0s autopkgtest [09:57:15]: starting date and time: 2024-11-15 09:57:15+0000
  0s autopkgtest [09:57:15]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [09:57:15]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.saqg13mi/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pyyaml --apt-upgrade idseq-bench --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=pyyaml/6.0.2-1build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-29.secgroup --name adt-plucky-amd64-idseq-bench-20241115-095715-juju-7f2275-prod-proposed-migration-environment-20-5f0dfe2f-8274-4ca4-8765-6516328230c4 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/
 37s autopkgtest [09:57:52]: testbed dpkg architecture: amd64
 37s autopkgtest [09:57:52]: testbed apt version: 2.9.8
 37s autopkgtest [09:57:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 38s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [95.8 kB]
 38s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 38s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB]
 38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1059 kB]
 38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB]
 38s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB]
 38s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 38s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [298 kB]
 38s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [835 kB]
 38s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B]
 38s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B]
 38s Fetched 2713 kB in 1s (3332 kB/s)
 39s Reading package lists...
 41s Reading package lists...
 41s Building dependency tree...
 41s Reading state information...
 41s Calculating upgrade...
 41s The following packages will be upgraded:
 41s   firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0
 41s   libexpat1 lxd-installer man-db pastebinit python3-systemd python3-yaml
 41s   xfsprogs
 41s 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 41s Need to get 13.8 MB of archives.
 41s After this operation, 765 kB of additional disk space will be used.
 41s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB]
 42s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB]
 42s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB]
 42s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-yaml amd64 6.0.2-1build1 [187 kB]
 42s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB]
 42s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB]
 42s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB]
 42s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB]
 42s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB]
 42s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B]
 42s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
 42s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB]
 42s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB]
 42s Preconfiguring packages ...
 43s Fetched 13.8 MB in 1s (13.4 MB/s)
 43s (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 ... 75542 files and directories currently installed.)
 43s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ...
 43s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ...
 43s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ...
 43s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ...
 43s Setting up libcap-ng0:amd64 (0.8.5-3build1) ...
 43s (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 ... 75568 files and directories currently installed.)
 43s Preparing to unpack .../00-libexpat1_2.6.4-1_amd64.deb ...
 43s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ...
 43s Preparing to unpack .../01-python3-yaml_6.0.2-1build1_amd64.deb ...
 43s Unpacking python3-yaml (6.0.2-1build1) over (6.0.2-1) ...
 43s Preparing to unpack .../02-man-db_2.13.0-1_amd64.deb ...
 43s Unpacking man-db (2.13.0-1) over (2.12.1-3) ...
 43s Preparing to unpack .../03-grub2-common_2.12-5ubuntu7_amd64.deb ...
 43s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 43s Preparing to unpack .../04-grub-pc_2.12-5ubuntu7_amd64.deb ...
 43s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 43s Preparing to unpack .../05-grub-pc-bin_2.12-5ubuntu7_amd64.deb ...
 43s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 43s Preparing to unpack .../06-grub-common_2.12-5ubuntu7_amd64.deb ...
 43s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 44s Preparing to unpack .../07-lxd-installer_9_all.deb ...
 44s Unpacking lxd-installer (9) over (8) ...
 44s Preparing to unpack .../08-pastebinit_1.7.1-1_all.deb ...
 44s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
 44s Preparing to unpack .../09-python3-systemd_235-1build5_amd64.deb ...
 44s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
 44s Preparing to unpack .../10-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ...
 44s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ...
 44s Setting up libexpat1:amd64 (2.6.4-1) ...
 44s Setting up firmware-sof-signed (2024.06-1ubuntu2) ...
 44s Setting up pastebinit (1.7.1-1) ...
 44s Setting up python3-yaml (6.0.2-1build1) ...
 44s Setting up man-db (2.13.0-1) ...
 44s Updating database of manual pages ...
 46s man-db.service is a disabled or a static unit not running, not starting it.
 46s Setting up grub-common (2.12-5ubuntu7) ...
 46s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
 46s Setting up xfsprogs (6.8.0-2.2ubuntu2) ...
 46s update-initramfs: deferring update (trigger activated)
 47s Setting up lxd-installer (9) ...
 47s Setting up python3-systemd (235-1build5) ...
 47s Setting up grub2-common (2.12-5ubuntu7) ...
 47s Setting up grub-pc-bin (2.12-5ubuntu7) ...
