0s autopkgtest [11:50:54]: starting date and time: 2025-11-17 11:50:54+0000
  0s autopkgtest [11:50:54]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [11:50:54]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zfcllhza/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade busco --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-8.secgroup --name adt-resolute-amd64-busco-20251117-115054-juju-7f2275-prod-proposed-migration-environment-2-6f46859c-71d3-4803-a55d-7f1f2c1b8ccd --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  4s Creating nova instance adt-resolute-amd64-busco-20251117-115054-juju-7f2275-prod-proposed-migration-environment-2-6f46859c-71d3-4803-a55d-7f1f2c1b8ccd from image adt/ubuntu-resolute-amd64-server-20251117.img (UUID 9762b0cc-7c5b-4854-acd5-cc74ad0de8c6)...
 50s autopkgtest [11:51:44]: testbed dpkg architecture: amd64
 51s autopkgtest [11:51:45]: testbed apt version: 3.1.11
 51s autopkgtest [11:51:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 51s autopkgtest [11:51:45]: testbed release detected to be: None
 52s autopkgtest [11:51:46]: updating testbed package index (apt update)
 52s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB]
 52s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 52s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 52s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 52s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB]
 52s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB]
 52s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B]
 52s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB]
 53s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [159 kB]
 53s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [118 kB]
 53s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3096 B]
 53s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B]
 53s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB]
 53s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B]
 53s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [279 kB]
 53s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [607 kB]
 53s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [21.2 kB]
 53s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [6516 B]
 53s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [13.4 kB]
 53s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [680 B]
 55s Fetched 2346 kB in 1s (1899 kB/s)
 55s Reading package lists...
 56s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 56s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 56s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 56s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 57s Reading package lists...
 57s Reading package lists...
 57s Building dependency tree...
 57s Reading state information...
 57s Calculating upgrade...
 57s The following packages will be upgraded:
 57s   libpython3-stdlib python3 python3-minimal usbutils
 57s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 57s Need to get 146 kB of archives.
 57s After this operation, 0 B of additional disk space will be used.
 57s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB]
 57s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB]
 57s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB]
 57s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 usbutils amd64 1:019-1 [83.9 kB]
 57s Fetched 146 kB in 0s (0 B/s)
 57s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 57s (Reading database ... 
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(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 ... 83372 files and directories currently installed.)
 57s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ...
 57s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ...
 57s Setting up python3-minimal (3.13.7-2) ...
 57s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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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 ... 83372 files and directories currently installed.)
 57s Preparing to unpack .../python3_3.13.7-2_amd64.deb ...
 57s running python pre-rtupdate hooks for python3.13...
 57s Unpacking python3 (3.13.7-2) over (3.13.7-1) ...
 57s Preparing to unpack .../libpython3-stdlib_3.13.7-2_amd64.deb ...
 57s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ...
 57s Preparing to unpack .../usbutils_1%3a019-1_amd64.deb ...
 57s Unpacking usbutils (1:019-1) over (1:018-2) ...
 57s Setting up usbutils (1:019-1) ...
 57s Setting up libpython3-stdlib:amd64 (3.13.7-2) ...
 57s Setting up python3 (3.13.7-2) ...
 57s running python rtupdate hooks for python3.13...
 57s running python post-rtupdate hooks for python3.13...
 58s Processing triggers for man-db (2.13.1-1) ...
 58s autopkgtest [11:51:52]: upgrading testbed (apt dist-upgrade and autopurge)
 58s Reading package lists...
 58s Building dependency tree...
 58s Reading state information...
 59s 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 Solving dependencies...
 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 61s autopkgtest [11:51:55]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025
 61s autopkgtest [11:51:55]: @@@@@@@@@@@@@@@@@@@@ apt-source busco
 63s Get:1 http://ftpmaster.internal/ubuntu resolute/universe busco 5.5.0-3 (dsc) [2079 B]
 63s Get:2 http://ftpmaster.internal/ubuntu resolute/universe busco 5.5.0-3 (tar) [392 kB]
 63s Get:3 http://ftpmaster.internal/ubuntu resolute/universe busco 5.5.0-3 (diff) [8608 B]
 63s gpgv: Signature made Thu Dec  5 18:33:36 2024 UTC
 63s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 63s gpgv:                issuer "tille@debian.org"
 63s gpgv: Can't check signature: No public key
 63s dpkg-source: warning: cannot verify inline signature for ./busco_5.5.0-3.dsc: no acceptable signature found
 63s autopkgtest [11:51:57]: testing package busco version 5.5.0-3
 63s autopkgtest [11:51:57]: build not needed
 64s autopkgtest [11:51:58]: test run-unit-test: preparing testbed
 64s Reading package lists...
 64s Building dependency tree...
 64s Reading state information...
 64s Solving dependencies...
