0s autopkgtest [03:03:07]: starting date and time: 2024-03-25 03:03:07+0000 0s autopkgtest [03:03:07]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [03:03:07]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f90vlmu4/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:python3-stdlib-extensions,src:gdbm --apt-upgrade ariba --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-stdlib-extensions/3.12.2-3ubuntu1.1 gdbm/1.23-5.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-arm64-18.secgroup --name adt-noble-arm64-ariba-20240325-030307-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/ 237s autopkgtest [03:07:04]: testbed dpkg architecture: arm64 238s autopkgtest [03:07:05]: testbed apt version: 2.7.12 238s autopkgtest [03:07:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 241s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 242s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.8 kB] 242s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 242s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4010 kB] 243s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 243s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 243s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 243s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 244s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 244s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4365 kB] 244s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 244s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [71.0 kB] 244s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 265s Fetched 9876 kB in 10s (969 kB/s) 267s Reading package lists... 277s Reading package lists... 278s Building dependency tree... 278s Reading state information... 281s Calculating upgrade... 282s The following packages will be REMOVED: 282s libgdbm6 282s The following NEW packages will be installed: 282s libgdbm6t64 283s The following packages will be upgraded: 283s python3-distutils python3-gdbm python3-lib2to3 283s 3 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 283s Need to get 266 kB of archives. 283s After this operation, 3072 B of additional disk space will be used. 283s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-gdbm arm64 3.12.2-3ubuntu1.1 [18.8 kB] 283s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB] 283s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-distutils all 3.12.2-3ubuntu1.1 [133 kB] 283s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-lib2to3 all 3.12.2-3ubuntu1.1 [79.1 kB] 286s Fetched 266 kB in 1s (353 kB/s) 287s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75911 files and directories currently installed.) 287s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu1.1_arm64.deb ... 287s Unpacking python3-gdbm:arm64 (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 288s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested: 288s man-db depends on libgdbm6 (>= 1.16). 288s libperl5.38:arm64 depends on libgdbm6 (>= 1.21). 288s libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16). 288s 288s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75911 files and directories currently installed.) 288s Removing libgdbm6:arm64 (1.23-5) ... 288s Selecting previously unselected package libgdbm6t64:arm64. 288s (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 ... 75906 files and directories currently installed.) 288s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ... 288s Unpacking libgdbm6t64:arm64 (1.23-5.1) ... 289s Preparing to unpack .../python3-distutils_3.12.2-3ubuntu1.1_all.deb ... 289s Unpacking python3-distutils (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 289s Preparing to unpack .../python3-lib2to3_3.12.2-3ubuntu1.1_all.deb ... 290s Unpacking python3-lib2to3 (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 291s Setting up libgdbm6t64:arm64 (1.23-5.1) ... 291s Setting up python3-gdbm:arm64 (3.12.2-3ubuntu1.1) ... 291s Setting up python3-lib2to3 (3.12.2-3ubuntu1.1) ... 293s Setting up python3-distutils (3.12.2-3ubuntu1.1) ... 294s python3.12: can't get files for byte-compilation 294s Processing triggers for libc-bin (2.39-0ubuntu6) ... 296s Reading package lists... 297s Building dependency tree... 297s Reading state information... 301s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 304s sh: Attempting to set up Debian/Ubuntu apt sources automatically 304s sh: Distribution appears to be Ubuntu 308s Reading package lists... 309s Building dependency tree... 309s Reading state information... 313s eatmydata is already the newest version (131-1). 313s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 313s Reading package lists... 314s Building dependency tree... 314s Reading state information... 317s dbus is already the newest version (1.14.10-4ubuntu1). 317s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 317s Reading package lists... 318s Building dependency tree... 318s Reading state information... 321s rng-tools-debian is already the newest version (2.4). 321s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 321s Reading package lists... 322s Building dependency tree... 322s Reading state information... 325s The following packages will be REMOVED: 325s cloud-init* python3-configobj* python3-debconf* 327s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 327s After this operation, 3256 kB disk space will be freed. 328s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75912 files and directories currently installed.) 328s Removing cloud-init (24.1.2-0ubuntu1) ... 333s Removing python3-configobj (5.0.8-3) ... 334s Removing python3-debconf (1.5.86) ... 334s Processing triggers for man-db (2.12.0-3) ... 337s (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 ... 75523 files and directories currently installed.) 337s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 343s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 343s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 344s invoke-rc.d: policy-rc.d denied execution of try-restart. 345s Reading package lists... 345s Building dependency tree... 345s Reading state information... 349s linux-generic is already the newest version (6.8.0-11.11+1). 349s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 350s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 350s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 350s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 370s Reading package lists... 370s Reading package lists... 371s Building dependency tree... 371s Reading state information... 