0s autopkgtest [02:02:47]: starting date: 2024-03-18
  0s autopkgtest [02:02:47]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt
  0s autopkgtest [02:02:47]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ljh0e2w3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade kleborate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-19.secgroup --name adt-noble-arm64-kleborate-20240318-020247-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
105s autopkgtest [02:04:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup
106s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
106s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB]
107s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB]
107s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
107s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
107s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB]
107s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
107s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
107s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
107s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB]
107s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
107s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB]
107s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
108s Fetched 9189 kB in 2s (5074 kB/s)
109s Reading package lists...
112s Reading package lists...
112s Building dependency tree...
112s Reading state information...
112s Calculating upgrade...
113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
113s Reading package lists...
113s Building dependency tree...
113s Reading state information...
114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
114s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
114s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
114s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
114s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
116s Reading package lists...
116s Reading package lists...
116s Building dependency tree...
116s Reading state information...
116s Calculating upgrade...
117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
117s Reading package lists...
117s Building dependency tree...
117s Reading state information...
117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
118s autopkgtest [02:04:45]: testbed dpkg architecture: arm64
119s autopkgtest [02:04:46]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
120s autopkgtest [02:04:47]: @@@@@@@@@@@@@@@@@@@@ apt-source kleborate
126s Get:1 http://ftpmaster.internal/ubuntu noble/universe kleborate 2.4.1-3 (dsc) [2331 B]
126s Get:2 http://ftpmaster.internal/ubuntu noble/universe kleborate 2.4.1-3 (tar) [91.6 MB]
126s Get:3 http://ftpmaster.internal/ubuntu noble/universe kleborate 2.4.1-3 (diff) [5997 kB]
126s gpgv: Signature made Sun Mar 10 19:05:38 2024 UTC
126s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
126s gpgv:                issuer "emollier@debian.org"
126s gpgv: Can't check signature: No public key
126s dpkg-source: warning: cannot verify inline signature for ./kleborate_2.4.1-3.dsc: no acceptable signature found
128s autopkgtest [02:04:55]: testing package kleborate version 2.4.1-3
128s autopkgtest [02:04:55]: build not needed
134s autopkgtest [02:05:01]: test run-unit-test: preparing testbed
137s Reading package lists...
137s Building dependency tree...
137s Reading state information...
137s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
137s Starting 2 pkgProblemResolver with broken count: 0
137s Done
138s  Done
138s Starting pkgProblemResolver with broken count: 0
138s Starting 2 pkgProblemResolver with broken count: 0
138s Done
139s The following additional packages will be installed:
139s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
139s   fonts-urw-base35 kaptive kaptive-data kleborate kleborate-examples libblas3
139s   libcairo2 libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libgfortran5
139s   libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libimagequant0
139s   libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4
139s   libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmurmurhash2
139s   libopenjp2-7 libpixman-1-0 libpython3.11-minimal libpython3.11-stdlib
139s   libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3
139s   libxcb-render0 libxcb-shm0 libxrender1 mash ncbi-blast+ ncbi-data
139s   python3-biopython python3-cairo python3-freetype python3-numpy python3-pil
139s   python3-reportlab python3-rlpycairo python3.11 python3.11-minimal sgml-base
139s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
139s Suggested packages:
139s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre kaptive-example
139s   gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblcms2-utils
139s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
139s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
139s   python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise
139s   gcc gfortran python3-dev python3-pytest python-pil-doc pdf-viewer
139s   python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm
139s   python3.11-venv python3.11-doc binfmt-support sgml-base-doc debhelper
139s Recommended packages:
139s   python-biopython-doc python3-olefile
139s The following NEW packages will be installed:
139s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
139s   fonts-urw-base35 kaptive kaptive-data kleborate kleborate-examples libblas3
139s   libcairo2 libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libgfortran5
139s   libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libimagequant0
139s   libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4
139s   libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmurmurhash2
139s   libopenjp2-7 libpixman-1-0 libpython3.11-minimal libpython3.11-stdlib
139s   libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3
139s   libxcb-render0 libxcb-shm0 libxrender1 mash ncbi-blast+ ncbi-data
139s   python3-biopython python3-cairo python3-freetype python3-numpy python3-pil
139s   python3-reportlab python3-rlpycairo python3.11 python3.11-minimal sgml-base
139s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
139s 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded.
139s 1 not fully installed or removed.
139s Need to get 73.6 MB of archives.
139s After this operation, 297 MB of additional disk space will be used.
