0s autopkgtest [09:23:22]: starting date and time: 2024-11-13 09:23:22+0000
  0s autopkgtest [09:23:22]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time
  0s autopkgtest [09:23:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l15n7kta/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade idseq-bench --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-30.secgroup --name adt-plucky-arm64-idseq-bench-20241113-092322-juju-7f2275-prod-proposed-migration-environment-2-a5521310-9ba2-4259-a3a9-1d86e6cf6c1c --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.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/
 75s autopkgtest [09:24:37]: testbed dpkg architecture: arm64
 75s autopkgtest [09:24:37]: testbed apt version: 2.9.8
 75s autopkgtest [09:24:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 77s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
 77s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
 77s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB]
 77s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
 77s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB]
 77s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB]
 78s Fetched 1793 kB in 1s (1809 kB/s)
 78s Reading package lists...
 81s Reading package lists...
 82s Building dependency tree...
 82s Reading state information...
 83s Calculating upgrade...
 84s The following NEW packages will be installed:
 84s   python3.13-gdbm
 84s The following packages will be upgraded:
 84s   libpython3-stdlib python3 python3-gdbm python3-minimal
 84s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 84s Need to get 101 kB of archives.
 84s After this operation, 141 kB of additional disk space will be used.
 84s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB]
 84s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB]
 84s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB]
 84s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB]
 84s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B]
 85s Fetched 101 kB in 0s (286 kB/s)
 85s (Reading database ... 
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(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 ... 79924 files and directories currently installed.)
 85s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ...
 85s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 85s Setting up python3-minimal (3.12.7-1) ...
 85s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 79924 files and directories currently installed.)
 85s Preparing to unpack .../python3_3.12.7-1_arm64.deb ...
 85s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 85s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ...
 85s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 85s Selecting previously unselected package python3.13-gdbm.
 85s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ...
 85s Unpacking python3.13-gdbm (3.13.0-2) ...
 85s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ...
 85s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 85s Setting up python3.13-gdbm (3.13.0-2) ...
 85s Setting up libpython3-stdlib:arm64 (3.12.7-1) ...
 85s Setting up python3 (3.12.7-1) ...
 86s Setting up python3-gdbm:arm64 (3.12.7-1) ...
 86s Processing triggers for man-db (2.12.1-3) ...
 87s Reading package lists...
 87s Building dependency tree...
 87s Reading state information...
 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 88s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 88s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 88s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 88s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 90s Reading package lists...
 90s Reading package lists...
 91s Building dependency tree...
 91s Reading state information...
 91s Calculating upgrade...
 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 92s Reading package lists...
 92s Building dependency tree...
 92s Reading state information...
 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 96s autopkgtest [09:24:58]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
 96s autopkgtest [09:24:58]: @@@@@@@@@@@@@@@@@@@@ apt-source idseq-bench
 98s Get:1 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (dsc) [2356 B]
 98s Get:2 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (tar) [17.3 kB]
 98s Get:3 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (diff) [4432 B]
 98s gpgv: Signature made Mon Jan 17 12:05:35 2022 UTC
 98s gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
 98s gpgv:                issuer "nilesh@debian.org"
 98s gpgv: Can't check signature: No public key
 98s dpkg-source: warning: cannot verify inline signature for ./idseq-bench_0.0~git20210602.27fb6dc-1.dsc: no acceptable signature found
 98s autopkgtest [09:25:00]: testing package idseq-bench version 0.0~git20210602.27fb6dc-1
 99s autopkgtest [09:25:01]: build not needed
100s autopkgtest [09:25:02]: test run-unit-test: preparing testbed
102s Reading package lists...
102s Building dependency tree...
102s Reading state information...