 64s The following NEW packages will be installed:
 64s   bbmap busco ca-certificates-java default-jre-headless diffstat
 64s   fontconfig-config fonts-urw-base35 gettext hmmer java-common
 64s   libapache-pom-java libblas3 libcairo2 libcommons-cli-java
 64s   libcommons-codec-java libcommons-io-java libcommons-parent-java libdeflate0
 64s   libdivsufsort3 libfontconfig1 libfontenc1 libgfortran5 libgomp1
 64s   libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8
 64s   liblapack3 liblcms2-2 liblerc4 liblog4j1.2-java libmpj-java libopenjp2-7
 64s   libpcsclite1 libpixman-1-0 libpython3.14-minimal libpython3.14-stdlib
 64s   libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3
 64s   libxcb-render0 libxcb-shm0 libxrender1 openjdk-21-jre-headless prodigal
 64s   python3-all python3-biopython python3-cairo python3-charset-normalizer
 64s   python3-freetype python3-numpy python3-numpy-dev python3-pandas
 64s   python3-pandas-lib python3-pil python3-pytz python3-reportlab
 64s   python3-rlpycairo python3.14 python3.14-minimal quilt sgml-base w3c-sgml-lib
 64s   x11-common xfonts-encodings xfonts-utils xml-core
 64s 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded.
 64s Need to get 109 MB of archives.
 64s After this operation, 429 MB of additional disk space will be used.
 64s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB]
 64s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB]
 64s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-7ubuntu1 [939 kB]
 65s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB]
 65s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB]
 66s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.0-4 [906 kB]
 66s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.0-4 [2559 kB]
 66s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-cli-java all 1.6.0-1 [59.9 kB]
 66s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapache-pom-java all 33-2 [5874 B]
 66s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-parent-java all 56-1 [10.7 kB]
 66s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-codec-java all 1.18.0-1 [303 kB]
 66s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-io-java all 2.19.0-1 [491 kB]
 66s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblog4j1.2-java all 1.2.17-11 [439 kB]
 66s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpj-java all 0.44+dfsg-4 [443 kB]
 66s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 ca-certificates-java all 20240118 [11.6 kB]
 66s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 java-common all 0.76 [6852 B]
 66s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB]
 66s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB]
 66s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
 66s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcsclite1 amd64 2.4.0-2 [24.3 kB]
 66s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 openjdk-21-jre-headless amd64 21.0.9+10-1 [46.5 MB]
 69s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B]
 69s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 bbmap all 39.20+dfsg-3 [10.6 MB]
 69s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB]
 69s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB]
 70s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB]
 70s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.3-1 [174 kB]
 70s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-7ubuntu1 [151 kB]
 70s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
 70s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB]
 70s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
 70s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB]
 70s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB]
 70s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB]
 70s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
 70s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
 70s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
 70s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
 70s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
 70s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB]
 70s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB]
 70s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu2 [504 kB]
 70s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB]
 70s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
 70s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
 70s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB]
 70s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB]
 70s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB]
 70s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB]
 70s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
 70s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB]
 70s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B]
 70s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
 70s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB]
 70s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB]
 70s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB]
 70s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B]
 70s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.4-2 [1147 kB]
 70s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB]
 70s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB]
 70s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB]
 70s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.85+dfsg-4 [1719 kB]
 70s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 libdivsufsort3 amd64 2.0.1-7 [46.8 kB]
 71s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 hmmer amd64 3.4+dfsg-2 [1147 kB]
 71s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 prodigal amd64 1:2.6.3-6 [643 kB]
 71s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 busco amd64 5.5.0-3 [295 kB]
 71s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 diffstat amd64 1.68-1 [30.3 kB]
 71s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.2-1 [1019 kB]
 71s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.0-4 [2397 kB]
 71s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.0-4 [805 kB]
 71s Get:71 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.13.7-2 [890 B]
 71s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 quilt all 0.68-1 [439 kB]
 71s Fetched 109 MB in 7s (16.2 MB/s)
 71s Selecting previously unselected package python3-numpy-dev:amd64.
 71s (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 ... 83372 files and directories currently installed.)
 71s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ...
 71s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ...
 71s Selecting previously unselected package libblas3:amd64.
 71s Preparing to unpack .../01-libblas3_3.12.1-7_amd64.deb ...
 71s Unpacking libblas3:amd64 (3.12.1-7) ...
 71s Selecting previously unselected package libgfortran5:amd64.
 71s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_amd64.deb ...
 71s Unpacking libgfortran5:amd64 (15.2.0-7ubuntu1) ...
 71s Selecting previously unselected package liblapack3:amd64.
 71s Preparing to unpack .../03-liblapack3_3.12.1-7_amd64.deb ...
 71s Unpacking liblapack3:amd64 (3.12.1-7) ...
 71s Selecting previously unselected package python3-numpy.
 71s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ...
 71s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ...
 71s Selecting previously unselected package libpython3.14-minimal:amd64.
 71s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_amd64.deb ...
 71s Unpacking libpython3.14-minimal:amd64 (3.14.0-4) ...
 71s Selecting previously unselected package python3.14-minimal.
 71s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_amd64.deb ...
 71s Unpacking python3.14-minimal (3.14.0-4) ...
 71s Selecting previously unselected package libcommons-cli-java.
 71s Preparing to unpack .../07-libcommons-cli-java_1.6.0-1_all.deb ...
 71s Unpacking libcommons-cli-java (1.6.0-1) ...
