0s autopkgtest [18:36:30]: starting date and time: 2025-03-15 18:36:30+0000 0s autopkgtest [18:36:30]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:36:30]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.govomtbg/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade ragout --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-17.secgroup --name adt-plucky-s390x-ragout-20250315-183630-juju-7f2275-prod-proposed-migration-environment-15-c446b663-2458-41d1-b930-fe9f0748b773 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 140s autopkgtest [18:38:50]: testbed dpkg architecture: s390x 140s autopkgtest [18:38:50]: testbed apt version: 2.9.33 140s autopkgtest [18:38:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s autopkgtest [18:38:50]: testbed release detected to be: None 141s autopkgtest [18:38:51]: updating testbed package index (apt update) 141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 142s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 142s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 142s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 142s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 143s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 143s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 143s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 143s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 143s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 143s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 143s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 143s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 143s Fetched 1073 kB in 2s (587 kB/s) 144s Reading package lists... 144s + lsb_release --codename --short 144s + RELEASE=plucky 144s + cat 144s + [ plucky != trusty ] 144s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s Calculating upgrade... 145s Calculating upgrade... 145s The following packages were automatically installed and are no longer required: 145s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 145s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 145s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 145s linux-tools-6.11.0-8-generic 145s Use 'sudo apt autoremove' to remove them. 146s The following packages will be upgraded: 146s pinentry-curses python3-jinja2 strace 146s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 652 kB of archives. 146s After this operation, 27.6 kB of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 146s Fetched 652 kB in 1s (743 kB/s) 146s (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 ... 81428 files and directories currently installed.) 146s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 146s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 146s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 146s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 146s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 146s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 146s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 146s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 146s Setting up strace (6.13+ds-1ubuntu1) ... 146s Processing triggers for man-db (2.13.0-1) ... 147s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 147s + /usr/lib/apt/apt-helper analyze-pattern ?true 147s + uname -r 147s + sed s/\./\\./g 147s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 147s + apt list ?obsolete 147s + tail -n+2 147s + cut -d/ -f1 147s + grep -v ^linux-.*6\.14\.0-10-generic.* 147s + obsolete_pkgs=linux-headers-6.11.0-8-generic 147s linux-headers-6.11.0-8 147s linux-modules-6.11.0-8-generic 147s linux-tools-6.11.0-8-generic 147s linux-tools-6.11.0-8 147s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 147s The following packages will be REMOVED: 147s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 147s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 147s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 147s linux-tools-6.11.0-8-generic* 147s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 147s After this operation, 167 MB disk space will be freed. 