373s Calculating upgrade... 374s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 375s Reading package lists... 376s Building dependency tree... 376s Reading state information... 379s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 379s autopkgtest [03:09:26]: rebooting testbed after setup commands that affected boot 561s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 578s autopkgtest [03:12:45]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 584s autopkgtest [03:12:51]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 591s Get:1 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (dsc) [2316 B] 591s Get:2 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (tar) [1920 kB] 591s Get:3 http://ftpmaster.internal/ubuntu noble/universe ariba 2.14.7+ds-2 (diff) [10.5 kB] 592s gpgv: Signature made Thu Feb 1 11:28:39 2024 UTC 592s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 592s gpgv: issuer "tille@debian.org" 592s gpgv: Can't check signature: No public key 592s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-2.dsc: no acceptable signature found 594s autopkgtest [03:13:01]: testing package ariba version 2.14.7+ds-2 595s autopkgtest [03:13:02]: build not needed 598s autopkgtest [03:13:05]: test test-example: preparing testbed 603s Reading package lists... 604s Building dependency tree... 604s Reading state information... 606s Starting pkgProblemResolver with broken count: 0 607s Starting 2 pkgProblemResolver with broken count: 0 607s Done 609s The following additional packages will be installed: 609s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 609s fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 609s libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 609s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 609s libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 609s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 609s libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 609s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 609s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 609s mummer python-matplotlib-data python3-appdirs python3-biopython 609s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 609s python3-dateutil python3-decorator python3-dendropy python3-fonttools 609s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 609s python3-matplotlib python3-mpmath python3-numpy python3-packaging 609s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 609s python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve 609s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 samtools 609s sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 609s xfonts-utils xml-core 609s Suggested packages: 609s spades blt-demo bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf 609s fonts-texgyre gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 609s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 609s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 609s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee 609s wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 609s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 609s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 609s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 609s python3-gmpy2 gcc gfortran python3-dev python3-pytest python-pil-doc 609s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 609s rl-renderpm python-scipy-doc texlive-fonts-extra python-sympy-doc tix 609s python3-tk-dbg cwltool sgml-base-doc debhelper 609s Recommended packages: 609s javascript-common python-biopython-doc ncbi-blast+ python3-cssselect 609s python3-html5lib python3-olefile g++ | c++-compiler isympy-common 610s The following NEW packages will be installed: 610s ariba autopkgtest-satdep blt bowtie2 cd-hit fastaq fontconfig-config 610s fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lyx 610s fonts-urw-base35 libblas3 libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 610s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 610s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 610s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 610s liblcms2-2 liblerc4 libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 610s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 610s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 610s libxslt1.1 libxss1 mash mummer python-matplotlib-data python3-appdirs 610s python3-biopython python3-brotli python3-bs4 python3-cairo python3-contourpy 610s python3-cycler python3-dateutil python3-decorator python3-dendropy 610s python3-fonttools python3-freetype python3-fs python3-kiwisolver 610s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 610s python3-packaging python3-pil python3-pil.imagetk python3-pymummer 610s python3-pysam python3-reportlab python3-rlpycairo python3-scipy 610s python3-soupsieve python3-sympy python3-tk python3-ufolib2 610s python3-unicodedata2 samtools sgml-base tk8.6-blt2.5 unicode-data 610s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 610s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 610s Need to get 92.3 MB/92.3 MB of archives. 610s After this operation, 423 MB of additional disk space will be used. 610s Get:1 /tmp/autopkgtest.kNcnMB/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 610s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 610s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 611s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 611s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 611s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 612s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 fastaq all 3.17.0-6 [47.9 kB] 612s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 612s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 612s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 613s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 614s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 614s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 614s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 614s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 614s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 614s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 614s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 614s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 615s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 615s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 615s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 