 71s Selecting previously unselected package libapache-pom-java.
 71s Preparing to unpack .../08-libapache-pom-java_33-2_all.deb ...
 71s Unpacking libapache-pom-java (33-2) ...
 71s Selecting previously unselected package libcommons-parent-java.
 71s Preparing to unpack .../09-libcommons-parent-java_56-1_all.deb ...
 71s Unpacking libcommons-parent-java (56-1) ...
 71s Selecting previously unselected package libcommons-codec-java.
 71s Preparing to unpack .../10-libcommons-codec-java_1.18.0-1_all.deb ...
 71s Unpacking libcommons-codec-java (1.18.0-1) ...
 71s Selecting previously unselected package libcommons-io-java.
 71s Preparing to unpack .../11-libcommons-io-java_2.19.0-1_all.deb ...
 71s Unpacking libcommons-io-java (2.19.0-1) ...
 71s Selecting previously unselected package liblog4j1.2-java.
 71s Preparing to unpack .../12-liblog4j1.2-java_1.2.17-11_all.deb ...
 71s Unpacking liblog4j1.2-java (1.2.17-11) ...
 71s Selecting previously unselected package libmpj-java.
 71s Preparing to unpack .../13-libmpj-java_0.44+dfsg-4_all.deb ...
 71s Unpacking libmpj-java (0.44+dfsg-4) ...
 71s Selecting previously unselected package ca-certificates-java.
 71s Preparing to unpack .../14-ca-certificates-java_20240118_all.deb ...
 71s Unpacking ca-certificates-java (20240118) ...
 71s Selecting previously unselected package java-common.
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 85s Adding debian:Izenpe.com.pem
 85s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
 85s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
 85s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
 85s Adding debian:NAVER_Global_Root_Certification_Authority.pem
 85s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
 85s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
 85s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
 85s Adding debian:QuoVadis_Root_CA_1_G3.pem
 85s Adding debian:QuoVadis_Root_CA_2.pem
 85s Adding debian:QuoVadis_Root_CA_2_G3.pem
 85s Adding debian:QuoVadis_Root_CA_3.pem
 85s Adding debian:QuoVadis_Root_CA_3_G3.pem
 85s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
 85s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
 85s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
 85s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
 85s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
 85s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
 85s Adding debian:SZAFIR_ROOT_CA2.pem
 85s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
 85s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
 85s Adding debian:SecureSign_Root_CA12.pem
 85s Adding debian:SecureSign_Root_CA14.pem
 85s Adding debian:SecureSign_Root_CA15.pem
 85s Adding debian:SecureTrust_CA.pem
 85s Adding debian:Secure_Global_CA.pem
 85s Adding debian:Security_Communication_ECC_RootCA1.pem
 85s Adding debian:Security_Communication_RootCA2.pem
 85s Adding debian:Starfield_Class_2_CA.pem
 85s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
 85s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
 85s Adding debian:SwissSign_Gold_CA_-_G2.pem
 85s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
 85s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
 85s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
 85s Adding debian:TWCA_CYBER_Root_CA.pem
 85s Adding debian:TWCA_Global_Root_CA.pem
 85s Adding debian:TWCA_Root_Certification_Authority.pem
 85s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
 85s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
 85s Adding debian:TeliaSonera_Root_CA_v1.pem
 85s Adding debian:Telia_Root_CA_v2.pem
 85s Adding debian:TrustAsia_Global_Root_CA_G3.pem
 85s Adding debian:TrustAsia_Global_Root_CA_G4.pem
 85s Adding debian:Trustwave_Global_Certification_Authority.pem
 85s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
 85s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
 85s Adding debian:TunTrust_Root_CA.pem
 85s Adding debian:UCA_Extended_Validation_Root.pem
 85s Adding debian:UCA_Global_G2_Root.pem
 85s Adding debian:USERTrust_ECC_Certification_Authority.pem
 85s Adding debian:USERTrust_RSA_Certification_Authority.pem
 85s Adding debian:XRamp_Global_CA_Root.pem
 85s Adding debian:certSIGN_ROOT_CA.pem
 85s Adding debian:certSIGN_Root_CA_G2.pem
 85s Adding debian:e-Szigno_Root_CA_2017.pem
 85s Adding debian:ePKI_Root_Certification_Authority.pem
 85s Adding debian:emSign_ECC_Root_CA_-_C3.pem
 85s Adding debian:emSign_ECC_Root_CA_-_G3.pem
 85s Adding debian:emSign_Root_CA_-_C1.pem
 85s Adding debian:emSign_Root_CA_-_G1.pem
 85s Adding debian:vTrus_ECC_Root_CA.pem
 85s Adding debian:vTrus_Root_CA.pem
 85s done.
 85s Setting up default-jre-headless (2:1.21-76) ...
 85s Setting up bbmap (39.20+dfsg-3) ...
 85s Processing triggers for sgml-base (1.31+nmu1) ...
 85s Setting up w3c-sgml-lib (1.3-3) ...
101s Setting up python3-biopython (1.85+dfsg-4) ...
102s Setting up busco (5.5.0-3) ...