103s Starting pkgProblemResolver with broken count: 0
103s Starting 2 pkgProblemResolver with broken count: 0
103s Done
104s The following additional packages will be installed:
104s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35
104s   idseq-bench insilicoseq libblas3 libcairo2 libdeflate0 libfontconfig1
104s   libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64
104s   libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
104s   liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0
104s   libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6
104s   libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1
104s   ncbi-acc-download python3-all python3-biopython python3-cairo
104s   python3-decorator python3-freetype python3-joblib python3-numpy python3-pil
104s   python3-pysam python3-reportlab python3-rlpycairo python3-scipy
104s   python3-sklearn python3-sklearn-lib python3-smart-open python3-threadpoolctl
104s   python3-wrapt python3.13 python3.13-minimal sgml-base w3c-sgml-lib
104s   x11-common xfonts-encodings xfonts-utils xml-core
104s Suggested packages:
104s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils
104s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
104s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
104s   python3-rdflib python3-psycopg2 raxml samtools t-coffee wise
104s   python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest
104s   python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc
104s   rl-accel rl-renderpm python-scipy-doc python3-dap python-sklearn-doc
104s   ipython3 python3-azure python3-azure-storage python3.13-venv python3.13-doc
104s   binfmt-support sgml-base-doc debhelper
104s Recommended packages:
104s   python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson
104s   python3-psutil python3-olefile fonts-dejavu-extra g++ | c++-compiler
104s   python3-matplotlib python3-boto3 python3-paramiko python3-zstandard
104s The following NEW packages will be installed:
104s   autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono
104s   fonts-urw-base35 idseq-bench insilicoseq libblas3 libcairo2 libdeflate0
104s   libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3
104s   libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0
104s   libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4
104s   libopenjp2-7 libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib
104s   libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3
104s   libxcb-render0 libxcb-shm0 libxrender1 ncbi-acc-download python3-all
104s   python3-biopython python3-cairo python3-decorator python3-freetype
104s   python3-joblib python3-numpy python3-pil python3-pysam python3-reportlab
104s   python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib
104s   python3-smart-open python3-threadpoolctl python3-wrapt python3.13
104s   python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings
104s   xfonts-utils xml-core
104s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded.
104s Need to get 63.0 MB/63.0 MB of archives.
104s After this operation, 254 MB of additional disk space will be used.
104s Get:1 /tmp/autopkgtest.LTiDeg/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [760 B]
105s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB]
105s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB]
105s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB]
105s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
105s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
105s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB]
105s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
105s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
105s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB]
105s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
106s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
106s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB]
106s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB]
106s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB]
106s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB]
106s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB]
106s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
106s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB]
106s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
106s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
106s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB]
106s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
106s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB]
106s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB]
106s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB]
106s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
106s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB]
106s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
106s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
106s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
106s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB]
106s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB]
106s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB]
106s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
106s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
107s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
107s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
107s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
107s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
107s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB]
107s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB]
107s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B]
107s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB]
107s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB]
107s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
107s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB]
107s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB]
107s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB]
107s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB]
107s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
107s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB]
107s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB]
108s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 insilicoseq all 2.0.1-1 [4247 kB]
108s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-acc-download all 0.2.8-3 [13.3 kB]
108s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB]
108s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB]
108s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB]
108s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB]
108s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wrapt arm64 1.15.0-3 [34.0 kB]
108s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-smart-open all 7.0.5-1 [89.9 kB]
108s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 idseq-bench all 0.0~git20210602.27fb6dc-1 [24.7 kB]
108s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB]
108s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB]
108s Get:65 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B]
109s Fetched 63.0 MB in 4s (15.6 MB/s)
109s Selecting previously unselected package libpython3.13-minimal:arm64.
109s (Reading database ... 
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(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 ... 79931 files and directories currently installed.)
109s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ...
109s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ...
109s Selecting previously unselected package python3.13-minimal.
109s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ...
109s Unpacking python3.13-minimal (3.13.0-2) ...
109s Selecting previously unselected package sgml-base.
109s Preparing to unpack .../02-sgml-base_1.31_all.deb ...
109s Unpacking sgml-base (1.31) ...
110s Selecting previously unselected package fonts-dejavu-mono.
110s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ...
110s Unpacking fonts-dejavu-mono (2.37-8) ...
110s Selecting previously unselected package fonts-dejavu-core.
110s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ...
110s Unpacking fonts-dejavu-core (2.37-8) ...
110s Selecting previously unselected package libfontenc1:arm64.
110s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_arm64.deb ...
110s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ...
110s Selecting previously unselected package x11-common.
110s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ...
110s Unpacking x11-common (1:7.7+23ubuntu3) ...
110s Selecting previously unselected package xfonts-encodings.
110s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
110s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
110s Selecting previously unselected package xfonts-utils.
110s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_arm64.deb ...
110s Unpacking xfonts-utils (1:7.7+7) ...
110s Selecting previously unselected package fonts-urw-base35.
110s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ...
110s Unpacking fonts-urw-base35 (20200910-8) ...
110s Selecting previously unselected package fontconfig-config.
110s Preparing to unpack .../10-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ...
111s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
111s Selecting previously unselected package libblas3:arm64.
111s Preparing to unpack .../11-libblas3_3.12.0-3build2_arm64.deb ...
111s Unpacking libblas3:arm64 (3.12.0-3build2) ...
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111s Selecting previously unselected package libgomp1:arm64.
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112s Selecting previously unselected package python3-pil:arm64.
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112s Selecting previously unselected package libfontconfig1:arm64.
