0s autopkgtest [16:07:05]: starting date and time: 2025-03-15 16:07:05+0000 0s autopkgtest [16:07:05]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:07:05]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s_g0eykq/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-9.secgroup --name adt-plucky-arm64-ragout-20250315-160704-juju-7f2275-prod-proposed-migration-environment-15-206f6e06-077a-4ce1-800e-68971d4ff2c8 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 243s autopkgtest [16:11:08]: testbed dpkg architecture: arm64 243s autopkgtest [16:11:08]: testbed apt version: 2.9.33 244s autopkgtest [16:11:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 244s autopkgtest [16:11:09]: testbed release detected to be: None 245s autopkgtest [16:11:10]: updating testbed package index (apt update) 245s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 246s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 246s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 246s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 246s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 246s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 246s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 247s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 247s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 247s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 247s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 248s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 248s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 248s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 248s Fetched 1078 kB in 3s (356 kB/s) 250s Reading package lists... 251s + lsb_release --codename --short 251s + RELEASE=plucky 251s + cat 251s + [ plucky != trusty ] 251s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 251s Reading package lists... 251s Building dependency tree... 251s Reading state information... 252s Calculating upgrade... 252s Calculating upgrade... 253s The following packages will be upgraded: 253s pinentry-curses python3-jinja2 strace 253s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 253s Need to get 647 kB of archives. 253s After this operation, 11.3 kB of additional disk space will be used. 253s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 254s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 254s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 255s Fetched 647 kB in 1s (448 kB/s) 255s (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 ... 117701 files and directories currently installed.) 255s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 255s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 256s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 256s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 256s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 256s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 256s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 256s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 256s Setting up strace (6.13+ds-1ubuntu1) ... 256s Processing triggers for man-db (2.13.0-1) ... 257s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 257s + /usr/lib/apt/apt-helper analyze-pattern ?true 257s + uname -r 257s + sed s/\./\\./g 257s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 257s + + apt list ?obsolete 257s tail -n+2 257s + cut -d/ -f1 257s + grep -v ^linux-.*6\.14\.0-10-generic.* 258s + obsolete_pkgs=linux-headers-6.11.0-8-generic 258s linux-headers-6.11.0-8 258s linux-image-6.11.0-8-generic 258s linux-modules-6.11.0-8-generic 258s linux-tools-6.11.0-8-generic 258s linux-tools-6.11.0-8 258s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 258s Reading package lists... 259s Building dependency tree... 259s Reading state information... 259s Solving dependencies... 260s The following packages will be REMOVED: 260s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 260s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 260s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 260s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 260s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 260s After this operation, 267 MB disk space will be freed. 261s (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 ... 117701 files and directories currently installed.) 261s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 261s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 261s Removing libpython3.12t64:arm64 (3.12.9-1) ... 261s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 261s Removing libnsl2:arm64 (1.3.0-3build3) ... 261s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 261s Removing libunwind8:arm64 (1.6.2-3.1) ... 261s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 261s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 264s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 264s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 264s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 264s /etc/kernel/postrm.d/initramfs-tools: 264s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 264s /etc/kernel/postrm.d/zz-flash-kernel: 264s flash-kernel: Kernel 6.11.0-8-generic has been removed. 264s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 264s /etc/kernel/postrm.d/zz-update-grub: 264s Sourcing file `/etc/default/grub' 264s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 264s Generating grub configuration file ... 265s Found linux image: /boot/vmlinuz-6.14.0-10-generic 265s Found initrd image: /boot/initrd.img-6.14.0-10-generic 265s Warning: os-prober will not be executed to detect other bootable partitions. 265s Systems on them will not be added to the GRUB boot configuration. 