102s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\['
102s   "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]"
102s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: "\[" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\["? A raw string is also an option.
102s   "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]"
103s /usr/lib/python3/dist-packages/busco/busco_tools/hmmer.py:225: SyntaxWarning: 'return' in a 'finally' block
103s   return hmmer_version
103s autopkgtest [11:52:37]: test run-unit-test: [-----------------------
103s File series fully applied, ends at patch debian/patches/python3.12-syntax.patch
103s Testing with python3.14 in /tmp/autopkgtest.KD6TJu/autopkgtest_tmp:
104s unittest_runner (unittest.loader._FailedTest.unittest_runner) ... ERROR
104s 
104s ======================================================================
104s ERROR: unittest_runner (unittest.loader._FailedTest.unittest_runner)
104s ----------------------------------------------------------------------
104s ImportError: Failed to import test module: unittest_runner
104s Traceback (most recent call last):
104s   File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName
104s     module = __import__(module_name)
104s   File "/tmp/autopkgtest.KD6TJu/autopkgtest_tmp/tests/unittest_runner.py", line 2, in <module>
104s     from tests.unittests import run_BUSCO_unittests
104s   File "/tmp/autopkgtest.KD6TJu/autopkgtest_tmp/tests/unittests/run_BUSCO_unittests.py", line 2, in <module>
104s     from busco import run_BUSCO
104s   File "/usr/lib/python3/dist-packages/busco/run_BUSCO.py", line 25, in <module>
104s     from busco.BuscoRunner import AnalysisRunner, BatchRunner, SingleRunner
104s   File "/usr/lib/python3/dist-packages/busco/BuscoRunner.py", line 2, in <module>
104s     from busco.analysis.BuscoAnalysis import BuscoAnalysis
104s   File "/usr/lib/python3/dist-packages/busco/analysis/BuscoAnalysis.py", line 14, in <module>
104s     from busco.BuscoConfig import BaseConfig, BuscoConfigAuto
104s   File "/usr/lib/python3/dist-packages/busco/BuscoConfig.py", line 9, in <module>
104s     from busco.BuscoDownloadManager import BuscoDownloadManager
104s   File "/usr/lib/python3/dist-packages/busco/BuscoDownloadManager.py", line 22, in <module>
104s     import pandas as pd
104s   File "/usr/lib/python3/dist-packages/pandas/__init__.py", line 19, in <module>
104s     raise ImportError(
104s         "Unable to import required dependencies:\n" + "\n".join(_missing_dependencies)
104s     )
104s ImportError: Unable to import required dependencies:
104s numpy: Error importing numpy: you should not try to import numpy from
104s         its source directory; please exit the numpy source tree, and relaunch
104s         your python interpreter from there.
104s 
104s 
104s ----------------------------------------------------------------------
104s Ran 1 test in 0.000s
104s 
104s FAILED (errors=1)
104s autopkgtest [11:52:38]: test run-unit-test: -----------------------]
104s run-unit-test        FAIL non-zero exit status 1
104s autopkgtest [11:52:38]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
105s autopkgtest [11:52:39]: test run-busco-analysis: preparing testbed
125s Creating nova instance adt-resolute-amd64-busco-20251117-115054-juju-7f2275-prod-proposed-migration-environment-2-6f46859c-71d3-4803-a55d-7f1f2c1b8ccd from image adt/ubuntu-resolute-amd64-server-20251117.img (UUID 9762b0cc-7c5b-4854-acd5-cc74ad0de8c6)...
166s autopkgtest [11:53:40]: testbed dpkg architecture: amd64
166s autopkgtest [11:53:40]: testbed apt version: 3.1.11
167s autopkgtest [11:53:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup
167s autopkgtest [11:53:41]: testbed release detected to be: resolute
168s autopkgtest [11:53:42]: updating testbed package index (apt update)
168s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB]
168s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
168s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
168s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
168s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB]
168s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B]
168s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB]
168s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB]
168s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [159 kB]
168s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [118 kB]
169s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3096 B]
169s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB]
169s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B]
169s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B]
169s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [607 kB]
169s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [279 kB]
169s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [21.2 kB]
169s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [13.4 kB]
169s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [6516 B]
169s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [680 B]
170s Fetched 2346 kB in 1s (1892 kB/s)
171s Reading package lists...
172s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
172s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
172s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
172s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
172s Reading package lists...
172s Reading package lists...
172s Building dependency tree...
172s Reading state information...
172s Calculating upgrade...
173s The following packages will be upgraded:
173s   libpython3-stdlib python3 python3-minimal usbutils
173s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
173s Need to get 146 kB of archives.
173s After this operation, 0 B of additional disk space will be used.
173s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB]
173s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB]
173s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB]
173s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 usbutils amd64 1:019-1 [83.9 kB]
173s dpkg-preconfigure: unable to re-open stdin: No such file or directory
173s Fetched 146 kB in 0s (13.0 MB/s)
173s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 83372 files and directories currently installed.)
173s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ...
173s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ...
173s Setting up python3-minimal (3.13.7-2) ...
173s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 83372 files and directories currently installed.)
173s Preparing to unpack .../python3_3.13.7-2_amd64.deb ...