 47s Setting up grub-pc (2.12-5ubuntu7) ...
 48s Installing for i386-pc platform.
 48s Installation finished. No error reported.
 48s Sourcing file `/etc/default/grub'
 48s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
 48s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
 48s Generating grub configuration file ...
 48s Found linux image: /boot/vmlinuz-6.11.0-8-generic
 48s Found initrd image: /boot/initrd.img-6.11.0-8-generic
 48s Warning: os-prober will not be executed to detect other bootable partitions.
 48s Systems on them will not be added to the GRUB boot configuration.
 48s Check GRUB_DISABLE_OS_PROBER documentation entry.
 48s Adding boot menu entry for UEFI Firmware Settings ...
 48s done
 48s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 48s Processing triggers for install-info (7.1.1-1) ...
 48s Processing triggers for initramfs-tools (0.142ubuntu34) ...
 49s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic
 49s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
 56s Reading package lists...
 56s Building dependency tree...
 56s Reading state information...
 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 57s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 57s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 57s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 57s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 58s Reading package lists...
 58s Reading package lists...
 58s Building dependency tree...
 58s Reading state information...
 58s Calculating upgrade...
 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 59s Reading package lists...
 59s Building dependency tree...
 59s Reading state information...
 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 59s autopkgtest [09:58:14]: rebooting testbed after setup commands that affected boot
 76s autopkgtest [09:58:31]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 78s autopkgtest [09:58:33]: @@@@@@@@@@@@@@@@@@@@ apt-source idseq-bench
 80s Get:1 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (dsc) [2356 B]
 80s Get:2 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (tar) [17.3 kB]
 80s Get:3 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (diff) [4432 B]
 80s gpgv: Signature made Mon Jan 17 12:05:35 2022 UTC
 80s gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
 80s gpgv:                issuer "nilesh@debian.org"
 80s gpgv: Can't check signature: No public key
 80s dpkg-source: warning: cannot verify inline signature for ./idseq-bench_0.0~git20210602.27fb6dc-1.dsc: no acceptable signature found
 80s autopkgtest [09:58:35]: testing package idseq-bench version 0.0~git20210602.27fb6dc-1
 80s autopkgtest [09:58:35]: build not needed
 80s autopkgtest [09:58:35]: test run-unit-test: preparing testbed
 82s Reading package lists...
 82s Building dependency tree...
 82s Reading state information...
 82s Starting pkgProblemResolver with broken count: 0
 82s Starting 2 pkgProblemResolver with broken count: 0
 82s Done
 82s The following additional packages will be installed:
 82s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35
 82s   idseq-bench insilicoseq libblas3 libcairo2 libdeflate0 libfontconfig1
 82s   libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64
 82s   libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
 82s   liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0
 82s   libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0
 82s   libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython
 82s   python3-cairo python3-decorator python3-freetype python3-joblib
 82s   python3-numpy python3-pil python3-pysam python3-reportlab python3-rlpycairo
 82s   python3-scipy python3-sklearn python3-sklearn-lib python3-smart-open
 82s   python3-threadpoolctl python3-wrapt sgml-base w3c-sgml-lib x11-common
 82s   xfonts-encodings xfonts-utils xml-core
 82s Suggested packages:
 82s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils
 82s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
 82s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
 82s   python3-rdflib python3-psycopg2 raxml samtools t-coffee wise
 82s   python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest
 82s   python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc
 82s   rl-accel rl-renderpm python-scipy-doc python3-dap python-sklearn-doc
 82s   ipython3 python3-azure python3-azure-storage sgml-base-doc debhelper
 82s Recommended packages:
 82s   python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson
 82s   python3-psutil python3-olefile fonts-dejavu-extra g++ | c++-compiler
 82s   python3-matplotlib python3-boto3 python3-paramiko python3-zstandard
 82s The following NEW packages will be installed:
 82s   autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono
 82s   fonts-urw-base35 idseq-bench insilicoseq libblas3 libcairo2 libdeflate0
 82s   libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3
 82s   libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0
 82s   libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4
 82s   libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7
 82s   libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1
 82s   ncbi-acc-download python3-all python3-biopython python3-cairo
 82s   python3-decorator python3-freetype python3-joblib python3-numpy python3-pil
 82s   python3-pysam python3-reportlab python3-rlpycairo python3-scipy
 82s   python3-sklearn python3-sklearn-lib python3-smart-open python3-threadpoolctl
 82s   python3-wrapt sgml-base w3c-sgml-lib x11-common xfonts-encodings
 82s   xfonts-utils xml-core
 82s 0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded.
