preparing to unpack .../030-python3-tk_3.11.5-1_arm64.deb ... 206s Unpacking python3-tk:arm64 (3.11.5-1) ... 206s Selecting previously unselected package python3-pil.imagetk:arm64. 206s Preparing to unpack .../031-python3-pil.imagetk_10.2.0-1_arm64.deb ... 206s Unpacking python3-pil.imagetk:arm64 (10.2.0-1) ... 206s Selecting previously unselected package libgomp1:arm64. 206s Preparing to unpack .../032-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 206s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 206s Selecting previously unselected package libimagequant0:arm64. 206s Preparing to unpack .../033-libimagequant0_2.18.0-1_arm64.deb ... 206s Unpacking libimagequant0:arm64 (2.18.0-1) ... 206s Selecting previously unselected package libjpeg-turbo8:arm64. 206s Preparing to unpack .../034-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 206s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 206s Selecting previously unselected package libjpeg8:arm64. 206s Preparing to unpack .../035-libjpeg8_8c-2ubuntu11_arm64.deb ... 206s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 206s Selecting previously unselected package liblcms2-2:arm64. 206s Preparing to unpack .../036-liblcms2-2_2.14-2_arm64.deb ... 206s Unpacking liblcms2-2:arm64 (2.14-2) ... 206s Selecting previously unselected package libopenjp2-7:arm64. 206s Preparing to unpack .../037-libopenjp2-7_2.5.0-2_arm64.deb ... 206s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 206s Selecting previously unselected package libgraphite2-3:arm64. 206s Preparing to unpack .../038-libgraphite2-3_1.3.14-2_arm64.deb ... 206s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 206s Selecting previously unselected package libharfbuzz0b:arm64. 207s Preparing to unpack .../039-libharfbuzz0b_8.3.0-2_arm64.deb ... 207s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 207s Selecting previously unselected package libraqm0:arm64. 207s Preparing to unpack .../040-libraqm0_0.10.1-1_arm64.deb ... 207s Unpacking libraqm0:arm64 (0.10.1-1) ... 207s Selecting previously unselected package libjbig0:arm64. 207s Preparing to unpack .../041-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 207s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 207s Selecting previously unselected package liblerc4:arm64. 207s Preparing to unpack .../042-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 207s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 207s Selecting previously unselected package libsharpyuv0:arm64. 207s Preparing to unpack .../043-libsharpyuv0_1.3.2-0.4_arm64.deb ... 207s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 207s Selecting previously unselected package libwebp7:arm64. 207s Preparing to unpack .../044-libwebp7_1.3.2-0.4_arm64.deb ... 207s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 207s Selecting previously unselected package libtiff6:arm64. 207s Preparing to unpack .../045-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 207s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 207s Selecting previously unselected package libwebpdemux2:arm64. 207s Preparing to unpack .../046-libwebpdemux2_1.3.2-0.4_arm64.deb ... 207s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 207s Selecting previously unselected package libwebpmux3:arm64. 207s Preparing to unpack .../047-libwebpmux3_1.3.2-0.4_arm64.deb ... 207s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 207s Selecting previously unselected package python3-pil:arm64. 207s Preparing to unpack .../048-python3-pil_10.2.0-1_arm64.deb ... 207s Unpacking python3-pil:arm64 (10.2.0-1) ... 207s Selecting previously unselected package libpixman-1-0:arm64. 207s Preparing to unpack .../049-libpixman-1-0_0.42.2-1_arm64.deb ... 207s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 207s Selecting previously unselected package libxcb-render0:arm64. 207s Preparing to unpack .../050-libxcb-render0_1.15-1_arm64.deb ... 207s Unpacking libxcb-render0:arm64 (1.15-1) ... 207s Selecting previously unselected package libxcb-shm0:arm64. 207s Preparing to unpack .../051-libxcb-shm0_1.15-1_arm64.deb ... 207s Unpacking libxcb-shm0:arm64 (1.15-1) ... 207s Selecting previously unselected package libcairo2:arm64. 