615s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 615s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 615s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.14-1 [767 kB] 615s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] 615s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] 615s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB] 615s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] 615s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 615s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 615s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 615s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 615s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 615s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 615s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 616s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 616s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 616s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 616s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 616s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 616s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 616s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 616s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 616s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 616s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 616s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 616s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 616s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 616s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 616s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 616s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 616s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 616s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 616s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 616s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 616s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 617s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 617s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 python3-soupsieve all 2.5-1 [33.0 kB] 617s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 python3-bs4 all 4.12.3-1 [109 kB] 617s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-dendropy all 4.6.1-1 [278 kB] 617s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 617s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 617s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB] 617s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 617s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 617s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB] 617s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B] 617s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB] 617s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 617s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 617s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 619s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 619s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 619s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB] 620s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 620s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] 620s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.39-0exp1 [166 kB] 620s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] 620s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB] 620s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1 [362 kB] 620s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 621s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB] 621s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-2 [48.5 kB] 621s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 621s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] 621s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] 622s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 622s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pymummer all 0.11.0-4 [17.1 kB] 622s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 623s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 libfml0 arm64 0.1+git20190320.b499514-1 [64.7 kB] 623s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 libminimap0 arm64 0.2-8 [22.6 kB] 623s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie2 arm64 2.5.2-1 [1261 kB] 623s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 cd-hit arm64 4.8.1-4 [522 kB] 623s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 libcapnp-1.0.1 arm64 1.0.1-3 [1326 kB] 623s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 624s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 624s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 libmurmurhash2 arm64 1.6-1 [6098 B] 624s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 mash arm64 2.3+dfsg-6 [145 kB] 624s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 ariba arm64 2.14.7+ds-2 [2042 kB] 626s Fetched 92.3 MB in 14s (6787 kB/s) 626s Selecting previously unselected package sgml-base. 628s (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 ... 75468 files and directories currently installed.) 628s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 628s Unpacking sgml-base (1.31) ... 628s Selecting previously unselected package libdeflate0:arm64. 628s Preparing to unpack .../01-libdeflate0_1.19-1_arm64.deb ... 628s Unpacking libdeflate0:arm64 (1.19-1) ... 628s Selecting previously unselected package libhtscodecs2:arm64. 628s Preparing to unpack .../02-libhtscodecs2_1.6.0-1_arm64.deb ... 628s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 628s Selecting previously unselected package libhts3:arm64. 628s Preparing to unpack .../03-libhts3_1.18+ds-1_arm64.deb ... 628s Unpacking libhts3:arm64 (1.18+ds-1) ... 628s Selecting previously unselected package samtools. 628s Preparing to unpack .../04-samtools_1.19.2-1_arm64.deb ... 628s Unpacking samtools (1.19.2-1) ... 629s Selecting previously unselected package fastaq. 629s Preparing to unpack .../05-fastaq_3.17.0-6_all.deb ... 629s Unpacking fastaq (3.17.0-6) ... 629s Selecting previously unselected package libblas3:arm64. 629s Preparing to unpack .../06-libblas3_3.12.0-3_arm64.deb ... 629s Unpacking libblas3:arm64 (3.12.0-3) ... 629s Selecting previously unselected package libgfortran5:arm64. 629s Preparing to unpack .../07-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 629s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 629s Selecting previously unselected package liblapack3:arm64. 