 82s Need to get 61.6 MB/61.6 MB of archives.
 82s After this operation, 245 MB of additional disk space will be used.
 82s Get:1 /tmp/autopkgtest.RoIl42/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [764 B]
 83s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB]
 83s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
 83s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
 83s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB]
 83s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
 83s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
 83s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB]
 83s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB]
 83s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
 83s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
 83s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
 83s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
 84s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB]
 84s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
 84s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
 84s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB]
 84s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
 84s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
 84s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB]
 84s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
 84s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB]
 84s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB]
 84s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
 84s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
 84s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB]
 84s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
 84s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
 84s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
 84s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB]
 84s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB]
 84s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB]
 84s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
 84s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
 84s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
 84s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
 84s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
 84s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
 84s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB]
 84s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB]
 84s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B]
 84s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB]
 84s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB]
 84s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB]
 84s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB]
 84s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB]
 84s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB]
 84s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB]
 84s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB]
 84s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB]
 84s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB]
 85s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 insilicoseq all 2.0.1-1 [4247 kB]
 85s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-acc-download all 0.2.8-3 [13.3 kB]
 85s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB]
 85s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB]
 85s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB]
 85s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB]
 86s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wrapt amd64 1.15.0-3 [34.6 kB]
 86s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-smart-open all 7.0.5-1 [89.9 kB]
 86s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 idseq-bench all 0.0~git20210602.27fb6dc-1 [24.7 kB]
 86s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B]
 86s Fetched 61.6 MB in 3s (20.1 MB/s)
 86s Selecting previously unselected package sgml-base.
 86s (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 ... 75576 files and directories currently installed.)
 86s Preparing to unpack .../00-sgml-base_1.31_all.deb ...
 86s Unpacking sgml-base (1.31) ...
 86s Selecting previously unselected package fonts-dejavu-mono.
 86s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ...
 86s Unpacking fonts-dejavu-mono (2.37-8) ...
 86s Selecting previously unselected package fonts-dejavu-core.
 86s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ...
 86s Unpacking fonts-dejavu-core (2.37-8) ...
 86s Selecting previously unselected package libfontenc1:amd64.
 86s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_amd64.deb ...
 86s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ...
 86s Selecting previously unselected package x11-common.
 86s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ...
 86s Unpacking x11-common (1:7.7+23ubuntu3) ...
 86s Selecting previously unselected package xfonts-encodings.
 86s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
 86s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
 86s Selecting previously unselected package xfonts-utils.
 86s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_amd64.deb ...
 86s Unpacking xfonts-utils (1:7.7+7) ...
 86s Selecting previously unselected package fonts-urw-base35.
 86s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ...
 86s Unpacking fonts-urw-base35 (20200910-8) ...
 86s Selecting previously unselected package fontconfig-config.
 86s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ...
 87s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
 87s Selecting previously unselected package libblas3:amd64.
 87s Preparing to unpack .../09-libblas3_3.12.0-3build2_amd64.deb ...
 87s Unpacking libblas3:amd64 (3.12.0-3build2) ...
 87s Selecting previously unselected package libgfortran5:amd64.
 87s Preparing to unpack .../10-libgfortran5_14.2.0-8ubuntu1_amd64.deb ...
 87s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ...
 87s Selecting previously unselected package liblapack3:amd64.
 87s Preparing to unpack .../11-liblapack3_3.12.0-3build2_amd64.deb ...
 87s Unpacking liblapack3:amd64 (3.12.0-3build2) ...
 87s Selecting previously unselected package python3-numpy.
 87s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ...
 87s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
 87s Selecting previously unselected package libgomp1:amd64.
 87s Preparing to unpack .../13-libgomp1_14.2.0-8ubuntu1_amd64.deb ...
 87s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ...
 87s Selecting previously unselected package libimagequant0:amd64.
 87s Preparing to unpack .../14-libimagequant0_2.18.0-1build1_amd64.deb ...
 87s Unpacking libimagequant0:amd64 (2.18.0-1build1) ...
 87s Selecting previously unselected package libjpeg-turbo8:amd64.