265s Check GRUB_DISABLE_OS_PROBER documentation entry. 265s Adding boot menu entry for UEFI Firmware Settings ... 265s done 265s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 266s Processing triggers for libc-bin (2.41-1ubuntu1) ... 266s (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 ... 81650 files and directories currently installed.) 266s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 266s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 266s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 266s + grep -q trusty /etc/lsb-release 266s + [ ! -d /usr/share/doc/unattended-upgrades ] 266s + [ ! -d /usr/share/doc/lxd ] 266s + [ ! -d /usr/share/doc/lxd-client ] 266s + [ ! -d /usr/share/doc/snapd ] 266s + type iptables 266s + cat 266s + chmod 755 /etc/rc.local 266s + . /etc/rc.local 266s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 266s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 266s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 266s + uname -m 266s + [ aarch64 = ppc64le ] 266s + [ -d /run/systemd/system ] 266s + systemd-detect-virt --quiet --vm 266s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 266s + cat 266s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 266s + echo COMPRESS=lz4 266s autopkgtest [16:11:31]: upgrading testbed (apt dist-upgrade and autopurge) 267s Reading package lists... 267s Building dependency tree... 267s Reading state information... 268s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 269s Starting 2 pkgProblemResolver with broken count: 0 269s Done 270s Entering ResolveByKeep 271s 271s Calculating upgrade... 273s The following packages will be upgraded: 273s libc-bin libc-dev-bin libc6 libc6-dev locales 273s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 273s Need to get 9530 kB of archives. 273s After this operation, 0 B of additional disk space will be used. 273s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 275s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 275s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 280s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 280s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 285s Preconfiguring packages ... 285s Fetched 9530 kB in 12s (801 kB/s) 285s (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 ... 81647 files and directories currently installed.) 285s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 285s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 286s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 286s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 286s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 286s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 286s Setting up libc6:arm64 (2.41-1ubuntu2) ... 287s (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 ... 81647 files and directories currently installed.) 287s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 287s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 287s Setting up libc-bin (2.41-1ubuntu2) ... 287s (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 ... 81647 files and directories currently installed.) 287s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 287s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 287s Setting up locales (2.41-1ubuntu2) ... 289s Generating locales (this might take a while)... 291s en_US.UTF-8... done 291s Generation complete. 291s Setting up libc-dev-bin (2.41-1ubuntu2) ... 291s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 291s Processing triggers for man-db (2.13.0-1) ... 292s Processing triggers for systemd (257.3-1ubuntu3) ... 293s Reading package lists... 293s Building dependency tree... 293s Reading state information... 294s Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 295s Solving dependencies... 296s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 296s autopkgtest [16:12:01]: rebooting testbed after setup commands that affected boot 321s autopkgtest [16:12:26]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 325s autopkgtest [16:12:30]: @@@@@@@@@@@@@@@@@@@@ apt-source ragout 342s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (dsc) [2117 B] 342s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (tar) [12.3 MB] 342s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (diff) [15.0 kB] 342s gpgv: Signature made Fri Feb 2 10:15:47 2024 UTC 342s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 342s gpgv: issuer "tille@debian.org" 342s gpgv: Can't check signature: No public key 342s dpkg-source: warning: cannot verify inline signature for ./ragout_2.3-5.dsc: no acceptable signature found 344s autopkgtest [16:12:49]: testing package ragout version 2.3-5 344s autopkgtest [16:12:49]: build not needed 348s autopkgtest [16:12:53]: test run-unit-test: preparing testbed 349s Reading package lists... 349s Building dependency tree... 349s Reading state information... 349s Starting pkgProblemResolver with broken count: 0 350s Starting 2 pkgProblemResolver with broken count: 0 350s Done 350s The following NEW packages will be installed: 351s lagan libdivsufsort3 python3-networkx python3-six ragout ragout-examples 351s sibelia 351s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 351s Need to get 32.6 MB of archives. 351s After this operation, 105 MB of additional disk space will be used. 351s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 lagan arm64 2.0-10 [196 kB] 351s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdivsufsort3 arm64 2.0.1-6 [41.0 kB] 351s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 364s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.17.0-1 [13.2 kB] 364s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 ragout arm64 2.3-5 [2159 kB] 366s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 ragout-examples all 2.3-5 [18.4 MB] 386s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 sibelia arm64 3.0.7+dfsg-3 [286 kB] 387s Fetched 32.6 MB in 36s (905 kB/s) 387s Selecting previously unselected package lagan. 