173s running python pre-rtupdate hooks for python3.13...
173s Unpacking python3 (3.13.7-2) over (3.13.7-1) ...
173s Preparing to unpack .../libpython3-stdlib_3.13.7-2_amd64.deb ...
173s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ...
173s Preparing to unpack .../usbutils_1%3a019-1_amd64.deb ...
173s Unpacking usbutils (1:019-1) over (1:018-2) ...
173s Setting up usbutils (1:019-1) ...
173s Setting up libpython3-stdlib:amd64 (3.13.7-2) ...
173s Setting up python3 (3.13.7-2) ...
173s running python rtupdate hooks for python3.13...
173s running python post-rtupdate hooks for python3.13...
173s Processing triggers for man-db (2.13.1-1) ...
174s autopkgtest [11:53:48]: upgrading testbed (apt dist-upgrade and autopurge)
174s Reading package lists...
174s Building dependency tree...
174s Reading state information...
174s Calculating upgrade...
174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
175s Reading package lists...
175s Building dependency tree...
175s Reading state information...
175s Solving dependencies...
175s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
177s Reading package lists...
178s Building dependency tree...
178s Reading state information...
178s Solving dependencies...
178s The following NEW packages will be installed:
178s   bbmap busco ca-certificates-java default-jre-headless fontconfig-config
178s   fonts-urw-base35 hmmer java-common libapache-pom-java libblas3 libcairo2
178s   libcommons-cli-java libcommons-codec-java libcommons-io-java
178s   libcommons-parent-java libdeflate0 libdivsufsort3 libfontconfig1 libfontenc1
178s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0
178s   libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblog4j1.2-java
178s   libmpj-java libopenjp2-7 libpcsclite1 libpixman-1-0 libpython3.14-minimal
178s   libpython3.14-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
178s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 openjdk-21-jre-headless
178s   prodigal python3-all python3-biopython python3-cairo
178s   python3-charset-normalizer python3-freetype python3-numpy python3-numpy-dev
178s   python3-pandas python3-pandas-lib python3-pil python3-pytz python3-reportlab
178s   python3-rlpycairo python3.14 python3.14-minimal sgml-base w3c-sgml-lib
178s   x11-common xfonts-encodings xfonts-utils xml-core
178s 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded.
178s Need to get 107 MB of archives.
178s After this operation, 425 MB of additional disk space will be used.
178s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB]
178s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB]
178s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-7ubuntu1 [939 kB]
178s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB]
178s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB]
178s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.0-4 [906 kB]
178s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.0-4 [2559 kB]
178s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-cli-java all 1.6.0-1 [59.9 kB]
178s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapache-pom-java all 33-2 [5874 B]
178s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-parent-java all 56-1 [10.7 kB]
178s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-codec-java all 1.18.0-1 [303 kB]
178s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-io-java all 2.19.0-1 [491 kB]
178s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblog4j1.2-java all 1.2.17-11 [439 kB]
178s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpj-java all 0.44+dfsg-4 [443 kB]
178s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 ca-certificates-java all 20240118 [11.6 kB]
178s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 java-common all 0.76 [6852 B]
178s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB]
178s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB]
178s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
178s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcsclite1 amd64 2.4.0-2 [24.3 kB]
178s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 openjdk-21-jre-headless amd64 21.0.9+10-1 [46.5 MB]
179s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B]
179s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 bbmap all 39.20+dfsg-3 [10.6 MB]
180s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB]
180s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB]
180s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB]
180s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.3-1 [174 kB]
180s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-7ubuntu1 [151 kB]
180s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
180s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB]
180s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
180s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB]
180s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB]
180s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB]
180s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
180s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
180s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
180s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
180s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
180s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB]
180s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB]
180s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu2 [504 kB]
180s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB]
180s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
180s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
180s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB]
180s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB]
180s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB]
180s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB]
180s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
180s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB]
180s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B]
180s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
180s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB]
180s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB]
180s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB]
180s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B]
180s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.4-2 [1147 kB]
180s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB]
180s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB]
180s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB]
181s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.85+dfsg-4 [1719 kB]
181s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 libdivsufsort3 amd64 2.0.1-7 [46.8 kB]
181s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 hmmer amd64 3.4+dfsg-2 [1147 kB]
181s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 prodigal amd64 1:2.6.3-6 [643 kB]
181s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 busco amd64 5.5.0-3 [295 kB]
181s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.0-4 [2397 kB]
181s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.0-4 [805 kB]
181s Get:69 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.13.7-2 [890 B]
181s Fetched 107 MB in 3s (34.1 MB/s)
181s Selecting previously unselected package python3-numpy-dev:amd64.
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181s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ...
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181s Selecting previously unselected package libblas3:amd64.
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181s Selecting previously unselected package liblapack3:amd64.
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183s Selecting previously unselected package libfontenc1:amd64.
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183s Selecting previously unselected package python3-biopython.
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183s Selecting previously unselected package libdivsufsort3:amd64.
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183s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
183s Setting up liblcms2-2:amd64 (2.17-1) ...
183s Setting up libpixman-1-0:amd64 (0.46.4-1) ...