 87s Preparing to unpack .../15-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ...
 87s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ...
 87s Selecting previously unselected package libjpeg8:amd64.
 87s Preparing to unpack .../16-libjpeg8_8c-2ubuntu11_amd64.deb ...
 87s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ...
 87s Selecting previously unselected package liblcms2-2:amd64.
 87s Preparing to unpack .../17-liblcms2-2_2.16-2_amd64.deb ...
 87s Unpacking liblcms2-2:amd64 (2.16-2) ...
 87s Selecting previously unselected package libopenjp2-7:amd64.
 87s Preparing to unpack .../18-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ...
 87s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ...
 87s Selecting previously unselected package libgraphite2-3:amd64.
 87s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ...
 87s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
 87s Selecting previously unselected package libharfbuzz0b:amd64.
 87s Preparing to unpack .../20-libharfbuzz0b_10.0.1-1_amd64.deb ...
 87s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ...
 87s Selecting previously unselected package libraqm0:amd64.
 87s Preparing to unpack .../21-libraqm0_0.10.1-1build1_amd64.deb ...
 87s Unpacking libraqm0:amd64 (0.10.1-1build1) ...
 87s Selecting previously unselected package libdeflate0:amd64.
 87s Preparing to unpack .../22-libdeflate0_1.22-1_amd64.deb ...
 87s Unpacking libdeflate0:amd64 (1.22-1) ...
 87s Selecting previously unselected package libjbig0:amd64.
 87s Preparing to unpack .../23-libjbig0_2.1-6.1ubuntu2_amd64.deb ...
 87s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ...
 87s Selecting previously unselected package liblerc4:amd64.
 87s Preparing to unpack .../24-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ...
 87s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ...
 87s Selecting previously unselected package libsharpyuv0:amd64.
 87s Preparing to unpack .../25-libsharpyuv0_1.4.0-0.1_amd64.deb ...
 87s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ...
 87s Selecting previously unselected package libwebp7:amd64.
 87s Preparing to unpack .../26-libwebp7_1.4.0-0.1_amd64.deb ...
 87s Unpacking libwebp7:amd64 (1.4.0-0.1) ...
 87s Selecting previously unselected package libtiff6:amd64.
 87s Preparing to unpack .../27-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ...
 87s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
 87s Selecting previously unselected package libwebpdemux2:amd64.
 87s Preparing to unpack .../28-libwebpdemux2_1.4.0-0.1_amd64.deb ...
 87s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ...
 87s Selecting previously unselected package libwebpmux3:amd64.
 87s Preparing to unpack .../29-libwebpmux3_1.4.0-0.1_amd64.deb ...
 87s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ...
 87s Selecting previously unselected package python3-pil:amd64.
 87s Preparing to unpack .../30-python3-pil_10.4.0-1ubuntu1_amd64.deb ...
 87s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ...
 87s Selecting previously unselected package libfontconfig1:amd64.
 87s Preparing to unpack .../31-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ...
 87s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
 87s Selecting previously unselected package libpixman-1-0:amd64.
 87s Preparing to unpack .../32-libpixman-1-0_0.44.0-3_amd64.deb ...
 87s Unpacking libpixman-1-0:amd64 (0.44.0-3) ...
 87s Selecting previously unselected package libxcb-render0:amd64.
 87s Preparing to unpack .../33-libxcb-render0_1.17.0-2_amd64.deb ...
 87s Unpacking libxcb-render0:amd64 (1.17.0-2) ...
 87s Selecting previously unselected package libxcb-shm0:amd64.
 87s Preparing to unpack .../34-libxcb-shm0_1.17.0-2_amd64.deb ...
 87s Unpacking libxcb-shm0:amd64 (1.17.0-2) ...
 87s Selecting previously unselected package libxrender1:amd64.
 87s Preparing to unpack .../35-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ...
 87s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ...
 87s Selecting previously unselected package libcairo2:amd64.
 87s Preparing to unpack .../36-libcairo2_1.18.2-2_amd64.deb ...
 87s Unpacking libcairo2:amd64 (1.18.2-2) ...
 87s Selecting previously unselected package python3-cairo.
 87s Preparing to unpack .../37-python3-cairo_1.26.1-2_amd64.deb ...
 87s Unpacking python3-cairo (1.26.1-2) ...
 87s Selecting previously unselected package python3-freetype.
 87s Preparing to unpack .../38-python3-freetype_2.5.1-1_all.deb ...