629s Preparing to unpack .../08-liblapack3_3.12.0-3_arm64.deb ... 629s Unpacking liblapack3:arm64 (3.12.0-3) ... 630s Selecting previously unselected package python3-numpy. 630s Preparing to unpack .../09-python3-numpy_1%3a1.24.2-2_arm64.deb ... 630s Unpacking python3-numpy (1:1.24.2-2) ... 633s Selecting previously unselected package libtcl8.6:arm64. 633s Preparing to unpack .../10-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 633s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 634s Selecting previously unselected package fonts-dejavu-mono. 634s Preparing to unpack .../11-fonts-dejavu-mono_2.37-8_all.deb ... 634s Unpacking fonts-dejavu-mono (2.37-8) ... 634s Selecting previously unselected package fonts-dejavu-core. 634s Preparing to unpack .../12-fonts-dejavu-core_2.37-8_all.deb ... 635s Unpacking fonts-dejavu-core (2.37-8) ... 635s Selecting previously unselected package libfontenc1:arm64. 635s Preparing to unpack .../13-libfontenc1_1%3a1.1.8-1_arm64.deb ... 635s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 635s Selecting previously unselected package x11-common. 635s Preparing to unpack .../14-x11-common_1%3a7.7+23ubuntu2_all.deb ... 635s Unpacking x11-common (1:7.7+23ubuntu2) ... 635s Selecting previously unselected package xfonts-encodings. 636s Preparing to unpack .../15-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 636s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 636s Selecting previously unselected package xfonts-utils. 636s Preparing to unpack .../16-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 636s Unpacking xfonts-utils (1:7.7+6build2) ... 636s Selecting previously unselected package fonts-urw-base35. 636s Preparing to unpack .../17-fonts-urw-base35_20200910-8_all.deb ... 637s Unpacking fonts-urw-base35 (20200910-8) ... 639s Selecting previously unselected package fontconfig-config. 639s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 641s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 641s Selecting previously unselected package libfontconfig1:arm64. 642s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 642s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 642s Selecting previously unselected package libxrender1:arm64. 642s Preparing to unpack .../20-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 642s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 642s Selecting previously unselected package libxft2:arm64. 642s Preparing to unpack .../21-libxft2_2.3.6-1_arm64.deb ... 642s Unpacking libxft2:arm64 (2.3.6-1) ... 642s Selecting previously unselected package libxss1:arm64. 642s Preparing to unpack .../22-libxss1_1%3a1.2.3-1build2_arm64.deb ... 642s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 643s Selecting previously unselected package libtk8.6:arm64. 643s Preparing to unpack .../23-libtk8.6_8.6.14-1_arm64.deb ... 643s Unpacking libtk8.6:arm64 (8.6.14-1) ... 643s Selecting previously unselected package tk8.6-blt2.5. 643s Preparing to unpack .../24-tk8.6-blt2.5_2.5.3+dfsg-7_arm64.deb ... 643s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... 643s Selecting previously unselected package blt. 643s Preparing to unpack .../25-blt_2.5.3+dfsg-7_arm64.deb ... 643s Unpacking blt (2.5.3+dfsg-7) ... 643s Selecting previously unselected package python3-tk:arm64. 643s Preparing to unpack .../26-python3-tk_3.11.5-1_arm64.deb ... 643s Unpacking python3-tk:arm64 (3.11.5-1) ... 644s Selecting previously unselected package python3-pil.imagetk:arm64. 644s Preparing to unpack .../27-python3-pil.imagetk_10.2.0-1_arm64.deb ... 644s Unpacking python3-pil.imagetk:arm64 (10.2.0-1) ... 644s Selecting previously unselected package libgomp1:arm64. 644s Preparing to unpack .../28-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 644s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 644s Selecting previously unselected package libimagequant0:arm64. 644s Preparing to unpack .../29-libimagequant0_2.18.0-1_arm64.deb ... 644s Unpacking libimagequant0:arm64 (2.18.0-1) ... 645s Selecting previously unselected package libjpeg-turbo8:arm64. 645s Preparing to unpack .../30-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 645s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 645s Selecting previously unselected package libjpeg8:arm64. 645s Preparing to unpack .../31-libjpeg8_8c-2ubuntu11_arm64.deb ... 645s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 645s Selecting previously unselected package liblcms2-2:arm64. 645s Preparing to unpack .../32-liblcms2-2_2.14-2_arm64.deb ... 645s Unpacking liblcms2-2:arm64 (2.14-2) ... 645s Selecting previously unselected package libopenjp2-7:arm64. 645s Preparing to unpack .../33-libopenjp2-7_2.5.0-2_arm64.deb ... 645s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 645s Selecting previously unselected package libgraphite2-3:arm64. 645s Preparing to unpack .../34-libgraphite2-3_1.3.14-2_arm64.deb ... 645s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 646s Selecting previously unselected package libharfbuzz0b:arm64. 646s Preparing to unpack .../35-libharfbuzz0b_8.3.0-2_arm64.deb ... 646s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 646s Selecting previously unselected package libraqm0:arm64. 646s Preparing to unpack .../36-libraqm0_0.10.1-1_arm64.deb ... 646s Unpacking libraqm0:arm64 (0.10.1-1) ... 646s Selecting previously unselected package libjbig0:arm64. 646s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 646s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 646s Selecting previously unselected package liblerc4:arm64. 646s Preparing to unpack .../38-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 646s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 646s Selecting previously unselected package libsharpyuv0:arm64. 647s Preparing to unpack .../39-libsharpyuv0_1.3.2-0.4_arm64.deb ... 647s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 647s Selecting previously unselected package libwebp7:arm64. 647s Preparing to unpack .../40-libwebp7_1.3.2-0.4_arm64.deb ... 647s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 647s Selecting previously unselected package libtiff6:arm64. 647s Preparing to unpack .../41-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 647s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 648s Selecting previously unselected package libwebpdemux2:arm64. 648s Preparing to unpack .../42-libwebpdemux2_1.3.2-0.4_arm64.deb ... 648s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 648s Selecting previously unselected package libwebpmux3:arm64. 