139s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
140s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
140s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
140s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
140s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
140s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
140s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
140s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
140s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
140s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB]
140s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
140s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
140s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB]
140s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB]
140s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
140s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
140s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB]
140s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
140s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
140s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
140s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
140s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
140s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
140s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB]
140s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB]
140s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB]
140s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
140s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
140s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB]
140s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
140s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
140s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB]
140s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
141s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
141s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
141s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
141s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
141s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
141s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
141s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
141s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB]
141s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB]
141s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B]
141s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB]
141s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB]
141s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB]
141s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB]
141s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
141s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB]
141s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
141s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB]
141s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB]
141s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB]
141s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB]
141s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 libcapnp-1.0.1 arm64 1.0.1-3 [1326 kB]
141s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB]
141s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB]
141s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 libmurmurhash2 arm64 1.6-1 [6098 B]
141s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 mash arm64 2.3+dfsg-6 [145 kB]
141s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 kaptive all 2.0.8-1 [28.1 kB]
141s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 kaptive-data all 2.0.8-1 [5432 kB]
141s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 kleborate arm64 2.4.1-3 [8743 kB]
141s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 kleborate-examples all 2.4.1-3 [5990 kB]
142s Fetched 73.6 MB in 3s (25.8 MB/s)
142s Selecting previously unselected package libpython3.11-minimal:arm64.
142s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 74758 files and directories currently installed.)
142s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ...
142s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ...
142s Selecting previously unselected package python3.11-minimal.
143s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ...
143s Unpacking python3.11-minimal (3.11.8-1) ...
143s Selecting previously unselected package libpython3.11-stdlib:arm64.
143s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ...
143s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
143s Selecting previously unselected package python3.11.
143s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ...
143s Unpacking python3.11 (3.11.8-1) ...
143s Selecting previously unselected package libblas3:arm64.
143s Preparing to unpack .../04-libblas3_3.12.0-3_arm64.deb ...
143s Unpacking libblas3:arm64 (3.12.0-3) ...
143s Selecting previously unselected package libgfortran5:arm64.
143s Preparing to unpack .../05-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
143s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
143s Selecting previously unselected package liblapack3:arm64.
143s Preparing to unpack .../06-liblapack3_3.12.0-3_arm64.deb ...
143s Unpacking liblapack3:arm64 (3.12.0-3) ...
143s Selecting previously unselected package python3-numpy.
143s Preparing to unpack .../07-python3-numpy_1%3a1.24.2-2_arm64.deb ...
143s Unpacking python3-numpy (1:1.24.2-2) ...
143s Selecting previously unselected package libgomp1:arm64.
143s Preparing to unpack .../08-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
143s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
143s Selecting previously unselected package libimagequant0:arm64.
143s Preparing to unpack .../09-libimagequant0_2.18.0-1_arm64.deb ...
143s Unpacking libimagequant0:arm64 (2.18.0-1) ...
143s Selecting previously unselected package libjpeg-turbo8:arm64.
143s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
143s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
143s Selecting previously unselected package libjpeg8:arm64.
143s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_arm64.deb ...
143s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
143s Selecting previously unselected package liblcms2-2:arm64.
143s Preparing to unpack .../12-liblcms2-2_2.14-2_arm64.deb ...
143s Unpacking liblcms2-2:arm64 (2.14-2) ...
143s Selecting previously unselected package libopenjp2-7:arm64.
143s Preparing to unpack .../13-libopenjp2-7_2.5.0-2_arm64.deb ...
143s Unpacking libopenjp2-7:arm64 (2.5.0-2) ...
143s Selecting previously unselected package libgraphite2-3:arm64.
143s Preparing to unpack .../14-libgraphite2-3_1.3.14-2_arm64.deb ...
143s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
143s Selecting previously unselected package libharfbuzz0b:arm64.
143s Preparing to unpack .../15-libharfbuzz0b_8.3.0-2_arm64.deb ...
143s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
143s Selecting previously unselected package libraqm0:arm64.
143s Preparing to unpack .../16-libraqm0_0.10.1-1_arm64.deb ...
143s Unpacking libraqm0:arm64 (0.10.1-1) ...
143s Selecting previously unselected package libdeflate0:arm64.
143s Preparing to unpack .../17-libdeflate0_1.19-1_arm64.deb ...
143s Unpacking libdeflate0:arm64 (1.19-1) ...
144s Selecting previously unselected package libjbig0:arm64.
144s Preparing to unpack .../18-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
144s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
144s Selecting previously unselected package liblerc4:arm64.