 87s Unpacking python3-freetype (2.5.1-1) ...
 88s Selecting previously unselected package python3-rlpycairo.
 88s Preparing to unpack .../39-python3-rlpycairo_0.3.0-3_all.deb ...
 88s Unpacking python3-rlpycairo (0.3.0-3) ...
 88s Selecting previously unselected package python3-reportlab.
 88s Preparing to unpack .../40-python3-reportlab_4.2.5-1_all.deb ...
 88s Unpacking python3-reportlab (4.2.5-1) ...
 88s Selecting previously unselected package xml-core.
 88s Preparing to unpack .../41-xml-core_0.19_all.deb ...
 88s Unpacking xml-core (0.19) ...
 88s Selecting previously unselected package w3c-sgml-lib.
 88s Preparing to unpack .../42-w3c-sgml-lib_1.3-3_all.deb ...
 88s Unpacking w3c-sgml-lib (1.3-3) ...
 88s Selecting previously unselected package python3-biopython.
 88s Preparing to unpack .../43-python3-biopython_1.84+dfsg-4_amd64.deb ...
 88s Unpacking python3-biopython (1.84+dfsg-4) ...
 88s Selecting previously unselected package libhtscodecs2:amd64.
 88s Preparing to unpack .../44-libhtscodecs2_1.6.1-1_amd64.deb ...
 88s Unpacking libhtscodecs2:amd64 (1.6.1-1) ...
 88s Selecting previously unselected package libhts3t64:amd64.
 88s Preparing to unpack .../45-libhts3t64_1.20+ds-1_amd64.deb ...
 88s Unpacking libhts3t64:amd64 (1.20+ds-1) ...
 88s Selecting previously unselected package python3-pysam.
 88s Preparing to unpack .../46-python3-pysam_0.22.1+ds-2_amd64.deb ...
 88s Unpacking python3-pysam (0.22.1+ds-2) ...
 88s Selecting previously unselected package python3-decorator.
 88s Preparing to unpack .../47-python3-decorator_5.1.1-5_all.deb ...
 88s Unpacking python3-decorator (5.1.1-5) ...
 88s Selecting previously unselected package liblbfgsb0:amd64.
 88s Preparing to unpack .../48-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ...
 88s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ...
 88s Selecting previously unselected package python3-scipy.
 88s Preparing to unpack .../49-python3-scipy_1.13.1-5_amd64.deb ...
 88s Unpacking python3-scipy (1.13.1-5) ...
 88s Selecting previously unselected package insilicoseq.
 88s Preparing to unpack .../50-insilicoseq_2.0.1-1_all.deb ...
 88s Unpacking insilicoseq (2.0.1-1) ...
 88s Selecting previously unselected package ncbi-acc-download.
 88s Preparing to unpack .../51-ncbi-acc-download_0.2.8-3_all.deb ...
 88s Unpacking ncbi-acc-download (0.2.8-3) ...
 88s Selecting previously unselected package python3-joblib.
 88s Preparing to unpack .../52-python3-joblib_1.3.2-5_all.deb ...
 88s Unpacking python3-joblib (1.3.2-5) ...
 89s Selecting previously unselected package python3-threadpoolctl.
 89s Preparing to unpack .../53-python3-threadpoolctl_3.1.0-1_all.deb ...
 89s Unpacking python3-threadpoolctl (3.1.0-1) ...
 89s Selecting previously unselected package python3-sklearn-lib:amd64.
 89s Preparing to unpack .../54-python3-sklearn-lib_1.4.2+dfsg-6_amd64.deb ...
 89s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ...
 89s Selecting previously unselected package python3-sklearn.
 89s Preparing to unpack .../55-python3-sklearn_1.4.2+dfsg-6_all.deb ...
 89s Unpacking python3-sklearn (1.4.2+dfsg-6) ...
 89s Selecting previously unselected package python3-wrapt.
 89s Preparing to unpack .../56-python3-wrapt_1.15.0-3_amd64.deb ...
 89s Unpacking python3-wrapt (1.15.0-3) ...
 89s Selecting previously unselected package python3-smart-open.
 89s Preparing to unpack .../57-python3-smart-open_7.0.5-1_all.deb ...
 89s Unpacking python3-smart-open (7.0.5-1) ...
 89s Selecting previously unselected package idseq-bench.