648s Preparing to unpack .../43-libwebpmux3_1.3.2-0.4_arm64.deb ... 648s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 648s Selecting previously unselected package python3-pil:arm64. 648s Preparing to unpack .../44-python3-pil_10.2.0-1_arm64.deb ... 648s Unpacking python3-pil:arm64 (10.2.0-1) ... 649s Selecting previously unselected package libpixman-1-0:arm64. 649s Preparing to unpack .../45-libpixman-1-0_0.42.2-1_arm64.deb ... 649s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 649s Selecting previously unselected package libxcb-render0:arm64. 649s Preparing to unpack .../46-libxcb-render0_1.15-1_arm64.deb ... 649s Unpacking libxcb-render0:arm64 (1.15-1) ... 650s Selecting previously unselected package libxcb-shm0:arm64. 650s Preparing to unpack .../47-libxcb-shm0_1.15-1_arm64.deb ... 650s Unpacking libxcb-shm0:arm64 (1.15-1) ... 650s Selecting previously unselected package libcairo2:arm64. 650s Preparing to unpack .../48-libcairo2_1.18.0-1_arm64.deb ... 650s Unpacking libcairo2:arm64 (1.18.0-1) ... 650s Selecting previously unselected package python3-cairo. 650s Preparing to unpack .../49-python3-cairo_1.25.1-2_arm64.deb ... 650s Unpacking python3-cairo (1.25.1-2) ... 650s Selecting previously unselected package python3-freetype. 650s Preparing to unpack .../50-python3-freetype_2.4.0-1_all.deb ... 650s Unpacking python3-freetype (2.4.0-1) ... 650s Selecting previously unselected package python3-rlpycairo. 651s Preparing to unpack .../51-python3-rlpycairo_0.3.0-3_all.deb ... 651s Unpacking python3-rlpycairo (0.3.0-3) ... 651s Selecting previously unselected package fonts-dejavu-extra. 651s Preparing to unpack .../52-fonts-dejavu-extra_2.37-8_all.deb ... 651s Unpacking fonts-dejavu-extra (2.37-8) ... 651s Selecting previously unselected package python3-reportlab. 651s Preparing to unpack .../53-python3-reportlab_4.1.0-1_all.deb ... 651s Unpacking python3-reportlab (4.1.0-1) ... 652s Selecting previously unselected package xml-core. 652s Preparing to unpack .../54-xml-core_0.19_all.deb ... 652s Unpacking xml-core (0.19) ... 652s Selecting previously unselected package w3c-sgml-lib. 652s Preparing to unpack .../55-w3c-sgml-lib_1.3-3_all.deb ... 652s Unpacking w3c-sgml-lib (1.3-3) ... 653s Selecting previously unselected package python3-biopython. 653s Preparing to unpack .../56-python3-biopython_1.81+dfsg-3_arm64.deb ... 653s Unpacking python3-biopython (1.81+dfsg-3) ... 656s Selecting previously unselected package python3-soupsieve. 656s Preparing to unpack .../57-python3-soupsieve_2.5-1_all.deb ... 656s Unpacking python3-soupsieve (2.5-1) ... 656s Selecting previously unselected package python3-bs4. 656s Preparing to unpack .../58-python3-bs4_4.12.3-1_all.deb ... 656s Unpacking python3-bs4 (4.12.3-1) ... 656s Selecting previously unselected package python3-dendropy. 656s Preparing to unpack .../59-python3-dendropy_4.6.1-1_all.deb ... 656s Unpacking python3-dendropy (4.6.1-1) ... 657s Selecting previously unselected package libjs-jquery. 657s Preparing to unpack .../60-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 657s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 657s Selecting previously unselected package libjs-jquery-ui. 657s Preparing to unpack .../61-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 657s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 659s Selecting previously unselected package fonts-lyx. 659s Preparing to unpack .../62-fonts-lyx_2.4.0~RC3-1_all.deb ... 659s Unpacking fonts-lyx (2.4.0~RC3-1) ... 659s Selecting previously unselected package python-matplotlib-data. 659s Preparing to unpack .../63-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ... 659s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ... 660s Selecting previously unselected package python3-dateutil. 660s Preparing to unpack .../64-python3-dateutil_2.8.2-3_all.deb ... 660s Unpacking python3-dateutil (2.8.2-3) ... 660s Selecting previously unselected package python3-contourpy. 660s Preparing to unpack .../65-python3-contourpy_1.0.7-1build2_arm64.deb ... 660s Unpacking python3-contourpy (1.0.7-1build2) ... 661s Selecting previously unselected package python3-cycler. 661s Preparing to unpack .../66-python3-cycler_0.11.0-2_all.deb ... 661s Unpacking python3-cycler (0.11.0-2) ... 661s Selecting previously unselected package python3-brotli. 661s Preparing to unpack .../67-python3-brotli_1.1.0-2_arm64.deb ... 661s Unpacking python3-brotli (1.1.0-2) ... 661s Selecting previously unselected package python3-decorator. 661s Preparing to unpack .../68-python3-decorator_5.1.1-5_all.deb ... 661s Unpacking python3-decorator (5.1.1-5) ... 661s Selecting previously unselected package liblbfgsb0:arm64. 661s Preparing to unpack .../69-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 661s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 662s Selecting previously unselected package python3-scipy. 662s Preparing to unpack .../70-python3-scipy_1.11.4-6_arm64.deb ... 662s Unpacking python3-scipy (1.11.4-6) ... 667s Selecting previously unselected package python3-ufolib2. 667s Preparing to unpack .../71-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 667s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 668s Selecting previously unselected package python3-mpmath. 668s Preparing to unpack .../72-python3-mpmath_1.2.1-3_all.deb ... 668s Unpacking python3-mpmath (1.2.1-3) ... 668s Selecting previously unselected package python3-sympy. 668s Preparing to unpack .../73-python3-sympy_1.12-7_all.deb ... 668s Unpacking python3-sympy (1.12-7) ... 671s Selecting previously unselected package python3-appdirs. 671s Preparing to unpack .../74-python3-appdirs_1.4.4-4_all.deb ... 671s Unpacking python3-appdirs (1.4.4-4) ... 671s Selecting previously unselected package python3-fs. 671s Preparing to unpack .../75-python3-fs_2.4.16-3_all.deb ... 671s Unpacking python3-fs (2.4.16-3) ... 671s Selecting previously unselected package libxslt1.1:arm64. 671s Preparing to unpack .../76-libxslt1.1_1.1.39-0exp1_arm64.deb ... 671s Unpacking libxslt1.1:arm64 (1.1.39-0exp1) ... 671s Selecting previously unselected package python3-lxml:arm64. 671s Preparing to unpack .../77-python3-lxml_5.1.0-1_arm64.deb ... 671s Unpacking python3-lxml:arm64 (5.1.0-1) ... 673s Selecting previously unselected package python3-lz4. 673s Preparing to unpack .../78-python3-lz4_4.0.2+dfsg-1build2_arm64.deb ... 673s Unpacking python3-lz4 (4.0.2+dfsg-1build2) ... 673s Selecting previously unselected package python3-unicodedata2. 