207s Preparing to unpack .../052-libcairo2_1.18.0-1_arm64.deb ... 207s Unpacking libcairo2:arm64 (1.18.0-1) ... 207s Selecting previously unselected package python3-cairo. 207s Preparing to unpack .../053-python3-cairo_1.25.1-2_arm64.deb ... 207s Unpacking python3-cairo (1.25.1-2) ... 207s Selecting previously unselected package python3-freetype. 207s Preparing to unpack .../054-python3-freetype_2.4.0-1_all.deb ... 207s Unpacking python3-freetype (2.4.0-1) ... 207s Selecting previously unselected package python3-rlpycairo. 207s Preparing to unpack .../055-python3-rlpycairo_0.3.0-3_all.deb ... 207s Unpacking python3-rlpycairo (0.3.0-3) ... 207s Selecting previously unselected package fonts-dejavu-extra. 207s Preparing to unpack .../056-fonts-dejavu-extra_2.37-8_all.deb ... 207s Unpacking fonts-dejavu-extra (2.37-8) ... 207s Selecting previously unselected package python3-reportlab. 207s Preparing to unpack .../057-python3-reportlab_4.1.0-1_all.deb ... 207s Unpacking python3-reportlab (4.1.0-1) ... 207s Selecting previously unselected package xml-core. 207s Preparing to unpack .../058-xml-core_0.19_all.deb ... 207s Unpacking xml-core (0.19) ... 207s Selecting previously unselected package w3c-sgml-lib. 207s Preparing to unpack .../059-w3c-sgml-lib_1.3-3_all.deb ... 207s Unpacking w3c-sgml-lib (1.3-3) ... 208s Selecting previously unselected package python3-biopython. 208s Preparing to unpack .../060-python3-biopython_1.81+dfsg-3_arm64.deb ... 208s Unpacking python3-biopython (1.81+dfsg-3) ... 208s Selecting previously unselected package python3-soupsieve. 208s Preparing to unpack .../061-python3-soupsieve_2.5-1_all.deb ... 208s Unpacking python3-soupsieve (2.5-1) ... 208s Selecting previously unselected package python3-bs4. 208s Preparing to unpack .../062-python3-bs4_4.12.3-1_all.deb ... 208s Unpacking python3-bs4 (4.12.3-1) ... 208s Selecting previously unselected package python3-dendropy. 208s Preparing to unpack .../063-python3-dendropy_4.6.1-1_all.deb ... 208s Unpacking python3-dendropy (4.6.1-1) ... 208s Selecting previously unselected package libjs-jquery. 208s Preparing to unpack .../064-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 208s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 208s Selecting previously unselected package libjs-jquery-ui. 208s Preparing to unpack .../065-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 208s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 208s Selecting previously unselected package fonts-lyx. 208s Preparing to unpack .../066-fonts-lyx_2.4.0~RC3-1_all.deb ... 208s Unpacking fonts-lyx (2.4.0~RC3-1) ... 208s Selecting previously unselected package python-matplotlib-data. 208s Preparing to unpack .../067-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ... 208s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ... 208s Selecting previously unselected package python3-dateutil. 208s Preparing to unpack .../068-python3-dateutil_2.8.2-3_all.deb ... 208s Unpacking python3-dateutil (2.8.2-3) ... 208s Selecting previously unselected package python3-contourpy. 208s Preparing to unpack .../069-python3-contourpy_1.0.7-1build2_arm64.deb ... 208s Unpacking python3-contourpy (1.0.7-1build2) ... 208s Selecting previously unselected package python3-cycler. 208s Preparing to unpack .../070-python3-cycler_0.11.0-2_all.deb ... 208s Unpacking python3-cycler (0.11.0-2) ... 208s Selecting previously unselected package python3-brotli. 208s Preparing to unpack .../071-python3-brotli_1.1.0-2_arm64.deb ... 208s Unpacking python3-brotli (1.1.0-2) ... 208s Selecting previously unselected package python3-decorator. 208s Preparing to unpack .../072-python3-decorator_5.1.1-5_all.deb ... 208s Unpacking python3-decorator (5.1.1-5) ... 208s Selecting previously unselected package liblbfgsb0:arm64. 208s Preparing to unpack .../073-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 208s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 208s Selecting previously unselected package python3-scipy. 208s Preparing to unpack .../074-python3-scipy_1.11.4-6_arm64.deb ... 208s Unpacking python3-scipy (1.11.4-6) ... 209s Selecting previously unselected package python3-ufolib2. 