147s (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 ... 81428 files and directories currently installed.) 147s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 147s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 147s Removing libpython3.12t64:s390x (3.12.9-1) ... 147s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 148s Removing libnsl2:s390x (1.3.0-3build3) ... 148s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 148s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 148s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 148s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 148s Processing triggers for libc-bin (2.41-1ubuntu1) ... 149s (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 ... 56328 files and directories currently installed.) 149s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 149s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 149s + grep -q trusty /etc/lsb-release 149s + [ ! -d /usr/share/doc/unattended-upgrades ] 149s + [ ! -d /usr/share/doc/lxd ] 149s + [ ! -d /usr/share/doc/lxd-client ] 149s + [ ! -d /usr/share/doc/snapd ] 149s + type iptables 149s + cat 149s + chmod 755 /etc/rc.local 149s + . /etc/rc.local 149s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 149s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 149s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 149s + uname -m 149s + [ s390x = ppc64le ] 149s + [ -d /run/systemd/system ] 149s + systemd-detect-virt --quiet --vm 149s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 149s + cat 149s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 149s + echo COMPRESS=lz4 149s autopkgtest [18:38:59]: upgrading testbed (apt dist-upgrade and autopurge) 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 149s Entering ResolveByKeep 150s 150s Calculating upgrade... 150s The following packages will be upgraded: 150s libc-bin libc-dev-bin libc6 libc6-dev locales 150s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 9512 kB of archives. 150s After this operation, 8192 B of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 151s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 153s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 154s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 157s Preconfiguring packages ... 157s Fetched 9512 kB in 7s (1385 kB/s) 157s (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 ... 56326 files and directories currently installed.) 157s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 157s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 157s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 157s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s Setting up libc6:s390x (2.41-1ubuntu2) ... 157s (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 ... 56326 files and directories currently installed.) 157s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 157s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s Setting up libc-bin (2.41-1ubuntu2) ... 157s (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 ... 56326 files and directories currently installed.) 157s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 157s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s Setting up locales (2.41-1ubuntu2) ... 158s Generating locales (this might take a while)... 159s en_US.UTF-8... done 159s Generation complete. 159s Setting up libc-dev-bin (2.41-1ubuntu2) ... 159s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 159s Processing triggers for man-db (2.13.0-1) ... 