673s Preparing to unpack .../79-python3-unicodedata2_15.1.0+ds-1_arm64.deb ... 673s Unpacking python3-unicodedata2 (15.1.0+ds-1) ... 673s Selecting previously unselected package unicode-data. 673s Preparing to unpack .../80-unicode-data_15.1.0-1_all.deb ... 673s Unpacking unicode-data (15.1.0-1) ... 675s Selecting previously unselected package python3-fonttools. 675s Preparing to unpack .../81-python3-fonttools_4.46.0-1_arm64.deb ... 675s Unpacking python3-fonttools (4.46.0-1) ... 676s Selecting previously unselected package python3-kiwisolver. 676s Preparing to unpack .../82-python3-kiwisolver_1.4.4-2_arm64.deb ... 676s Unpacking python3-kiwisolver (1.4.4-2) ... 676s Selecting previously unselected package python3-packaging. 676s Preparing to unpack .../83-python3-packaging_23.2-1_all.deb ... 676s Unpacking python3-packaging (23.2-1) ... 676s Selecting previously unselected package libqhull-r8.0:arm64. 676s Preparing to unpack .../84-libqhull-r8.0_2020.2-6_arm64.deb ... 676s Unpacking libqhull-r8.0:arm64 (2020.2-6) ... 676s Selecting previously unselected package python3-matplotlib. 676s Preparing to unpack .../85-python3-matplotlib_3.6.3-1ubuntu3_arm64.deb ... 676s Unpacking python3-matplotlib (3.6.3-1ubuntu3) ... 678s Selecting previously unselected package mummer. 678s Preparing to unpack .../86-mummer_3.23+dfsg-8_arm64.deb ... 678s Unpacking mummer (3.23+dfsg-8) ... 679s Selecting previously unselected package python3-pymummer. 679s Preparing to unpack .../87-python3-pymummer_0.11.0-4_all.deb ... 679s Unpacking python3-pymummer (0.11.0-4) ... 679s Selecting previously unselected package python3-pysam. 679s Preparing to unpack .../88-python3-pysam_0.22.0+ds-1_arm64.deb ... 679s Unpacking python3-pysam (0.22.0+ds-1) ... 684s Selecting previously unselected package libfml0:arm64. 684s Preparing to unpack .../89-libfml0_0.1+git20190320.b499514-1_arm64.deb ... 684s Unpacking libfml0:arm64 (0.1+git20190320.b499514-1) ... 684s Selecting previously unselected package libminimap0:arm64. 684s Preparing to unpack .../90-libminimap0_0.2-8_arm64.deb ... 684s Unpacking libminimap0:arm64 (0.2-8) ... 684s Selecting previously unselected package bowtie2. 685s Preparing to unpack .../91-bowtie2_2.5.2-1_arm64.deb ... 685s Unpacking bowtie2 (2.5.2-1) ... 685s Selecting previously unselected package cd-hit. 685s Preparing to unpack .../92-cd-hit_4.8.1-4_arm64.deb ... 685s Unpacking cd-hit (4.8.1-4) ... 685s Selecting previously unselected package libcapnp-1.0.1:arm64. 685s Preparing to unpack .../93-libcapnp-1.0.1_1.0.1-3_arm64.deb ... 685s Unpacking libcapnp-1.0.1:arm64 (1.0.1-3) ... 686s Selecting previously unselected package libgslcblas0:arm64. 686s Preparing to unpack .../94-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 686s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 686s Selecting previously unselected package libgsl27:arm64. 686s Preparing to unpack .../95-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 686s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 686s Selecting previously unselected package libmurmurhash2:arm64. 686s Preparing to unpack .../96-libmurmurhash2_1.6-1_arm64.deb ... 686s Unpacking libmurmurhash2:arm64 (1.6-1) ... 687s Selecting previously unselected package mash. 687s Preparing to unpack .../97-mash_2.3+dfsg-6_arm64.deb ... 687s Unpacking mash (2.3+dfsg-6) ... 687s Selecting previously unselected package ariba. 687s Preparing to unpack .../98-ariba_2.14.7+ds-2_arm64.deb ... 687s Unpacking ariba (2.14.7+ds-2) ... 690s Selecting previously unselected package autopkgtest-satdep. 690s Preparing to unpack .../99-1-autopkgtest-satdep.deb ... 690s Unpacking autopkgtest-satdep (0) ... 690s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 690s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 690s Setting up liblcms2-2:arm64 (2.14-2) ... 690s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 690s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 690s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 690s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 690s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 690s Setting up libmurmurhash2:arm64 (1.6-1) ... 690s Setting up libcapnp-1.0.1:arm64 (1.0.1-3) ... 690s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 692s Setting up libxcb-render0:arm64 (1.15-1) ... 692s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 692s Setting up fonts-lyx (2.4.0~RC3-1) ... 692s Setting up x11-common (1:7.7+23ubuntu2) ... 696s Setting up libdeflate0:arm64 (1.19-1) ... 696s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 696s Setting up libqhull-r8.0:arm64 (2020.2-6) ... 696s Setting up libxcb-shm0:arm64 (1.15-1) ... 696s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 696s Setting up python3-freetype (2.4.0-1) ... 698s Setting up libfml0:arm64 (0.1+git20190320.b499514-1) ... 698s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 698s Setting up bowtie2 (2.5.2-1) ... 698s Setting up unicode-data (15.1.0-1) ... 698s Setting up python3-decorator (5.1.1-5) ... 699s Setting up libminimap0:arm64 (0.2-8) ... 699s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 699s Setting up libblas3:arm64 (3.12.0-3) ... 699s 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 699s Setting up python3-packaging (23.2-1) ... 700s Setting up python3-brotli (1.1.0-2) ... 702s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 702s Setting up python3-cycler (0.11.0-2) ... 704s Setting up libimagequant0:arm64 (2.18.0-1) ... 704s Setting up fonts-dejavu-mono (2.37-8) ... 704s Setting up python3-kiwisolver (1.4.4-2) ... 704s Setting up mash (2.3+dfsg-6) ... 704s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 704s Setting up fonts-dejavu-core (2.37-8) ... 704s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 704s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 704s Setting up libwebp7:arm64 (1.3.2-0.4) ... 704s Setting up fonts-dejavu-extra (2.37-8) ... 704s Setting up libxslt1.1:arm64 (1.1.39-0exp1) ... 704s Setting up mummer (3.23+dfsg-8) ... 704s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 704s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 704s Setting up python3-dateutil (2.8.2-3) ... 707s Setting up sgml-base (1.31) ... 708s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 708s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 708s Setting up python3-mpmath (1.2.1-3) ... 712s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 712s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 712s Setting up python3-dendropy (4.6.1-1) ... 