183s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ...
183s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
183s Setting up java-common (0.76) ...
183s Setting up libxrender1:amd64 (1:0.9.12-1) ...
183s Setting up libcommons-cli-java (1.6.0-1) ...
183s Setting up libxcb-render0:amd64 (1.17.0-2build1) ...
183s Setting up prodigal (1:2.6.3-6) ...
183s Setting up python3-charset-normalizer (3.4.3-1) ...
183s Setting up libpython3.14-minimal:amd64 (3.14.0-4) ...
183s Setting up x11-common (1:7.7+24ubuntu1) ...
184s Setting up libdeflate0:amd64 (1.23-2) ...
184s Setting up liblog4j1.2-java (1.2.17-11) ...
184s Setting up python3-pytz (2025.2-4) ...
184s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ...
184s Setting up libgomp1:amd64 (15.2.0-7ubuntu1) ...
184s Setting up python3-freetype (2.5.1-2) ...
184s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
184s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ...
184s Setting up libblas3:amd64 (3.12.1-7) ...
184s 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
184s Setting up libapache-pom-java (33-2) ...
184s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
184s Setting up libimagequant0:amd64 (2.18.0-1build1) ...
184s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ...
184s Setting up libpcsclite1:amd64 (2.4.0-2) ...
184s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ...
184s Setting up libgfortran5:amd64 (15.2.0-7ubuntu1) ...
184s Setting up libwebp7:amd64 (1.5.0-0.1) ...
184s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ...
184s Setting up libharfbuzz0b:amd64 (12.1.0-1) ...
184s Setting up sgml-base (1.31+nmu1) ...
184s Setting up ca-certificates-java (20240118) ...
184s No JRE found. Skipping Java certificates setup.
184s Setting up libdivsufsort3:amd64 (2.0.1-7) ...
184s Setting up libwebpmux3:amd64 (1.5.0-0.1) ...
184s Setting up python3.14-minimal (3.14.0-4) ...
184s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
184s Setting up liblapack3:amd64 (3.12.1-7) ...
184s 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
184s Setting up openjdk-21-jre-headless:amd64 (21.0.9+10-1) ...
184s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
184s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
184s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
184s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
184s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
184s Setting up libpython3.14-stdlib:amd64 (3.14.0-4) ...
184s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ...
184s Setting up libcommons-parent-java (56-1) ...
184s Setting up xfonts-utils (1:7.7+7) ...
184s Setting up libraqm0:amd64 (0.10.3-1) ...
184s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ...
187s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ...
187s Setting up xml-core (0.19) ...
187s Setting up hmmer (3.4+dfsg-2) ...
187s Setting up python3.14 (3.14.0-4) ...
187s Setting up libcommons-codec-java (1.18.0-1) ...
187s Setting up libcommons-io-java (2.19.0-1) ...
187s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ...
187s Setting up python3-all (3.13.7-2) ...
187s Setting up fonts-urw-base35 (20200910-8) ...
187s Setting up libmpj-java (0.44+dfsg-4) ...
187s Setting up python3-pil:amd64 (11.3.0-1ubuntu2) ...
188s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ...
193s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ...
193s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ...
193s Setting up libcairo2:amd64 (1.18.4-1build1) ...
193s Setting up python3-cairo (1.27.0-2build1) ...
193s Setting up python3-rlpycairo (0.3.0-4) ...
193s Setting up python3-reportlab (4.4.4-2) ...
194s Processing triggers for libc-bin (2.42-2ubuntu2) ...
194s Processing triggers for systemd (257.9-0ubuntu2) ...
194s Processing triggers for man-db (2.13.1-1) ...
195s Processing triggers for ca-certificates-java (20240118) ...