159s Processing triggers for systemd (257.3-1ubuntu3) ... 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 161s Solving dependencies... 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s autopkgtest [18:39:11]: rebooting testbed after setup commands that affected boot 181s autopkgtest [18:39:31]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 183s autopkgtest [18:39:33]: @@@@@@@@@@@@@@@@@@@@ apt-source ragout 195s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (dsc) [2117 B] 195s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (tar) [12.3 MB] 195s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (diff) [15.0 kB] 195s gpgv: Signature made Fri Feb 2 10:15:47 2024 UTC 195s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 195s gpgv: issuer "tille@debian.org" 195s gpgv: Can't check signature: No public key 195s dpkg-source: warning: cannot verify inline signature for ./ragout_2.3-5.dsc: no acceptable signature found 195s autopkgtest [18:39:45]: testing package ragout version 2.3-5 196s autopkgtest [18:39:46]: build not needed 200s autopkgtest [18:39:50]: test run-unit-test: preparing testbed 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 201s Starting pkgProblemResolver with broken count: 0 201s Starting 2 pkgProblemResolver with broken count: 0 201s Done 201s The following NEW packages will be installed: 201s lagan libdivsufsort3 python3-networkx python3-six ragout ragout-examples 201s sibelia 201s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 201s Need to get 32.7 MB of archives. 201s After this operation, 104 MB of additional disk space will be used. 201s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x lagan s390x 2.0-10 [221 kB] 201s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libdivsufsort3 s390x 2.0.1-6 [62.7 kB] 202s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 210s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3-six all 1.17.0-1 [13.2 kB] 211s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x ragout s390x 2.3-5 [2176 kB] 212s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x ragout-examples all 2.3-5 [18.4 MB] 229s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x sibelia s390x 3.0.7+dfsg-3 [299 kB] 229s Fetched 32.7 MB in 28s (1168 kB/s) 229s Selecting previously unselected package lagan. 229s (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 ... 56326 files and directories currently installed.) 229s Preparing to unpack .../0-lagan_2.0-10_s390x.deb ... 229s Unpacking lagan (2.0-10) ... 229s Selecting previously unselected package libdivsufsort3:s390x. 229s Preparing to unpack .../1-libdivsufsort3_2.0.1-6_s390x.deb ... 229s Unpacking libdivsufsort3:s390x (2.0.1-6) ... 229s Selecting previously unselected package python3-networkx. 229s Preparing to unpack .../2-python3-networkx_3.2.1-4ubuntu1_all.deb ... 229s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 230s Selecting previously unselected package python3-six. 230s Preparing to unpack .../3-python3-six_1.17.0-1_all.deb ... 230s Unpacking python3-six (1.17.0-1) ... 230s Selecting previously unselected package ragout. 230s Preparing to unpack .../4-ragout_2.3-5_s390x.deb ... 230s Unpacking ragout (2.3-5) ... 230s Selecting previously unselected package ragout-examples. 230s Preparing to unpack .../5-ragout-examples_2.3-5_all.deb ... 230s Unpacking ragout-examples (2.3-5) ... 230s Selecting previously unselected package sibelia. 230s Preparing to unpack .../6-sibelia_3.0.7+dfsg-3_s390x.deb ... 230s Unpacking sibelia (3.0.7+dfsg-3) ... 230s Setting up ragout-examples (2.3-5) ... 230s Setting up python3-networkx (3.2.1-4ubuntu1) ... 231s Setting up python3-six (1.17.0-1) ... 231s Setting up ragout (2.3-5) ... 231s Setting up lagan (2.0-10) ... 231s Setting up libdivsufsort3:s390x (2.0.1-6) ... 231s Setting up sibelia (3.0.7+dfsg-3) ... 