144s Preparing to unpack .../19-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
144s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
144s Selecting previously unselected package libsharpyuv0:arm64.
144s Preparing to unpack .../20-libsharpyuv0_1.3.2-0.4_arm64.deb ...
144s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
144s Selecting previously unselected package libwebp7:arm64.
144s Preparing to unpack .../21-libwebp7_1.3.2-0.4_arm64.deb ...
144s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
144s Selecting previously unselected package libtiff6:arm64.
144s Preparing to unpack .../22-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
144s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
144s Selecting previously unselected package libwebpdemux2:arm64.
144s Preparing to unpack .../23-libwebpdemux2_1.3.2-0.4_arm64.deb ...
144s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ...
144s Selecting previously unselected package libwebpmux3:arm64.
144s Preparing to unpack .../24-libwebpmux3_1.3.2-0.4_arm64.deb ...
144s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ...
144s Selecting previously unselected package python3-pil:arm64.
144s Preparing to unpack .../25-python3-pil_10.2.0-1_arm64.deb ...
144s Unpacking python3-pil:arm64 (10.2.0-1) ...
144s Selecting previously unselected package fonts-dejavu-mono.
144s Preparing to unpack .../26-fonts-dejavu-mono_2.37-8_all.deb ...
144s Unpacking fonts-dejavu-mono (2.37-8) ...
144s Selecting previously unselected package fonts-dejavu-core.
144s Preparing to unpack .../27-fonts-dejavu-core_2.37-8_all.deb ...
144s Unpacking fonts-dejavu-core (2.37-8) ...
144s Selecting previously unselected package libfontenc1:arm64.
144s Preparing to unpack .../28-libfontenc1_1%3a1.1.8-1_arm64.deb ...
144s Unpacking libfontenc1:arm64 (1:1.1.8-1) ...
144s Selecting previously unselected package x11-common.
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179s Setting up kaptive (2.0.8-1) ...
179s Setting up kleborate (2.4.1-3) ...
180s Setting up autopkgtest-satdep (0) ...
185s (Reading database ... 79161 files and directories currently installed.)
185s Removing autopkgtest-satdep (0) ...
186s autopkgtest [02:05:53]: test run-unit-test: [-----------------------
187s /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
187s   warnings.warn(
249s strain	species	ST	virulence_score	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	RmpADC	RmST	rmpA2	wzi	K_locus
249s Klebs_HS11286	Klebsiella pneumoniae	ST11	1	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	0	-	wzi74	KL103
249s Klebs_Kp1084	Klebsiella pneumoniae	ST23	2	ybt 1; ICEKp10	47	clb 2	37	-	0	-	0	-	0	-	wzi172	KL1
249s MGH78578	Klebsiella pneumoniae	ST38	0	-	0	-	0	-	0	-	0	-	0	-	wzi50	KL15 (KL17,KL51,KL52)
249s NTUH-K2044	Klebsiella pneumoniae	ST23	4	ybt 2; ICEKp1	326	-	0	iuc 1	1	iro 1,iro 3	19,18	rmp 1; KpVP-1 (truncated),rmp 3; ICEKp1 (truncated)	26-1LV,119	rmpA2_3-47%	wzi1	KL1
249s /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
249s   warnings.warn(
344s strain	species	ST	virulence_score	resistance_score	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	RmpADC	RmST	rmpA2	wzi	K_locus	AGly_acquired	Col_acquired	Fcyn_acquired	Flq_acquired	Gly_acquired	MLS_acquired	Phe_acquired	Rif_acquired	Sul_acquired	Tet_acquired	Tgc_acquired	Tmt_acquired	Bla_acquired	Bla_inhR_acquired	Bla_ESBL_acquired	Bla_ESBL_inhR_acquired	Bla_Carb_acquired	Bla_chr	SHV_mutations	Omp_mutations	Col_mutations	Flq_mutations	truncated_resistance_hits	spurious_resistance_hits