 89s Preparing to unpack .../58-idseq-bench_0.0~git20210602.27fb6dc-1_all.deb ...
 89s Unpacking idseq-bench (0.0~git20210602.27fb6dc-1) ...
 89s Selecting previously unselected package python3-all.
 89s Preparing to unpack .../59-python3-all_3.12.6-0ubuntu1_amd64.deb ...
 89s Unpacking python3-all (3.12.6-0ubuntu1) ...
 89s Selecting previously unselected package autopkgtest-satdep.
 89s Preparing to unpack .../60-1-autopkgtest-satdep.deb ...
 89s Unpacking autopkgtest-satdep (0) ...
 89s Setting up libhtscodecs2:amd64 (1.6.1-1) ...
 89s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
 89s Setting up liblcms2-2:amd64 (2.16-2) ...
 89s Setting up libpixman-1-0:amd64 (0.44.0-3) ...
 89s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ...
 89s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ...
 89s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
 89s Setting up python3-joblib (1.3.2-5) ...
 89s Setting up libxcb-render0:amd64 (1.17.0-2) ...
 89s Setting up python3-threadpoolctl (3.1.0-1) ...
 89s Setting up x11-common (1:7.7+23ubuntu3) ...
 89s Setting up libdeflate0:amd64 (1.22-1) ...
 89s Setting up python3-all (3.12.6-0ubuntu1) ...
 89s Setting up libxcb-shm0:amd64 (1.17.0-2) ...
 89s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ...
 89s Setting up python3-freetype (2.5.1-1) ...
 90s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
 90s Setting up python3-decorator (5.1.1-5) ...
 90s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ...
 90s Setting up libblas3:amd64 (3.12.0-3build2) ...
 90s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
 90s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
 90s Setting up libimagequant0:amd64 (2.18.0-1build1) ...
 90s Setting up fonts-dejavu-mono (2.37-8) ...
 90s Setting up python3-wrapt (1.15.0-3) ...
 90s Setting up fonts-dejavu-core (2.37-8) ...
 90s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ...
 90s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ...
 90s Setting up libwebp7:amd64 (1.4.0-0.1) ...
 90s Setting up libhts3t64:amd64 (1.20+ds-1) ...
 90s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ...
 90s Setting up ncbi-acc-download (0.2.8-3) ...
 90s Setting up libharfbuzz0b:amd64 (10.0.1-1) ...
 90s Setting up sgml-base (1.31) ...
 90s Setting up libwebpmux3:amd64 (1.4.0-0.1) ...
 90s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
 90s Setting up liblapack3:amd64 (3.12.0-3build2) ...
 90s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
 90s Setting up python3-pysam (0.22.1+ds-2) ...
 90s Setting up python3-smart-open (7.0.5-1) ...
 90s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
 90s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ...
 90s Setting up xfonts-utils (1:7.7+7) ...
 90s Setting up libraqm0:amd64 (0.10.1-1build1) ...
 90s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
 92s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
 92s Setting up xml-core (0.19) ...
 92s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
 92s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ...
 92s Setting up python3-scipy (1.13.1-5) ...
 94s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ...
 94s Setting up fonts-urw-base35 (20200910-8) ...
 95s Setting up libcairo2:amd64 (1.18.2-2) ...
 95s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ...
 95s Setting up python3-sklearn (1.4.2+dfsg-6) ...
 96s Setting up python3-cairo (1.26.1-2) ...
 96s Setting up python3-rlpycairo (0.3.0-3) ...
 96s Setting up python3-reportlab (4.2.5-1) ...
 97s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 97s Processing triggers for man-db (2.13.0-1) ...
 98s Processing triggers for sgml-base (1.31) ...
 98s Setting up w3c-sgml-lib (1.3-3) ...
120s Setting up python3-biopython (1.84+dfsg-4) ...
121s Setting up insilicoseq (2.0.1-1) ...
121s Setting up idseq-bench (0.0~git20210602.27fb6dc-1) ...
121s Setting up autopkgtest-satdep (0) ...
124s (Reading database ... 81895 files and directories currently installed.)
124s Removing autopkgtest-satdep (0) ...