231s Processing triggers for man-db (2.13.0-1) ... 231s Processing triggers for libc-bin (2.41-1ubuntu2) ... 233s autopkgtest [18:40:23]: test run-unit-test: [----------------------- 233s + ragout E.Coli/ecoli.rcp --outdir E.Coli/out/ --refine 233s [18:40:23] INFO: Starting Ragout v2.3 233s [18:40:23] INFO: Running withs synteny block sizes '[5000, 500, 100]' 233s [18:40:23] INFO: Running Sibelia with block size 5000 258s [18:40:48] INFO: Running Sibelia with block size 500 284s [18:41:14] INFO: Running Sibelia with block size 100 309s [18:41:39] INFO: Inferring phylogeny from synteny blocks data 309s [18:41:39] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 309s [18:41:39] INFO: "dh1" synteny blocks coverage: 99.86% 309s [18:41:39] INFO: "mg1655" synteny blocks coverage: 99.56% 309s [18:41:39] INFO: Inferred tree: ('dh1' : 1.5, 'mg1655' : 1.5) 309s [18:41:39] INFO: 'dh1' is chosen as a naming reference 309s [18:41:39] INFO: Processing permutation files 309s [18:41:39] INFO: Reading E.Coli/out/sibelia-workdir/5000/blocks_coords.txt 309s [18:41:39] INFO: "dh1" synteny blocks coverage: 96.41% 309s [18:41:39] INFO: "mg1655" synteny blocks coverage: 99.45% 309s [18:41:39] INFO: Reading E.Coli/out/sibelia-workdir/500/blocks_coords.txt 309s [18:41:39] INFO: "dh1" synteny blocks coverage: 99.58% 309s [18:41:39] INFO: "mg1655" synteny blocks coverage: 99.66% 309s [18:41:39] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 309s [18:41:39] INFO: "dh1" synteny blocks coverage: 99.86% 309s [18:41:39] INFO: "mg1655" synteny blocks coverage: 99.56% 309s [18:41:39] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 309s [18:41:39] INFO: "dh1" synteny blocks coverage: 99.86% 309s [18:41:39] INFO: "mg1655" synteny blocks coverage: 99.56% 309s [18:41:39] INFO: Reading contigs file 309s [18:41:39] INFO: Detecting chimeric adjacencies 309s [18:41:39] INFO: Stage "5000" 309s [18:41:39] INFO: Removing chimeric adjacencies 309s [18:41:39] INFO: Inferring missing adjacencies 309s [18:41:39] INFO: Stage "500" 309s [18:41:39] INFO: Removing chimeric adjacencies 309s [18:41:39] INFO: Inferring missing adjacencies 309s [18:41:39] INFO: Removing chimeric adjacencies 309s [18:41:39] INFO: Merging two iterations 309s [18:41:39] INFO: Stage "100" 309s [18:41:39] INFO: Removing chimeric adjacencies 309s [18:41:39] INFO: Inferring missing adjacencies 309s [18:41:39] INFO: Removing chimeric adjacencies 309s [18:41:39] INFO: Merging two iterations 309s [18:41:39] INFO: Stage "refine" 309s [18:41:39] INFO: Removing chimeric adjacencies 309s [18:41:39] INFO: Inferring missing adjacencies 309s [18:41:39] INFO: Removing chimeric adjacencies 310s [18:41:39] INFO: Merging two iterations 310s [18:41:40] INFO: Building assembly graph 310s Reading FASTA 310s Building FM-index 310s Overapping 310s Kmer size is set to 55 310s [18:41:40] INFO: Refining with assembly graph 310s [18:41:40] INFO: Generating FASTA output 310s [18:41:40] INFO: Assembly statistics: 310s 310s Scaffolds: 1 310s Used fragments: 145 310s Scaffolds length: 4635053 310s 310s Unplaced fragments: 37 310s Unplaced length: 13411 (0.29%) 310s Introduced Ns length: 69544 (1.50%) 310s 310s Fragments N50: 125773 310s Assembly N50: 4635053 310s 310s [18:41:40] INFO: Done! 310s + ragout H.Pylori/helicobacter.rcp --outdir H.Pylori/out/ --refine 310s [18:41:40] INFO: Starting Ragout v2.3 310s [18:41:40] INFO: Running withs synteny block sizes '[5000, 500, 100]' 310s [18:41:40] INFO: Running Sibelia with block size 5000 361s [18:42:31] INFO: Running Sibelia with block size 500 419s [18:43:29] INFO: Running Sibelia with block size 100 474s [18:44:24] INFO: Phylogeny is taken from the recipe 474s [18:44:24] INFO: 'els' is chosen as a naming reference 474s [18:44:24] INFO: Processing permutation files 474s [18:44:24] INFO: Reading