209s Preparing to unpack .../075-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 209s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 209s Selecting previously unselected package python3-mpmath. 209s Preparing to unpack .../076-python3-mpmath_1.2.1-3_all.deb ... 209s Unpacking python3-mpmath (1.2.1-3) ... 209s Selecting previously unselected package python3-sympy. 209s Preparing to unpack .../077-python3-sympy_1.12-7_all.deb ... 209s Unpacking python3-sympy (1.12-7) ... 209s Selecting previously unselected package python3-appdirs. 209s Preparing to unpack .../078-python3-appdirs_1.4.4-4_all.deb ... 209s Unpacking python3-appdirs (1.4.4-4) ... 209s Selecting previously unselected package python3-fs. 209s Preparing to unpack .../079-python3-fs_2.4.16-3_all.deb ... 209s Unpacking python3-fs (2.4.16-3) ... 209s Selecting previously unselected package libxslt1.1:arm64. 209s Preparing to unpack .../080-libxslt1.1_1.1.39-0exp1_arm64.deb ... 209s Unpacking libxslt1.1:arm64 (1.1.39-0exp1) ... 209s Selecting previously unselected package python3-lxml:arm64. 209s Preparing to unpack .../081-python3-lxml_5.1.0-1_arm64.deb ... 209s Unpacking python3-lxml:arm64 (5.1.0-1) ... 209s Selecting previously unselected package python3-lz4. 209s Preparing to unpack .../082-python3-lz4_4.0.2+dfsg-1build2_arm64.deb ... 209s Unpacking python3-lz4 (4.0.2+dfsg-1build2) ... 209s Selecting previously unselected package python3-unicodedata2. 209s Preparing to unpack .../083-python3-unicodedata2_15.1.0+ds-1_arm64.deb ... 209s Unpacking python3-unicodedata2 (15.1.0+ds-1) ... 209s Selecting previously unselected package unicode-data. 209s Preparing to unpack .../084-unicode-data_15.1.0-1_all.deb ... 209s Unpacking unicode-data (15.1.0-1) ... 209s Selecting previously unselected package python3-fonttools. 209s Preparing to unpack .../085-python3-fonttools_4.46.0-1_arm64.deb ... 209s Unpacking python3-fonttools (4.46.0-1) ... 210s Selecting previously unselected package python3-kiwisolver. 210s Preparing to unpack .../086-python3-kiwisolver_1.4.4-2_arm64.deb ... 210s Unpacking python3-kiwisolver (1.4.4-2) ... 210s Selecting previously unselected package python3-packaging. 210s Preparing to unpack .../087-python3-packaging_23.2-1_all.deb ... 210s Unpacking python3-packaging (23.2-1) ... 210s Selecting previously unselected package libqhull-r8.0:arm64. 210s Preparing to unpack .../088-libqhull-r8.0_2020.2-6_arm64.deb ... 210s Unpacking libqhull-r8.0:arm64 (2020.2-6) ... 210s Selecting previously unselected package python3-matplotlib. 210s Preparing to unpack .../089-python3-matplotlib_3.6.3-1ubuntu3_arm64.deb ... 210s Unpacking python3-matplotlib (3.6.3-1ubuntu3) ... 210s Selecting previously unselected package mummer. 210s Preparing to unpack .../090-mummer_3.23+dfsg-8_arm64.deb ... 210s Unpacking mummer (3.23+dfsg-8) ... 210s Selecting previously unselected package python3-pymummer. 210s Preparing to unpack .../091-python3-pymummer_0.11.0-4_all.deb ... 210s Unpacking python3-pymummer (0.11.0-4) ... 210s Selecting previously unselected package python3-pysam. 210s Preparing to unpack .../092-python3-pysam_0.22.0+ds-1_arm64.deb ... 210s Unpacking python3-pysam (0.22.0+ds-1) ... 210s Selecting previously unselected package libfml0:arm64. 210s Preparing to unpack .../093-libfml0_0.1+git20190320.b499514-1_arm64.deb ... 210s Unpacking libfml0:arm64 (0.1+git20190320.b499514-1) ... 210s Selecting previously unselected package libminimap0:arm64. 210s Preparing to unpack .../094-libminimap0_0.2-8_arm64.deb ... 210s Unpacking libminimap0:arm64 (0.2-8) ... 210s Selecting previously unselected package bowtie2. 210s Preparing to unpack .../095-bowtie2_2.5.2-1_arm64.deb ... 210s Unpacking bowtie2 (2.5.2-1) ... 210s Selecting previously unselected package cd-hit. 210s Preparing to unpack .../096-cd-hit_4.8.1-4_arm64.deb ... 210s Unpacking cd-hit (4.8.1-4) ... 210s Selecting previously unselected package libcapnp-1.0.1:arm64. 210s Preparing to unpack .../097-libcapnp-1.0.1_1.0.1-3_arm64.deb ... 210s Unpacking libcapnp-1.0.1:arm64 (1.0.1-3) ... 210s Selecting previously unselected package libgslcblas0:arm64. 210s Preparing to unpack .../098-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 210s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 210s Selecting previously unselected package libgsl27:arm64. 