344s Klebs_HS11286	Klebsiella pneumoniae	ST11	1	3	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	0	-	wzi74	KL103	aadA2^;rmtB;strA.v1^;strB.v1	-	-	-	-	-	-	-	sul2	tet(G).v1	-	dfrA12*	TEM-1;TEM-1;TEM-1	-	CTX-M-14;CTX-M-14	-	KPC-2	SHV-11	35Q	OmpK35-40%	PmrB-10%	GyrA-83I;ParC-80I	aac(3)-IId*?-0%	floR.v2*?;sul1?-63%
344s Klebs_Kp1084	Klebsiella pneumoniae	ST23	2	0	ybt 1; ICEKp10	47	clb 2	37	-	0	-	0	-	0	-	wzi172	KL1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	SHV-11^	35Q	-	-	-	-	-
344s MGH78578	Klebsiella pneumoniae	ST38	0	1	-	0	-	0	-	0	-	0	-	0	-	wzi50	KL15 (KL17,KL51,KL52)	aac(6')-Ib'.v1;aadA*;ant(2'')-Ia;aph(3')-Ia;strA.v1;strB.v1	-	-	-	-	-	catA1*;cmlA5	-	sul1;sul2	tet(D)	-	-	TEM-1D.v1^;TEM-1D.v1^	-	SHV-12	-	-	SHV-11^	238S;240K;35Q;35Q	OmpK35-86%	-	GyrA-83Y	OXA-9.v1*-42%	-
344s NTUH-K2044	Klebsiella pneumoniae	ST23	4	0	ybt 2; ICEKp1	326	-	0	iuc 1	1	iro 1,iro 3	19,18	rmp 1; KpVP-1 (truncated),rmp 3; ICEKp1 (truncated)	26-1LV,119	rmpA2_3-47%	wzi1	KL1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	SHV-11^	35Q	-	-	-	-	-
345s /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
345s   warnings.warn(
855s strain	species	ST	virulence_score	resistance_score	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	RmpADC	RmST	rmpA2	wzi	K_locus	K_locus_confidence	O_locus	O_locus_confidence	AGly_acquired	Col_acquired	Fcyn_acquired	Flq_acquired	Gly_acquired	MLS_acquired	Phe_acquired	Rif_acquired	Sul_acquired	Tet_acquired	Tgc_acquired	Tmt_acquired	Bla_acquired	Bla_inhR_acquired	Bla_ESBL_acquired	Bla_ESBL_inhR_acquired	Bla_Carb_acquired	Bla_chr	SHV_mutations	Omp_mutations	Col_mutations	Flq_mutations	truncated_resistance_hits	spurious_resistance_hits
855s Klebs_HS11286	Klebsiella pneumoniae	ST11	1	3	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	0	-	wzi74	KL103	Very high	O1/O2v1	Very high	aadA2^;rmtB;strA.v1^;strB.v1	-	-	-	-	-	-	-	sul2	tet(G).v1	-	dfrA12*	TEM-1;TEM-1;TEM-1	-	CTX-M-14;CTX-M-14	-	KPC-2	SHV-11	35Q	OmpK35-40%	PmrB-10%	GyrA-83I;ParC-80I	aac(3)-IId*?-0%	floR.v2*?;sul1?-63%
855s Klebs_Kp1084	Klebsiella pneumoniae	ST23	2	0	ybt 1; ICEKp10	47	clb 2	37	-	0	-	0	-	0	-	wzi172	unknown (KL1)	None	O1/O2v2	High	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	SHV-11^	35Q	-	-	-	-	-
855s MGH78578	Klebsiella pneumoniae	ST38	0	1	-	0	-	0	-	0	-	0	-	0	-	wzi50	KL52	Perfect	OL13	High	aac(6')-Ib'.v1;aadA*;ant(2'')-Ia;aph(3')-Ia;strA.v1;strB.v1	-	-	-	-	-	catA1*;cmlA5	-	sul1;sul2	tet(D)	-	-	TEM-1D.v1^;TEM-1D.v1^	-	SHV-12	-	-	SHV-11^	238S;240K;35Q;35Q	OmpK35-86%	-	GyrA-83Y	OXA-9.v1*-42%	-
855s NTUH-K2044	Klebsiella pneumoniae	ST23	4	0	ybt 2; ICEKp1	326	-	0	iuc 1	1	iro 1,iro 3	19,18	rmp 1; KpVP-1 (truncated),rmp 3; ICEKp1 (truncated)	26-1LV,119	rmpA2_3-47%	wzi1	KL1	Perfect	O1/O2v2	Very high	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	SHV-11^	35Q	-	-	-	-	-
855s autopkgtest [02:17:02]: test run-unit-test: -----------------------]
856s autopkgtest [02:17:03]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
856s run-unit-test        PASS
856s autopkgtest [02:17:03]: @@@@@@@@@@@@@@@@@@@@ summary
856s run-unit-test        PASS
860s Creating nova instance adt-noble-arm64-kleborate-20240318-020247-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...