715s Setting up python3-appdirs (1.4.4-4) ... 717s Setting up python3-soupsieve (2.5-1) ... 718s Setting up cd-hit (4.8.1-4) ... 718s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 718s Setting up python3-sympy (1.12-7) ... 766s Setting up liblapack3:arm64 (3.12.0-3) ... 766s 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 766s Setting up libhts3:arm64 (1.18+ds-1) ... 766s Setting up python3-pysam (0.22.0+ds-1) ... 768s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 769s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 769s Setting up xfonts-utils (1:7.7+6build2) ... 770s Setting up python3-bs4 (4.12.3-1) ... 771s Setting up samtools (1.19.2-1) ... 771s Setting up python3-fs (2.4.16-3) ... 774s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 774s Setting up libraqm0:arm64 (0.10.1-1) ... 774s Setting up python3-numpy (1:1.24.2-2) ... 791s Setting up python3-lxml:arm64 (5.1.0-1) ... 792s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 792s Setting up xml-core (0.19) ... 793s Setting up python3-contourpy (1.0.7-1build2) ... 795s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 795s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 795s Setting up libxft2:arm64 (2.3.6-1) ... 795s Setting up python3-scipy (1.11.4-6) ... 823s Setting up libtk8.6:arm64 (8.6.14-1) ... 823s Setting up fastaq (3.17.0-6) ... 824s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 824s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 824s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 824s gbk_regex = re.compile('^LOCUS\s+\S') 824s Setting up fonts-urw-base35 (20200910-8) ... 826s Setting up libcairo2:arm64 (1.18.0-1) ... 826s Setting up python3-pymummer (0.11.0-4) ... 827s Setting up python3-pil:arm64 (10.2.0-1) ... 831s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 831s Setting up python3-cairo (1.25.1-2) ... 831s Setting up blt (2.5.3+dfsg-7) ... 831s Setting up python3-tk:arm64 (3.11.5-1) ... 833s Setting up python3-pil.imagetk:arm64 (10.2.0-1) ... 834s Setting up python3-rlpycairo (0.3.0-3) ... 835s Setting up python3-reportlab (4.1.0-1) ... 840s Setting up python3-fonttools (4.46.0-1) ... 848s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 848s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 860s Processing triggers for libc-bin (2.39-0ubuntu6) ... 860s Processing triggers for man-db (2.12.0-3) ... 867s Processing triggers for sgml-base (1.31) ... 867s Setting up w3c-sgml-lib (1.3-3) ... 1063s Setting up python3-biopython (1.81+dfsg-3) ... 1070s Setting up ariba (2.14.7+ds-2) ... 1071s /usr/lib/python3/dist-packages/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.' 1071s 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), 1071s /usr/lib/python3/dist-packages/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.' 1071s 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), 1071s /usr/lib/python3/dist-packages/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.' 1071s 'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)')) 1072s Setting up autopkgtest-satdep (0) ... 1091s (Reading database ... 86153 files and directories currently installed.) 1091s Removing autopkgtest-satdep (0) ... 1093s autopkgtest [03:21:20]: test test-example: [----------------------- 1107s ARIBA version: 2.14.6 1107s 1107s External dependencies: 1107s bowtie2 2.5.2 /usr/bin/bowtie2 1107s cdhit 4.8.1 /usr/bin/cd-hit-est 1107s nucmer 3.1 /usr/bin/nucmer 1107s 1107s External dependencies OK: True 1107s 1107s Python version: 1107s 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 1107s 1107s Python packages: 1107s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 1107s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 1107s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 1107s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 1107s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 1107s pysam 0.22.0 /usr/lib/python3/dist-packages/pysam/__init__.py 1107s 1107s Python packages OK: True 1107s 1107s Everything looks OK: True 1107s 1107s Loading and checking input data 1107s 1107s Running cdhit 1108s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.f99f3E16ci/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.f99f3E16ci/foo/tmp.run_cd-hit._ucdk2dx/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 1108s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.f99f3E16ci/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.f99f3E16ci/foo/tmp.run_cd-hit.r6g0t3c3/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 1109s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.f99f3E16ci/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.f99f3E16ci/foo/tmp.run_cd-hit.dmnwrrqn/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 1109s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.f99f3E16ci/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.f99f3E16ci/foo/tmp.run_cd-hit.hbqb08hs/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 1110s 1110s Writing clusters to file. 10 in total 1114s Found reads file: reads_1.fq 1114s Found reads file: reads_2.fq 1114s ARIBA version: 2.14.6 1114s 1114s External dependencies: 1114s bowtie2 2.5.2 /usr/bin/bowtie2 1114s cdhit 4.8.1 /usr/bin/cd-hit-est 1114s nucmer 3.1 /usr/bin/nucmer 1114s 1114s External dependencies OK: True 1114s 1114s Python version: 1114s 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 1114s 1114s Python packages: 1114s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 1114s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 1114s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 1114s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 1114s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 1114s pysam 0.22.0 /usr/lib/python3/dist-packages/pysam/__init__.py 1114s 1114s Python packages OK: True 1114s 1114s Everything looks OK: True 1114s Temporary directory: /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j 1114s ______________________ Mapping reads to clustered genes _______________________ 1114s Finished mapping 1114s 1114s _____________________________ Generating clusters _____________________________ 1114s syscall: sort -k1,1 -k 2,2n /tmp/tmp.f99f3E16ci/foo/OUT/minimap.reads > /tmp/tmp.f99f3E16ci/foo/OUT/read_store 1114s Compressing file /tmp/tmp.f99f3E16ci/foo/OUT/read_store 1114s Found 51 proper read pairs from minimap 1114s Total clusters to perform local assemblies: 9 1114s 1114s Insert size information from reads mapped to reference genes: 1114s Insert size: 185.0 1114s Insert sspace