210s Preparing to unpack .../099-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 210s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 210s Selecting previously unselected package libmurmurhash2:arm64. 210s Preparing to unpack .../100-libmurmurhash2_1.6-1_arm64.deb ... 210s Unpacking libmurmurhash2:arm64 (1.6-1) ... 210s Selecting previously unselected package mash. 210s Preparing to unpack .../101-mash_2.3+dfsg-6_arm64.deb ... 210s Unpacking mash (2.3+dfsg-6) ... 211s Selecting previously unselected package ariba. 211s Preparing to unpack .../102-ariba_2.14.7+ds-2_arm64.deb ... 211s Unpacking ariba (2.14.7+ds-2) ... 211s Selecting previously unselected package autopkgtest-satdep. 211s Preparing to unpack .../103-1-autopkgtest-satdep.deb ... 211s Unpacking autopkgtest-satdep (0) ... 211s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 211s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 211s Setting up liblcms2-2:arm64 (2.14-2) ... 211s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 211s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 211s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 211s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 211s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 211s Setting up libmurmurhash2:arm64 (1.6-1) ... 211s Setting up libcapnp-1.0.1:arm64 (1.0.1-3) ... 211s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 211s Setting up libxcb-render0:arm64 (1.15-1) ... 211s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 211s Setting up fonts-lyx (2.4.0~RC3-1) ... 211s Setting up x11-common (1:7.7+23ubuntu2) ... 211s Setting up libdeflate0:arm64 (1.19-1) ... 211s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 211s Setting up libqhull-r8.0:arm64 (2020.2-6) ... 211s Setting up libxcb-shm0:arm64 (1.15-1) ... 211s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 211s Setting up python3-freetype (2.4.0-1) ... 211s Setting up libfml0:arm64 (0.1+git20190320.b499514-1) ... 211s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 211s Setting up bowtie2 (2.5.2-1) ... 211s Setting up unicode-data (15.1.0-1) ... 211s Setting up python3-decorator (5.1.1-5) ... 212s Setting up libminimap0:arm64 (0.2-8) ... 212s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 212s Setting up libblas3:arm64 (3.12.0-3) ... 212s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 212s Setting up python3-packaging (23.2-1) ... 212s Setting up python3-brotli (1.1.0-2) ... 212s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 212s Setting up python3-cycler (0.11.0-2) ... 212s Setting up libimagequant0:arm64 (2.18.0-1) ... 212s Setting up fonts-dejavu-mono (2.37-8) ... 212s Setting up python3-kiwisolver (1.4.4-2) ... 212s Setting up mash (2.3+dfsg-6) ... 212s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 212s Setting up fonts-dejavu-core (2.37-8) ... 212s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 212s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 212s Setting up libwebp7:arm64 (1.3.2-0.4) ... 212s Setting up fonts-dejavu-extra (2.37-8) ... 212s Setting up libxslt1.1:arm64 (1.1.39-0exp1) ... 212s Setting up mummer (3.23+dfsg-8) ... 212s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 212s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 212s Setting up python3-dateutil (2.8.2-3) ... 212s Setting up sgml-base (1.31) ... 212s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 212s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 212s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 212s Setting up python3-mpmath (1.2.1-3) ... 213s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 213s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 213s Setting up python3-dendropy (4.6.1-1) ... 213s Setting up python3-appdirs (1.4.4-4) ... 213s Setting up python3-soupsieve (2.5-1) ... 213s Setting up cd-hit (4.8.1-4) ... 213s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 213s Setting up python3.11-minimal (3.11.8-1) ... 214s Setting up python3-sympy (1.12-7) ... 219s Setting up liblapack3:arm64 (3.12.0-3) ... 219s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 219s Setting up libhts3:arm64 (1.18+ds-1) ... 