195s Adding debian:ACCVRAIZ1.pem
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195s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
195s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
195s Adding debian:BJCA_Global_Root_CA1.pem
195s Adding debian:BJCA_Global_Root_CA2.pem
195s Adding debian:Baltimore_CyberTrust_Root.pem
195s Adding debian:Buypass_Class_2_Root_CA.pem
195s Adding debian:Buypass_Class_3_Root_CA.pem
195s Adding debian:CA_Disig_Root_R2.pem
195s Adding debian:CFCA_EV_ROOT.pem
195s Adding debian:COMODO_Certification_Authority.pem
195s Adding debian:COMODO_ECC_Certification_Authority.pem
195s Adding debian:COMODO_RSA_Certification_Authority.pem
195s Adding debian:Certainly_Root_E1.pem
195s Adding debian:Certainly_Root_R1.pem
195s Adding debian:Certigna.pem
195s Adding debian:Certigna_Root_CA.pem
195s Adding debian:Certum_EC-384_CA.pem
195s Adding debian:Certum_Trusted_Network_CA.pem
195s Adding debian:Certum_Trusted_Network_CA_2.pem
195s Adding debian:Certum_Trusted_Root_CA.pem
195s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
195s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
195s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
195s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
195s Adding debian:Comodo_AAA_Services_root.pem
195s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
195s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem
195s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
195s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem
195s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
195s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
195s Adding debian:DigiCert_Assured_ID_Root_CA.pem
195s Adding debian:DigiCert_Assured_ID_Root_G2.pem
195s Adding debian:DigiCert_Assured_ID_Root_G3.pem
195s Adding debian:DigiCert_Global_Root_CA.pem
195s Adding debian:DigiCert_Global_Root_G2.pem
195s Adding debian:DigiCert_Global_Root_G3.pem
195s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
195s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
195s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
195s Adding debian:DigiCert_Trusted_Root_G4.pem
195s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
195s Adding debian:Entrust_Root_Certification_Authority.pem
195s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
195s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
195s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
195s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
195s Adding debian:GLOBALTRUST_2020.pem
195s Adding debian:GTS_Root_R1.pem
195s Adding debian:GTS_Root_R2.pem
195s Adding debian:GTS_Root_R3.pem
195s Adding debian:GTS_Root_R4.pem
195s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
195s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
195s Adding debian:GlobalSign_Root_CA.pem
195s Adding debian:GlobalSign_Root_CA_-_R3.pem
195s Adding debian:GlobalSign_Root_CA_-_R6.pem
195s Adding debian:GlobalSign_Root_E46.pem
195s Adding debian:GlobalSign_Root_R46.pem
195s Adding debian:Go_Daddy_Class_2_CA.pem
195s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
195s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
195s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
195s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
195s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
195s Adding debian:HiPKI_Root_CA_-_G1.pem
195s Adding debian:Hongkong_Post_Root_CA_3.pem
195s Adding debian:ISRG_Root_X1.pem
195s Adding debian:ISRG_Root_X2.pem
195s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
195s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
195s Adding debian:Izenpe.com.pem
195s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
195s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
195s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
195s Adding debian:NAVER_Global_Root_Certification_Authority.pem
195s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
195s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
195s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
195s Adding debian:QuoVadis_Root_CA_1_G3.pem
195s Adding debian:QuoVadis_Root_CA_2.pem
195s Adding debian:QuoVadis_Root_CA_2_G3.pem
195s Adding debian:QuoVadis_Root_CA_3.pem
195s Adding debian:QuoVadis_Root_CA_3_G3.pem
195s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
195s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
195s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
195s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
195s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
195s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
195s Adding debian:SZAFIR_ROOT_CA2.pem
195s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
195s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
195s Adding debian:SecureSign_Root_CA12.pem
195s Adding debian:SecureSign_Root_CA14.pem
195s Adding debian:SecureSign_Root_CA15.pem
195s Adding debian:SecureTrust_CA.pem
195s Adding debian:Secure_Global_CA.pem
195s Adding debian:Security_Communication_ECC_RootCA1.pem
195s Adding debian:Security_Communication_RootCA2.pem
195s Adding debian:Starfield_Class_2_CA.pem
195s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
195s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
195s Adding debian:SwissSign_Gold_CA_-_G2.pem
195s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
195s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
195s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
195s Adding debian:TWCA_CYBER_Root_CA.pem
195s Adding debian:TWCA_Global_Root_CA.pem
195s Adding debian:TWCA_Root_Certification_Authority.pem
195s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
195s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
195s Adding debian:TeliaSonera_Root_CA_v1.pem
195s Adding debian:Telia_Root_CA_v2.pem
195s Adding debian:TrustAsia_Global_Root_CA_G3.pem
195s Adding debian:TrustAsia_Global_Root_CA_G4.pem
195s Adding debian:Trustwave_Global_Certification_Authority.pem
195s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
195s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
195s Adding debian:TunTrust_Root_CA.pem
195s Adding debian:UCA_Extended_Validation_Root.pem
195s Adding debian:UCA_Global_G2_Root.pem
195s Adding debian:USERTrust_ECC_Certification_Authority.pem
195s Adding debian:USERTrust_RSA_Certification_Authority.pem
195s Adding debian:XRamp_Global_CA_Root.pem
195s Adding debian:certSIGN_ROOT_CA.pem
195s Adding debian:certSIGN_Root_CA_G2.pem
195s Adding debian:e-Szigno_Root_CA_2017.pem
195s Adding debian:ePKI_Root_Certification_Authority.pem
195s Adding debian:emSign_ECC_Root_CA_-_C3.pem
195s Adding debian:emSign_ECC_Root_CA_-_G3.pem
195s Adding debian:emSign_Root_CA_-_C1.pem
195s Adding debian:emSign_Root_CA_-_G1.pem
195s Adding debian:vTrus_ECC_Root_CA.pem
195s Adding debian:vTrus_Root_CA.pem
195s done.
195s Setting up default-jre-headless (2:1.21-76) ...
195s Setting up bbmap (39.20+dfsg-3) ...
195s Processing triggers for sgml-base (1.31+nmu1) ...
195s Setting up w3c-sgml-lib (1.3-3) ...
211s Setting up python3-biopython (1.85+dfsg-4) ...
212s Setting up busco (5.5.0-3) ...
212s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\['
212s   "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]"
212s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: "\[" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\["? A raw string is also an option.