sd: 0.27 1114s Max insert: 220.55 1114s 1114s ___________________________ Assembling each cluster ___________________________ 1114s Will run 1 cluster(s) in parallel 1115s Not constructing cluster cluster because it only has 2 reads (1 of 9) 1115s Constructing cluster cluster_1 (2 of 9) 1115s Constructing cluster cluster_2 (3 of 9) 1115s Constructing cluster cluster_3 (4 of 9) 1115s Constructing cluster cluster_4 (5 of 9) 1115s Constructing cluster gene (6 of 9) 1115s Constructing cluster gene_1 (7 of 9) 1115s Constructing cluster noncoding (8 of 9) 1115s Constructing cluster noncoding_1 (9 of 9) 1115s Start running cluster cluster_1 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_1 1125s cluster_1 detected 1 threads available to it 1125s cluster_1 reported completion 1125s Finished running cluster cluster_1 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_1 1125s Deleting cluster dir /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_1 1125s Start running cluster cluster_2 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_2 1136s cluster_2 detected 1 threads available to it 1136s cluster_2 reported completion 1136s Finished running cluster cluster_2 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_2 1136s Deleting cluster dir /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_2 1136s Start running cluster cluster_3 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_3 1146s cluster_3 detected 1 threads available to it 1146s cluster_3 reported completion 1146s Finished running cluster cluster_3 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_3 1146s Deleting cluster dir /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_3 1146s Start running cluster cluster_4 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_4 1156s cluster_4 detected 1 threads available to it 1156s cluster_4 reported completion 1156s Finished running cluster cluster_4 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_4 1156s Deleting cluster dir /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/cluster_4 1156s Start running cluster gene in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/gene 1165s gene detected 1 threads available to it 1165s gene reported completion 1165s Finished running cluster gene in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/gene 1165s Deleting cluster dir /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/gene 1165s Start running cluster gene_1 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/gene_1 1175s gene_1 detected 1 threads available to it 1175s gene_1 reported completion 1175s Finished running cluster gene_1 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/gene_1 1175s Deleting cluster dir /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/gene_1 1175s Start running cluster noncoding in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/noncoding 1185s noncoding detected 1 threads available to it 1185s noncoding reported completion 1185s Finished running cluster noncoding in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/noncoding 1185s Deleting cluster dir /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/noncoding 1185s Start running cluster noncoding_1 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/noncoding_1 1195s noncoding_1 detected 1 threads available to it 1195s noncoding_1 reported completion 1195s Finished running cluster noncoding_1 in directory /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/noncoding_1 1195s Deleting cluster dir /tmp/tmp.f99f3E16ci/foo/OUT/ariba.tmp.liotd90j/noncoding_1 1195s Final value of remaining_clusters counter: Value('l', 0) 1195s Finished assembling clusters 1195s 1195s _______________________________ Writing reports _______________________________ 1195s Making /tmp/tmp.f99f3E16ci/foo/OUT/debug.report.tsv 1195s Making /tmp/tmp.f99f3E16ci/foo/OUT/report.tsv 1195s 1195s ____________________ Writing fasta of assembled sequences _____________________ 1195s /tmp/tmp.f99f3E16ci/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.f99f3E16ci/foo/OUT/assembled_genes.fa.gz 1195s 1195s __________________________ Catting cluster log files __________________________ 1195s Writing file /tmp/tmp.f99f3E16ci/foo/OUT/log.clusters.gz 1196s 1196s _______________________________ Cleaning files ________________________________ 1196s Deleting Logs directory /tmp/tmp.f99f3E16ci/foo/OUT/Logs 1196s Deleting reads store files /tmp/tmp.f99f3E16ci/foo/OUT/read_store.gz[.tbi] 1196s 1196s All done! 1196s 1196s Running ARIBA on test data... 1196s ------------------------------------------------------------------------------- 1196s |=============================================================================| 1196s | Preparing input data | 1196s |=============================================================================| 1196s ------------------------------------------------------------------------------- 1196s Made output directory ./foo. Copying test data files into it: 1196s copied ref_seqs.fa 1196s copied metadata.tsv 1196s copied reads_1.fq 1196s copied reads_2.fq 1196s ------------------------------------------------------------------------------- 1196s |=============================================================================| 1196s | Try running ariba prepareref | 1196s |=============================================================================| 1196s ------------------------------------------------------------------------------- 1196s 1196s Running ariba prepareref with: 1196s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 1196s 1196s 1196s ariba prepareref finished OK 1196s ------------------------------------------------------------------------------- 1196s |=============================================================================| 1196s | Try running ariba run | 1196s |=============================================================================| 1196s ------------------------------------------------------------------------------- 1196s 1196s Running ARIBA with: 1196s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 1196s 1196s 1196s ariba run finished OK 1196s Finished run on test data OK 1198s autopkgtest [03:23:05]: test test-example: -----------------------] 1198s autopkgtest [03:23:05]: test test-example: - - - - - - - - - - results - - - - - - - - - - 1198s test-example PASS 1199s autopkgtest [03:23:06]: @@@@@@@@@@@@@@@@@@@@ summary 1199s test-example PASS 1238s Creating nova instance adt-noble-arm64-ariba-20240325-030307-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...