219s Setting up python3-pysam (0.22.0+ds-1) ... 219s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 219s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 219s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 219s Setting up xfonts-utils (1:7.7+6build2) ... 219s Setting up python3-bs4 (4.12.3-1) ... 219s Setting up samtools (1.19.2-1) ... 219s Setting up python3-fs (2.4.16-3) ... 219s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 219s Setting up libraqm0:arm64 (0.10.1-1) ... 219s Setting up python3-lxml:arm64 (5.1.0-1) ... 219s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 219s Setting up xml-core (0.19) ... 220s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 220s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 220s Setting up python3.11 (3.11.8-1) ... 220s Setting up libxft2:arm64 (2.3.6-1) ... 220s Setting up libtk8.6:arm64 (8.6.14-1) ... 220s Setting up fastaq (3.17.0-6) ... 220s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 220s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 220s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 220s gbk_regex = re.compile('^LOCUS\s+\S') 220s Setting up fonts-urw-base35 (20200910-8) ... 221s Setting up libcairo2:arm64 (1.18.0-1) ... 221s Setting up python3-pymummer (0.11.0-4) ... 221s Setting up python3-pil:arm64 (10.2.0-1) ... 221s Setting up python3-numpy (1:1.24.2-2) ... 223s Setting up python3-contourpy (1.0.7-1build2) ... 223s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 223s Setting up python3-scipy (1.11.4-6) ... 226s Setting up python3-cairo (1.25.1-2) ... 226s Setting up blt (2.5.3+dfsg-7) ... 226s Setting up python3-tk:arm64 (3.11.5-1) ... 226s Setting up python3-pil.imagetk:arm64 (10.2.0-1) ... 226s Setting up python3-rlpycairo (0.3.0-3) ... 226s Setting up python3-reportlab (4.1.0-1) ... 227s Setting up python3-fonttools (4.46.0-1) ... 228s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 228s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 229s Processing triggers for libc-bin (2.39-0ubuntu6) ... 229s Processing triggers for systemd (255.2-3ubuntu2) ... 229s Processing triggers for man-db (2.12.0-3) ... 230s Processing triggers for sgml-base (1.31) ... 230s Setting up w3c-sgml-lib (1.3-3) ... 254s Setting up python3-biopython (1.81+dfsg-3) ... 255s Setting up ariba (2.14.7+ds-2) ... 255s /usr/lib/python3/dist-packages/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.' 255s 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), 255s /usr/lib/python3/dist-packages/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.' 255s 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), 255s /usr/lib/python3/dist-packages/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.' 255s 'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)')) 255s Setting up autopkgtest-satdep (0) ... 261s (Reading database ... 85758 files and directories currently installed.) 261s Removing autopkgtest-satdep (0) ... 261s autopkgtest [16:49:02]: test test-example: [----------------------- 264s ARIBA version: 2.14.6 264s 264s External dependencies: 264s bowtie2 2.5.2 /usr/bin/bowtie2 264s cdhit 4.8.1 /usr/bin/cd-hit-est 264s nucmer 3.1 /usr/bin/nucmer 264s 264s External dependencies OK: True 264s 264s Python version: 264s 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 264s 264s Python packages: 264s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 264s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 264s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 264s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 264s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 264s pysam 0.22.0 /usr/lib/python3/dist-packages/pysam/__init__.py 264s 264s Python packages OK: True 264s 264s Everything looks OK: True 264s 264s Loading and checking input data 264s 264s Running cdhit 264s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.D74kdZBC4w/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.D74kdZBC4w/foo/tmp.run_cd-hit.qt3pkp2z/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 264s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.D74kdZBC4w/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.D74kdZBC4w/foo/tmp.run_cd-hit.vrz17a4q/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 