125s autopkgtest [09:59:20]: test run-unit-test: [-----------------------
427s INFO:iss.app:Starting iss generate
427s INFO:iss.generator:Using kde ErrorModel
427s INFO:iss.util:Stitching input files together
427s INFO:iss.generator:Using abundance file:norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_3798_abundance.txt
427s INFO:iss.app:Using 2 cpus for read generation
427s INFO:iss.app:Generating 60000 reads
449s INFO:iss.util:Stitching input files together
449s INFO:iss.util:Stitching input files together
449s INFO:iss.util:Cleaning up
449s INFO:iss.app:Read generation complete
455s Generating IDseq benchmark data...
455s 'cd downloads; ncbi-acc-download --format fasta NC_016845.1 -e all'
455s 'cat downloads/NC_016845.1.fa > downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta'
455s "grep -v '^>' downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta | tr -d '\n' | wc > bateria__klebsiella_pneumoniae_HS11286__1125630.size"
455s Genome bateria__klebsiella_pneumoniae_HS11286__1125630 size 5333942 bases.
455s 'cd downloads; ncbi-acc-download --format fasta NC_007194.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_007195.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_007196.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_007197.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_007198.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_007199.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_007200.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_007201.1 -e all'
455s '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'
455s "grep -v '^>' downloads/fungi__aspergillus_fumigatus__330879.fasta | tr -d '\n' | wc > fungi__aspergillus_fumigatus__330879.size"
455s Genome fungi__aspergillus_fumigatus__330879 size 29384958 bases.
455s 'cd downloads; ncbi-acc-download --format fasta MG148341.1 -e all'
455s 'cat downloads/MG148341.1.fa > downloads/viruses__rhinovirus_c__463676.fasta'
455s "grep -v '^>' downloads/viruses__rhinovirus_c__463676.fasta | tr -d '\n' | wc > viruses__rhinovirus_c__463676.size"
455s Genome viruses__rhinovirus_c__463676 size 7056 bases.
455s 'cd downloads; ncbi-acc-download --format fasta MG049915.1 -e all'
455s 'cat downloads/MG049915.1.fa > downloads/viruses__chikungunya__37124.fasta'
455s "grep -v '^>' downloads/viruses__chikungunya__37124.fasta | tr -d '\n' | wc > viruses__chikungunya__37124.size"
455s Genome viruses__chikungunya__37124 size 11604 bases.
455s 'cd downloads; ncbi-acc-download --format fasta NC_007795.1 -e all'
455s 'cat downloads/NC_007795.1.fa > downloads/bateria__staphylococcus_aureus__93061.fasta'
455s "grep -v '^>' downloads/bateria__staphylococcus_aureus__93061.fasta | tr -d '\n' | wc > bateria__staphylococcus_aureus__93061.size"
455s Genome bateria__staphylococcus_aureus__93061 size 2821361 bases.
455s 'cd downloads; ncbi-acc-download --format fasta NC_004325.2 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_037280.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_000521.4 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_004318.2 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_004326.2 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_004327.3 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_004328.3 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_004329.3 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_004330.2 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_037281.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_037282.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_037284.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_004331.3 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_037283.1 -e all'
455s 'cd downloads; ncbi-acc-download --format fasta NC_036769.1 -e all'
455s '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'
455s "grep -v '^>' downloads/protista__plasmodium_falciuparum__36329.fasta | tr -d '\n' | wc > protista__plasmodium_falciuparum__36329.size"
455s Genome protista__plasmodium_falciuparum__36329 size 23326872 bases.
455s Initializing and downloading genomes...
455s GENERATING norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6
455s 'iss --version > iss_version.txt'
455s '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_3798_genomes.fasta'
455s 'iss generate --n_reads 60000 --genomes norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_3798_genomes.fasta --model hiseq --abundance_file norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_3798_abundance.txt --gc_bias --output norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_3798 --cpus 2'
455s *** 100.0 percent done, 0.5 minutes elapsed, 0.0 minutes remaining, ETA 10:04:50 ***
455s 
455s autopkgtest [10:04:50]: test run-unit-test: -----------------------]
456s autopkgtest [10:04:51]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
456s run-unit-test        PASS
456s autopkgtest [10:04:51]: @@@@@@@@@@@@@@@@@@@@ summary
456s run-unit-test        PASS
468s nova [W] Skipping flock for amd64
468s Creating nova instance adt-plucky-amd64-idseq-bench-20241115-095715-juju-7f2275-prod-proposed-migration-environment-20-5f0dfe2f-8274-4ca4-8765-6516328230c4 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...