H.Pylori/out/sibelia-workdir/5000/blocks_coords.txt 474s [18:44:24] INFO: "els" synteny blocks coverage: 80.53% 474s [18:44:24] INFO: "g27" synteny blocks coverage: 81.02% 474s [18:44:24] INFO: "gambia" synteny blocks coverage: 80.04% 474s [18:44:24] INFO: "puno" synteny blocks coverage: 80.58% 474s [18:44:24] INFO: "sjm180" synteny blocks coverage: 83.86% 474s [18:44:24] INFO: Reading H.Pylori/out/sibelia-workdir/500/blocks_coords.txt 474s [18:44:24] INFO: "els" synteny blocks coverage: 96.82% 474s [18:44:24] INFO: "g27" synteny blocks coverage: 94.8% 474s [18:44:24] INFO: "gambia" synteny blocks coverage: 94.9% 474s [18:44:24] INFO: "puno" synteny blocks coverage: 92.43% 474s [18:44:24] INFO: "sjm180" synteny blocks coverage: 96.75% 474s [18:44:24] INFO: Reading H.Pylori/out/sibelia-workdir/100/blocks_coords.txt 474s [18:44:24] INFO: "els" synteny blocks coverage: 97.08% 474s [18:44:24] INFO: "g27" synteny blocks coverage: 95.16% 474s [18:44:24] INFO: "gambia" synteny blocks coverage: 95.13% 474s [18:44:24] INFO: "puno" synteny blocks coverage: 92.78% 474s [18:44:24] INFO: "sjm180" synteny blocks coverage: 96.5% 474s [18:44:24] INFO: Reading H.Pylori/out/sibelia-workdir/100/blocks_coords.txt 474s [18:44:24] INFO: "els" synteny blocks coverage: 97.08% 474s [18:44:24] INFO: "g27" synteny blocks coverage: 95.16% 474s [18:44:24] INFO: "gambia" synteny blocks coverage: 95.13% 474s [18:44:24] INFO: "puno" synteny blocks coverage: 92.78% 474s [18:44:24] INFO: "sjm180" synteny blocks coverage: 96.5% 474s [18:44:24] INFO: Reading contigs file 474s [18:44:24] INFO: Detecting chimeric adjacencies 474s [18:44:24] INFO: Stage "5000" 474s [18:44:24] INFO: Removing chimeric adjacencies 474s [18:44:24] INFO: Inferring missing adjacencies 474s [18:44:24] INFO: Stage "500" 474s [18:44:24] INFO: Removing chimeric adjacencies 474s [18:44:24] INFO: Inferring missing adjacencies 474s [18:44:24] INFO: Removing chimeric adjacencies 474s [18:44:24] INFO: Merging two iterations 474s [18:44:24] INFO: Stage "100" 474s [18:44:24] INFO: Removing chimeric adjacencies 474s [18:44:24] INFO: Inferring missing adjacencies 474s [18:44:24] INFO: Removing chimeric adjacencies 474s [18:44:24] INFO: Merging two iterations 474s [18:44:24] INFO: Stage "refine" 474s [18:44:24] INFO: Removing chimeric adjacencies 474s [18:44:24] INFO: Inferring missing adjacencies 474s [18:44:24] INFO: Removing chimeric adjacencies 474s [18:44:24] INFO: Merging two iterations 474s [18:44:24] INFO: Building assembly graph 474s Reading FASTA 474s Building FM-index 474s Overapping 474s Kmer size is set to 54 474s [18:44:24] INFO: Refining with assembly graph 474s [18:44:24] INFO: Generating FASTA output 474s [18:44:24] INFO: Assembly statistics: 474s 474s Scaffolds: 1 474s Used fragments: 133 474s Scaffolds length: 1654315 474s 474s Unplaced fragments: 78 474s Unplaced length: 18234 (1.10%) 474s Introduced Ns length: 11306 (0.68%) 474s 474s Fragments N50: 75870 474s Assembly N50: 1654315 474s 474s [18:44:24] INFO: Done! 474s + ragout S.Aureus/aureus.rcp --outdir S.Aureus/out/ --refine 474s [18:44:24] INFO: Starting Ragout v2.3 474s [18:44:24] INFO: Running withs synteny block sizes '[5000, 500, 100]' 474s [18:44:24] INFO: Running Sibelia with block size 5000 537s [18:45:26] INFO: Running Sibelia with block size 500 600s [18:46:30] INFO: Running Sibelia with block size 100 668s [18:47:38] INFO: Inferring phylogeny from synteny blocks data 668s [18:47:38] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 668s [18:47:38] INFO: "col" synteny blocks coverage: 98.34% 668s [18:47:38] INFO: "jkd" synteny blocks coverage: 94.31% 668s [18:47:38] INFO: "rf122" synteny blocks coverage: 93.71% 668s [18:47:38] INFO: "n315" synteny blocks coverage: 97.19% 668s [18:47:38] INFO: "usa" synteny blocks coverage: 96.35% 668s [18:47:38] INFO: Inferred