265s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.D74kdZBC4w/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.D74kdZBC4w/foo/tmp.run_cd-hit.jlor4xys/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 265s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.D74kdZBC4w/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.D74kdZBC4w/foo/tmp.run_cd-hit.x4sfjn5u/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 265s 265s Writing clusters to file. 10 in total 266s Found reads file: reads_1.fq 266s Found reads file: reads_2.fq 266s ARIBA version: 2.14.6 266s 266s External dependencies: 266s bowtie2 2.5.2 /usr/bin/bowtie2 266s cdhit 4.8.1 /usr/bin/cd-hit-est 266s nucmer 3.1 /usr/bin/nucmer 266s 266s External dependencies OK: True 266s 266s Python version: 266s 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 266s 266s Python packages: 266s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 266s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 266s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 266s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 266s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 266s pysam 0.22.0 /usr/lib/python3/dist-packages/pysam/__init__.py 266s 266s Python packages OK: True 266s 266s Everything looks OK: True 266s Temporary directory: /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx 266s ______________________ Mapping reads to clustered genes _______________________ 266s Finished mapping 266s 266s _____________________________ Generating clusters _____________________________ 266s syscall: sort -k1,1 -k 2,2n /tmp/tmp.D74kdZBC4w/foo/OUT/minimap.reads > /tmp/tmp.D74kdZBC4w/foo/OUT/read_store 266s Compressing file /tmp/tmp.D74kdZBC4w/foo/OUT/read_store 266s Found 51 proper read pairs from minimap 266s Total clusters to perform local assemblies: 9 266s 266s Insert size information from reads mapped to reference genes: 266s Insert size: 185.0 266s Insert sspace sd: 0.27 266s Max insert: 220.55 266s 266s ___________________________ Assembling each cluster ___________________________ 266s Will run 1 cluster(s) in parallel 266s Not constructing cluster cluster because it only has 2 reads (1 of 9) 266s Constructing cluster cluster_1 (2 of 9) 266s Constructing cluster cluster_2 (3 of 9) 266s Constructing cluster cluster_3 (4 of 9) 266s Constructing cluster cluster_4 (5 of 9) 266s Constructing cluster gene (6 of 9) 266s Constructing cluster gene_1 (7 of 9) 266s Constructing cluster noncoding (8 of 9) 266s Constructing cluster noncoding_1 (9 of 9) 266s Start running cluster cluster_1 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_1 268s cluster_1 detected 1 threads available to it 268s cluster_1 reported completion 268s Finished running cluster cluster_1 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_1 268s Deleting cluster dir /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_1 268s Start running cluster cluster_2 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_2 270s cluster_2 detected 1 threads available to it 270s cluster_2 reported completion 270s Finished running cluster cluster_2 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_2 270s Deleting cluster dir /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_2 270s Start running cluster cluster_3 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_3 272s cluster_3 detected 1 threads available to it 272s cluster_3 reported completion 272s Finished running cluster cluster_3 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_3 272s Deleting cluster dir /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_3 272s Start running cluster cluster_4 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_4 273s cluster_4 detected 1 threads available to it 273s cluster_4 reported completion 273s Finished running cluster cluster_4 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_4 273s Deleting cluster dir /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/cluster_4 273s Start running cluster gene in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/gene 275s gene detected 1 threads available to it 275s gene reported completion 275s Finished running