212s   "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]"
212s /usr/lib/python3/dist-packages/busco/busco_tools/hmmer.py:225: SyntaxWarning: 'return' in a 'finally' block
212s   return hmmer_version
214s autopkgtest [11:54:28]: test run-busco-analysis: [-----------------------
214s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
214s   "cannot import name '(?P<module_name>[\w]+)", err.msg
215s 2025-11-17 11:54:29 INFO:	***** Start a BUSCO v5.5.0 analysis, current time: 11/17/2025 11:54:29 *****
215s 2025-11-17 11:54:29 INFO:	Configuring BUSCO with local environment
215s 2025-11-17 11:54:29 INFO:	Mode is genome
215s 2025-11-17 11:54:29 INFO:	Downloading information on latest versions of BUSCO data...
217s 2025-11-17 11:54:31 INFO:	Input file is /tmp/autopkgtest.KD6TJu/autopkgtest_tmp/genome.fna
217s 2025-11-17 11:54:31 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz'
218s 2025-11-17 11:54:32 INFO:	Decompressing file '/tmp/autopkgtest.KD6TJu/autopkgtest_tmp/busco_downloads/lineages/bacteria_odb10.tar.gz'
219s 2025-11-17 11:54:33 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2024-01-08)
219s 2025-11-17 11:54:33 INFO:	Running 1 job(s) on bbmap, starting at 11/17/2025 11:54:33
219s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
219s   "cannot import name '(?P<module_name>[\w]+)", err.msg
219s 2025-11-17 11:54:33 INFO:	[bbmap]	1 of 1 task(s) completed
219s 2025-11-17 11:54:33 INFO:	***** Run Prodigal on input to predict and extract genes *****
219s 2025-11-17 11:54:33 INFO:	Running Prodigal with genetic code 11 in single mode
219s 2025-11-17 11:54:33 INFO:	Running 1 job(s) on prodigal, starting at 11/17/2025 11:54:33
219s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
219s   "cannot import name '(?P<module_name>[\w]+)", err.msg
220s 2025-11-17 11:54:34 INFO:	[prodigal]	1 of 1 task(s) completed
220s 2025-11-17 11:54:34 INFO:	Genetic code 11 selected as optimal
220s 2025-11-17 11:54:34 INFO:	***** Run HMMER on gene sequences *****
220s 2025-11-17 11:54:34 INFO:	Running 124 job(s) on hmmsearch, starting at 11/17/2025 11:54:34
220s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
220s   "cannot import name '(?P<module_name>[\w]+)", err.msg
220s 2025-11-17 11:54:34 INFO:	[hmmsearch]	13 of 124 task(s) completed
220s 2025-11-17 11:54:34 INFO:	[hmmsearch]	25 of 124 task(s) completed
220s 2025-11-17 11:54:34 INFO:	[hmmsearch]	38 of 124 task(s) completed
220s 2025-11-17 11:54:34 INFO:	[hmmsearch]	50 of 124 task(s) completed
220s 2025-11-17 11:54:34 INFO:	[hmmsearch]	63 of 124 task(s) completed
220s 2025-11-17 11:54:34 INFO:	[hmmsearch]	75 of 124 task(s) completed
220s 2025-11-17 11:54:34 INFO:	[hmmsearch]	87 of 124 task(s) completed
220s 2025-11-17 11:54:34 INFO:	[hmmsearch]	100 of 124 task(s) completed
221s 2025-11-17 11:54:35 INFO:	[hmmsearch]	112 of 124 task(s) completed
221s 2025-11-17 11:54:35 INFO:	[hmmsearch]	124 of 124 task(s) completed
221s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
221s   "cannot import name '(?P<module_name>[\w]+)", err.msg
221s 2025-11-17 11:54:35 INFO:	Results:	C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124	   
221s 
221s 2025-11-17 11:54:35 INFO:	
221s 
221s 	---------------------------------------------------
221s 	|Results from dataset bacteria_odb10               |
221s 	---------------------------------------------------
221s 	|C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124      |
221s 	|26	Complete BUSCOs (C)                        |
221s 	|26	Complete and single-copy BUSCOs (S)        |
221s 	|0	Complete and duplicated BUSCOs (D)         |
221s 	|1	Fragmented BUSCOs (F)                      |
221s 	|97	Missing BUSCOs (M)                         |
221s 	|124	Total BUSCO groups searched                |
221s 	---------------------------------------------------
221s 2025-11-17 11:54:35 INFO:	BUSCO analysis done. Total running time: 4 seconds
221s 2025-11-17 11:54:35 INFO:	Results written in /tmp/autopkgtest.KD6TJu/autopkgtest_tmp/test_bacteria
221s 2025-11-17 11:54:35 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
221s 
221s 2025-11-17 11:54:35 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
221s Output Directory Generated
221s PASS
221s autopkgtest [11:54:35]: test run-busco-analysis: -----------------------]
222s autopkgtest [11:54:36]: test run-busco-analysis:  - - - - - - - - - - results - - - - - - - - - -
222s run-busco-analysis   PASS
222s autopkgtest [11:54:36]: @@@@@@@@@@@@@@@@@@@@ summary
222s run-unit-test        FAIL non-zero exit status 1
222s run-busco-analysis   PASS