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112s Selecting previously unselected package libpixman-1-0:arm64.
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112s Selecting previously unselected package libxcb-render0:arm64.
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116s Setting up libhtscodecs2:arm64 (1.6.1-1) ...
116s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
116s Setting up liblcms2-2:arm64 (2.16-2) ...
116s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
116s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ...
116s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ...
116s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
116s Setting up python3-joblib (1.3.2-5) ...
117s Setting up libxcb-render0:arm64 (1.17.0-2) ...
117s Setting up python3-threadpoolctl (3.1.0-1) ...
117s Setting up x11-common (1:7.7+23ubuntu3) ...
118s Setting up libdeflate0:arm64 (1.22-1) ...
118s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
118s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ...
118s Setting up python3-freetype (2.5.1-1) ...
118s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
118s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ...
118s Setting up python3-decorator (5.1.1-5) ...
118s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ...
118s Setting up libblas3:arm64 (3.12.0-3build2) ...
118s 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
118s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
118s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
118s Setting up fonts-dejavu-mono (2.37-8) ...
118s Setting up python3-wrapt (1.15.0-3) ...
119s Setting up fonts-dejavu-core (2.37-8) ...
119s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
119s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ...
119s Setting up libwebp7:arm64 (1.4.0-0.1) ...
119s Setting up libhts3t64:arm64 (1.20+ds-1) ...
119s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ...
119s Setting up python3.13-minimal (3.13.0-2) ...
120s Setting up ncbi-acc-download (0.2.8-3) ...
121s Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
121s Setting up sgml-base (1.31) ...
121s Setting up libwebpmux3:arm64 (1.4.0-0.1) ...
121s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ...
121s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
121s Setting up liblapack3:arm64 (3.12.0-3build2) ...
121s 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
121s Setting up python3-pysam (0.22.1+ds-2) ...
121s Setting up python3-smart-open (7.0.5-1) ...
122s Setting up python3.13 (3.13.0-2) ...
123s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
124s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ...
124s Setting up python3-all (3.12.7-1) ...
124s Setting up xfonts-utils (1:7.7+7) ...
124s Setting up libraqm0:arm64 (0.10.1-1build1) ...
124s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
129s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
129s Setting up xml-core (0.19) ...
129s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
129s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
129s Setting up python3-scipy (1.13.1-5) ...
139s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ...
139s Setting up fonts-urw-base35 (20200910-8) ...
140s Setting up libcairo2:arm64 (1.18.2-2) ...
140s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ...
141s Setting up python3-sklearn (1.4.2+dfsg-6) ...
148s Setting up python3-cairo (1.26.1-2) ...
148s Setting up python3-rlpycairo (0.3.0-3) ...
148s Setting up python3-reportlab (4.2.5-1) ...
151s Processing triggers for libc-bin (2.40-1ubuntu3) ...
151s Processing triggers for systemd (256.5-2ubuntu4) ...
151s Processing triggers for man-db (2.12.1-3) ...
152s Processing triggers for sgml-base (1.31) ...
152s Setting up w3c-sgml-lib (1.3-3) ...
191s Setting up python3-biopython (1.84+dfsg-4) ...
195s Setting up insilicoseq (2.0.1-1) ...
196s Setting up idseq-bench (0.0~git20210602.27fb6dc-1) ...
196s Setting up autopkgtest-satdep (0) ...
204s (Reading database ... 86984 files and directories currently installed.)
204s Removing autopkgtest-satdep (0) ...
204s autopkgtest [09:26:46]: test run-unit-test: [-----------------------
441s INFO:iss.app:Starting iss generate
441s INFO:iss.generator:Using kde ErrorModel
441s INFO:iss.util:Stitching input files together
442s INFO:iss.generator:Using abundance file:norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4708_abundance.txt
442s INFO:iss.app:Using 2 cpus for read generation
442s INFO:iss.app:Generating 60000 reads
474s INFO:iss.util:Stitching input files together
474s INFO:iss.util:Stitching input files together
474s INFO:iss.util:Cleaning up
474s INFO:iss.app:Read generation complete
482s Generating IDseq benchmark data...
482s 'cd downloads; ncbi-acc-download --format fasta NC_016845.1 -e all'
482s 'cat downloads/NC_016845.1.fa > downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta'
482s "grep -v '^>' downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta | tr -d '\n' | wc > bateria__klebsiella_pneumoniae_HS11286__1125630.size"
482s Genome bateria__klebsiella_pneumoniae_HS11286__1125630 size 5333942 bases.