tree: (('jkd' : 47.625, ('col' : 5.375, 'usa' : 40.625) : 14.375) : 11.4375, ('n315' : 35.333333333333336, 'rf122' : 61.666666666666664) : 11.4375) 668s [18:47:38] INFO: 'col' is chosen as a naming reference 668s [18:47:38] INFO: Processing permutation files 668s [18:47:38] INFO: Reading S.Aureus/out/sibelia-workdir/5000/blocks_coords.txt 668s [18:47:38] INFO: "col" synteny blocks coverage: 84.15% 668s [18:47:38] INFO: "jkd" synteny blocks coverage: 80.65% 668s [18:47:38] INFO: "rf122" synteny blocks coverage: 83.55% 668s [18:47:38] INFO: "n315" synteny blocks coverage: 83.81% 668s [18:47:38] INFO: "usa" synteny blocks coverage: 89.64% 668s [18:47:38] INFO: Reading S.Aureus/out/sibelia-workdir/500/blocks_coords.txt 668s [18:47:38] INFO: "col" synteny blocks coverage: 97.78% 668s [18:47:38] INFO: "jkd" synteny blocks coverage: 93.69% 668s [18:47:38] INFO: "rf122" synteny blocks coverage: 93.63% 668s [18:47:38] INFO: "n315" synteny blocks coverage: 96.93% 668s [18:47:38] INFO: "usa" synteny blocks coverage: 97.32% 668s [18:47:38] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 668s [18:47:38] INFO: "col" synteny blocks coverage: 98.34% 668s [18:47:38] INFO: "jkd" synteny blocks coverage: 94.31% 668s [18:47:38] INFO: "rf122" synteny blocks coverage: 93.71% 668s [18:47:38] INFO: "n315" synteny blocks coverage: 97.19% 668s [18:47:38] INFO: "usa" synteny blocks coverage: 96.35% 668s [18:47:38] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 668s [18:47:38] INFO: "col" synteny blocks coverage: 98.34% 668s [18:47:38] INFO: "jkd" synteny blocks coverage: 94.31% 668s [18:47:38] INFO: "rf122" synteny blocks coverage: 93.71% 668s [18:47:38] INFO: "n315" synteny blocks coverage: 97.19% 668s [18:47:38] INFO: "usa" synteny blocks coverage: 96.35% 668s [18:47:38] INFO: Reading contigs file 668s [18:47:38] INFO: Detecting chimeric adjacencies 668s [18:47:38] INFO: Stage "5000" 668s [18:47:38] INFO: Removing chimeric adjacencies 668s [18:47:38] INFO: Inferring missing adjacencies 668s [18:47:38] INFO: Stage "500" 668s [18:47:38] INFO: Removing chimeric adjacencies 668s [18:47:38] INFO: Inferring missing adjacencies 668s [18:47:38] INFO: Removing chimeric adjacencies 668s [18:47:38] INFO: Merging two iterations 668s [18:47:38] INFO: Stage "100" 668s [18:47:38] INFO: Removing chimeric adjacencies 668s [18:47:38] INFO: Inferring missing adjacencies 668s [18:47:38] INFO: Removing chimeric adjacencies 668s [18:47:38] INFO: Merging two iterations 668s [18:47:38] INFO: Stage "refine" 668s [18:47:38] INFO: Removing chimeric adjacencies 668s [18:47:38] INFO: Inferring missing adjacencies 668s [18:47:38] INFO: Removing chimeric adjacencies 668s [18:47:38] INFO: Merging two iterations 668s [18:47:38] INFO: Building assembly graph 668s Reading FASTA 668s Building FM-index 669s Overapping 669s Kmer size is set to 55 669s [18:47:38] INFO: Refining with assembly graph 669s [18:47:39] INFO: Generating FASTA output 669s [18:47:39] INFO: Assembly statistics: 669s 669s Scaffolds: 1 669s Used fragments: 169 669s Scaffolds length: 2828340 669s 669s Unplaced fragments: 633 669s Unplaced length: 441368 (13.88%) 669s Introduced Ns length: 83415 (2.95%) 669s 669s Fragments N50: 45930 669s Assembly N50: 2828340 669s 669s [18:47:39] INFO: Done! 669s + ragout V.Cholerae/cholerae.rcp --outdir V.Cholerae/out/ --refine 669s [18:47:39] INFO: Starting Ragout v2.3 669s [18:47:39] INFO: Running withs synteny block sizes '[5000, 500, 100]' 669s [18:47:39] INFO: Running Sibelia with block size 5000 723s [18:48:33] INFO: Running Sibelia with block size 500 780s [18:49:30] INFO: Running Sibelia with block size 100 841s [18:50:30] INFO: Inferring phylogeny from synteny blocks data 841s [18:50:30] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 841s [18:50:30] INFO: "biovar" synteny blocks coverage: 99.26% 841s [18:50:30] INFO: "inaba" synteny blocks coverage: 97.98% 841s [18:50:30] INFO: "o395" synteny blocks coverage: 97.85% 841s [18:50:30] INFO: "h1" synteny blocks coverage: 99.19% 841s [18:50:30] INFO: Inferred tree: (('biovar' : 4.75, 'o395' : 13.25) : 4.625, ('h1' : 1e-06, 'inaba' : 6.75) : 4.625) 841s [18:50:30] INFO: 'inaba' is chosen as a naming reference 841s [18:50:30] INFO: Processing permutation files 841s [18:50:30] INFO: Reading V.Cholerae/out/sibelia-workdir/5000/blocks_coords.txt 841s [18:50:30] INFO: "biovar" synteny blocks coverage: 92.08% 841s [18:50:30] INFO: "inaba" synteny blocks coverage: 91.94% 841s [18:50:30] INFO: "o395" synteny blocks coverage: 91.08% 841s [18:50:30] INFO: "h1" synteny blocks coverage: 98.87% 841s [18:50:30] INFO: Reading V.Cholerae/out/sibelia-workdir/500/blocks_coords.txt 841s [18:50:30] INFO: "biovar" synteny blocks coverage: 99.0% 841s [18:50:30] INFO: "inaba" synteny blocks coverage: 97.68% 841s [18:50:30] INFO: "o395" synteny blocks coverage: 97.52% 841s [18:50:30] INFO: "h1" synteny blocks coverage: 99.3% 841s [18:50:31] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 841s [18:50:31] INFO: "biovar" synteny blocks coverage: 99.26% 841s [18:50:31] INFO: "inaba" synteny blocks coverage: 97.98% 841s [18:50:31] INFO: "o395" synteny blocks coverage: 97.85% 841s [18:50:31] INFO: "h1" synteny blocks coverage: 99.19% 841s [18:50:31] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 841s [18:50:31] INFO: "biovar" synteny blocks coverage: 99.26% 841s [18:50:31] INFO: "inaba" synteny blocks coverage: 97.98% 841s [18:50:31] INFO: "o395" synteny blocks coverage: 97.85% 841s [18:50:31] INFO: "h1" synteny blocks coverage: 99.19% 841s [18:50:31] INFO: Reading contigs file 841s [18:50:31] INFO: Detecting chimeric adjacencies 841s [18:50:31] INFO: Stage "5000" 841s [18:50:31] INFO: Removing chimeric adjacencies 841s [18:50:31] INFO: Inferring missing adjacencies 841s [18:50:31] INFO: Stage "500" 841s [18:50:31] INFO: Removing chimeric adjacencies 841s [18:50:31] INFO: Inferring missing adjacencies 841s [18:50:31] INFO: Removing chimeric adjacencies 841s [18:50:31] INFO: Merging two iterations 841s [18:50:31] INFO: Stage "100" 841s [18:50:31] INFO: Removing chimeric adjacencies 841s [18:50:31] INFO: Inferring missing adjacencies 841s [18:50:31] INFO: Removing chimeric adjacencies 841s [18:50:31] INFO: Merging two iterations 841s [18:50:31] INFO: Stage "refine" 841s [18:50:31] INFO: Removing chimeric adjacencies 841s [18:50:31] INFO: Inferring missing adjacencies 841s [18:50:31] INFO: Removing chimeric adjacencies 841s [18:50:31] INFO: Merging two iterations 841s [18:50:31] INFO: Building assembly graph 841s Reading FASTA 841s Building FM-index 841s Overapping 841s Kmer size is set to 33 841s [18:50:31] INFO: Refining with assembly graph 842s [18:50:32] INFO: Generating FASTA output 842s [18:50:32] INFO: Assembly statistics: 842s 842s Scaffolds: 4 842s Used fragments: 816 842s Scaffolds length: 4062392 842s 842s Unplaced fragments: 885 842s Unplaced length: 76312 (1.89%) 842s Introduced Ns length: 76706 (1.89%) 842s 842s Fragments N50: 38091 842s Assembly N50: 2150683 842s 842s [18:50:32] INFO: Done! 842s autopkgtest [18:50:32]: test run-unit-test: -----------------------] 843s run-unit-test PASS 843s autopkgtest [18:50:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 843s autopkgtest [18:50:33]: @@@@@@@@@@@@@@@@@@@@ summary 843s run-unit-test PASS 848s nova [W] Using flock in prodstack6-s390x 848s flock: timeout while waiting to get lock 848s Creating nova instance adt-plucky-s390x-ragout-20250315-183630-juju-7f2275-prod-proposed-migration-environment-15-c446b663-2458-41d1-b930-fe9f0748b773 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 848s nova [W] Timed out waiting for eb41684f-4cec-4302-b43b-bc027d4e5dc3 to get deleted.