cluster gene in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/gene 275s Deleting cluster dir /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/gene 275s Start running cluster gene_1 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/gene_1 278s gene_1 detected 1 threads available to it 278s gene_1 reported completion 278s Finished running cluster gene_1 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/gene_1 278s Deleting cluster dir /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/gene_1 278s Start running cluster noncoding in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/noncoding 279s noncoding detected 1 threads available to it 279s noncoding reported completion 279s Finished running cluster noncoding in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/noncoding 279s Deleting cluster dir /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/noncoding 279s Start running cluster noncoding_1 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/noncoding_1 281s noncoding_1 detected 1 threads available to it 281s noncoding_1 reported completion 281s Finished running cluster noncoding_1 in directory /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/noncoding_1 281s Deleting cluster dir /tmp/tmp.D74kdZBC4w/foo/OUT/ariba.tmp.3k3zw4gx/noncoding_1 281s Final value of remaining_clusters counter: Value('l', 0) 281s Finished assembling clusters 281s 281s _______________________________ Writing reports _______________________________ 281s Making /tmp/tmp.D74kdZBC4w/foo/OUT/debug.report.tsv 281s Making /tmp/tmp.D74kdZBC4w/foo/OUT/report.tsv 281s 281s ____________________ Writing fasta of assembled sequences _____________________ 281s /tmp/tmp.D74kdZBC4w/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.D74kdZBC4w/foo/OUT/assembled_genes.fa.gz 281s 281s __________________________ Catting cluster log files __________________________ 281s Writing file /tmp/tmp.D74kdZBC4w/foo/OUT/log.clusters.gz 281s 281s _______________________________ Cleaning files ________________________________ 281s Deleting Logs directory /tmp/tmp.D74kdZBC4w/foo/OUT/Logs 281s Deleting reads store files /tmp/tmp.D74kdZBC4w/foo/OUT/read_store.gz[.tbi] 281s 281s All done! 281s 281s Running ARIBA on test data... 281s ------------------------------------------------------------------------------- 281s |=============================================================================| 281s | Preparing input data | 281s |=============================================================================| 281s ------------------------------------------------------------------------------- 281s Made output directory ./foo. Copying test data files into it: 281s copied ref_seqs.fa 281s copied metadata.tsv 281s copied reads_1.fq 281s copied reads_2.fq 281s ------------------------------------------------------------------------------- 281s |=============================================================================| 281s | Try running ariba prepareref | 281s |=============================================================================| 281s ------------------------------------------------------------------------------- 281s 281s Running ariba prepareref with: 281s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 281s 281s 281s ariba prepareref finished OK 281s ------------------------------------------------------------------------------- 281s |=============================================================================| 281s | Try running ariba run | 281s |=============================================================================| 281s ------------------------------------------------------------------------------- 281s 281s Running ARIBA with: 281s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 281s 281s 281s ariba run finished OK 281s Finished run on test data OK 282s autopkgtest [16:49:23]: test test-example: -----------------------] 282s test-example PASS 282s autopkgtest [16:49:23]: test test-example: - - - - - - - - - - results - - - - - - - - - - 283s autopkgtest [16:49:24]: @@@@@@@@@@@@@@@@@@@@ summary 283s test-example PASS 287s Creating nova instance adt-noble-arm64-ariba-20240324-164441-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...