482s 'cd downloads; ncbi-acc-download --format fasta NC_007194.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_007195.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_007196.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_007197.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_007198.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_007199.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_007200.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_007201.1 -e all'
482s 'cat downloads/NC_007194.1.fa downloads/NC_007195.1.fa downloads/NC_007196.1.fa downloads/NC_007197.1.fa downloads/NC_007198.1.fa downloads/NC_007199.1.fa downloads/NC_007200.1.fa downloads/NC_007201.1.fa > downloads/fungi__aspergillus_fumigatus__330879.fasta'
482s "grep -v '^>' downloads/fungi__aspergillus_fumigatus__330879.fasta | tr -d '\n' | wc > fungi__aspergillus_fumigatus__330879.size"
482s Genome fungi__aspergillus_fumigatus__330879 size 29384958 bases.
482s 'cd downloads; ncbi-acc-download --format fasta MG148341.1 -e all'
482s 'cat downloads/MG148341.1.fa > downloads/viruses__rhinovirus_c__463676.fasta'
482s "grep -v '^>' downloads/viruses__rhinovirus_c__463676.fasta | tr -d '\n' | wc > viruses__rhinovirus_c__463676.size"
482s Genome viruses__rhinovirus_c__463676 size 7056 bases.
482s 'cd downloads; ncbi-acc-download --format fasta MG049915.1 -e all'
482s 'cat downloads/MG049915.1.fa > downloads/viruses__chikungunya__37124.fasta'
482s "grep -v '^>' downloads/viruses__chikungunya__37124.fasta | tr -d '\n' | wc > viruses__chikungunya__37124.size"
482s Genome viruses__chikungunya__37124 size 11604 bases.
482s 'cd downloads; ncbi-acc-download --format fasta NC_007795.1 -e all'
482s 'cat downloads/NC_007795.1.fa > downloads/bateria__staphylococcus_aureus__93061.fasta'
482s "grep -v '^>' downloads/bateria__staphylococcus_aureus__93061.fasta | tr -d '\n' | wc > bateria__staphylococcus_aureus__93061.size"
482s Genome bateria__staphylococcus_aureus__93061 size 2821361 bases.
482s 'cd downloads; ncbi-acc-download --format fasta NC_004325.2 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_037280.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_000521.4 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_004318.2 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_004326.2 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_004327.3 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_004328.3 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_004329.3 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_004330.2 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_037281.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_037282.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_037284.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_004331.3 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_037283.1 -e all'
482s 'cd downloads; ncbi-acc-download --format fasta NC_036769.1 -e all'
482s 'cat downloads/NC_004325.2.fa downloads/NC_037280.1.fa downloads/NC_000521.4.fa downloads/NC_004318.2.fa downloads/NC_004326.2.fa downloads/NC_004327.3.fa downloads/NC_004328.3.fa downloads/NC_004329.3.fa downloads/NC_004330.2.fa downloads/NC_037281.1.fa downloads/NC_037282.1.fa downloads/NC_037284.1.fa downloads/NC_004331.3.fa downloads/NC_037283.1.fa downloads/NC_036769.1.fa > downloads/protista__plasmodium_falciuparum__36329.fasta'
482s "grep -v '^>' downloads/protista__plasmodium_falciuparum__36329.fasta | tr -d '\n' | wc > protista__plasmodium_falciuparum__36329.size"
482s Genome protista__plasmodium_falciuparum__36329 size 23326872 bases.
482s Initializing and downloading genomes...
482s GENERATING norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6
482s 'iss --version > iss_version.txt'
482s 'cat downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta downloads/fungi__aspergillus_fumigatus__330879.fasta downloads/viruses__rhinovirus_c__463676.fasta downloads/viruses__chikungunya__37124.fasta downloads/bateria__staphylococcus_aureus__93061.fasta downloads/protista__plasmodium_falciuparum__36329.fasta > norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4708_genomes.fasta'
482s 'iss generate --n_reads 60000 --genomes norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4708_genomes.fasta --model hiseq --abundance_file norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4708_abundance.txt --gc_bias --output norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4708 --cpus 2'
482s *** 100.0 percent done, 0.7 minutes elapsed, 0.0 minutes remaining, ETA 09:31:24 ***
482s 
483s autopkgtest [09:31:25]: test run-unit-test: -----------------------]
483s autopkgtest [09:31:25]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
483s run-unit-test        PASS
484s autopkgtest [09:31:26]: @@@@@@@@@@@@@@@@@@@@ summary
484s run-unit-test        PASS
503s virt: nova [W] Skipping flock in bos03-arm64
503s virt: Creating nova instance adt-plucky-arm64-idseq-bench-20241113-092322-juju-7f2275-prod-proposed-migration-environment-2-a5521310-9ba2-4259-a3a9-1d86e6cf6c1c from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...