388s (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 ... 81647 files and directories currently installed.) 388s Preparing to unpack .../0-lagan_2.0-10_arm64.deb ... 388s Unpacking lagan (2.0-10) ... 388s Selecting previously unselected package libdivsufsort3:arm64. 388s Preparing to unpack .../1-libdivsufsort3_2.0.1-6_arm64.deb ... 388s Unpacking libdivsufsort3:arm64 (2.0.1-6) ... 388s Selecting previously unselected package python3-networkx. 388s Preparing to unpack .../2-python3-networkx_3.2.1-4ubuntu1_all.deb ... 388s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 389s Selecting previously unselected package python3-six. 389s Preparing to unpack .../3-python3-six_1.17.0-1_all.deb ... 389s Unpacking python3-six (1.17.0-1) ... 389s Selecting previously unselected package ragout. 389s Preparing to unpack .../4-ragout_2.3-5_arm64.deb ... 389s Unpacking ragout (2.3-5) ... 389s Selecting previously unselected package ragout-examples. 389s Preparing to unpack .../5-ragout-examples_2.3-5_all.deb ... 389s Unpacking ragout-examples (2.3-5) ... 389s Selecting previously unselected package sibelia. 389s Preparing to unpack .../6-sibelia_3.0.7+dfsg-3_arm64.deb ... 389s Unpacking sibelia (3.0.7+dfsg-3) ... 390s Setting up ragout-examples (2.3-5) ... 390s Setting up python3-networkx (3.2.1-4ubuntu1) ... 392s Setting up python3-six (1.17.0-1) ... 392s Setting up ragout (2.3-5) ... 393s Setting up lagan (2.0-10) ... 393s Setting up libdivsufsort3:arm64 (2.0.1-6) ... 393s Setting up sibelia (3.0.7+dfsg-3) ... 393s Processing triggers for man-db (2.13.0-1) ... 394s Processing triggers for libc-bin (2.41-1ubuntu2) ... 395s autopkgtest [16:13:40]: test run-unit-test: [----------------------- 396s + ragout E.Coli/ecoli.rcp --outdir E.Coli/out/ --refine 397s [16:13:42] INFO: Starting Ragout v2.3 397s [16:13:42] INFO: Running withs synteny block sizes '[5000, 500, 100]' 397s [16:13:42] INFO: Running Sibelia with block size 5000 458s [16:14:43] INFO: Running Sibelia with block size 500 512s [16:15:37] INFO: Running Sibelia with block size 100 562s [16:16:27] INFO: Inferring phylogeny from synteny blocks data 562s [16:16:27] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 562s [16:16:27] INFO: "dh1" synteny blocks coverage: 99.86% 562s [16:16:27] INFO: "mg1655" synteny blocks coverage: 99.56% 562s [16:16:27] INFO: Inferred tree: ('dh1' : 1.5, 'mg1655' : 1.5) 562s [16:16:27] INFO: 'dh1' is chosen as a naming reference 562s [16:16:27] INFO: Processing permutation files 562s [16:16:27] INFO: Reading E.Coli/out/sibelia-workdir/5000/blocks_coords.txt 562s [16:16:27] INFO: "dh1" synteny blocks coverage: 96.41% 562s [16:16:27] INFO: "mg1655" synteny blocks coverage: 99.45% 562s [16:16:27] INFO: Reading E.Coli/out/sibelia-workdir/500/blocks_coords.txt 562s [16:16:27] INFO: "dh1" synteny blocks coverage: 99.58% 562s [16:16:27] INFO: "mg1655" synteny blocks coverage: 99.66% 562s [16:16:27] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 562s [16:16:27] INFO: "dh1" synteny blocks coverage: 99.86% 562s [16:16:27] INFO: "mg1655" synteny blocks coverage: 99.56% 562s [16:16:27] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 562s [16:16:27] INFO: "dh1" synteny blocks coverage: 99.86% 562s [16:16:27] INFO: "mg1655" synteny blocks coverage: 99.56% 562s [16:16:27] INFO: Reading contigs file 562s [16:16:27] INFO: Detecting chimeric adjacencies 562s [16:16:27] INFO: Stage "5000" 562s [16:16:27] INFO: Removing chimeric adjacencies 562s [16:16:27] INFO: Inferring missing adjacencies 562s [16:16:27] INFO: Stage "500" 562s [16:16:27] INFO: Removing chimeric adjacencies 562s [16:16:27] INFO: Inferring missing adjacencies 562s [16:16:27] INFO: Removing chimeric adjacencies 562s [16:16:27] INFO: Merging two iterations 562s [16:16:27] INFO: Stage "100" 562s [16:16:27] INFO: Removing chimeric adjacencies 562s [16:16:27] INFO: Inferring missing adjacencies 562s [16:16:27] INFO: Removing chimeric adjacencies 562s [16:16:27] INFO: Merging two iterations 562s [16:16:27] INFO: Stage "refine" 562s [16:16:27] INFO: Removing chimeric adjacencies 562s [16:16:27] INFO: Inferring missing adjacencies 562s [16:16:27] INFO: Removing chimeric adjacencies 562s [16:16:27] INFO: Merging two iterations 562s [16:16:27] INFO: Building assembly graph 562s Reading FASTA 562s Building FM-index 562s Overapping 562s Kmer size is set to 55 562s [16:16:27] INFO: Refining with assembly graph 562s [16:16:27] INFO: Generating FASTA output 562s [16:16:27] INFO: Assembly statistics: 562s 562s Scaffolds: 1 562s Used fragments: 145 562s Scaffolds length: 4635053 562s 562s Unplaced fragments: 37 562s Unplaced length: 13411 (0.29%) 562s Introduced Ns length: 69544 (1.50%) 562s 562s Fragments N50: 125773 562s Assembly N50: 4635053 562s 562s [16:16:27] INFO: Done! 562s + ragout H.Pylori/helicobacter.rcp --outdir H.Pylori/out/ --refine 562s [16:16:27] INFO: Starting Ragout v2.3 562s [16:16:27] INFO: Running withs synteny block sizes '[5000, 500, 100]' 563s [16:16:27] INFO: Running Sibelia with block size 5000 657s [16:18:02] INFO: Running Sibelia with block size 500 746s [16:19:31] INFO: Running Sibelia with block size 100 837s [16:21:02] INFO: Phylogeny is taken from the recipe 837s [16:21:02] INFO: 'els' is chosen as a naming reference 837s [16:21:02] INFO: Processing permutation files 837s [16:21:02] INFO: Reading H.Pylori/out/sibelia-workdir/5000/blocks_coords.txt 837s [16:21:02] INFO: "els" synteny blocks coverage: 80.53% 837s [16:21:02] INFO: "g27" synteny blocks coverage: 81.02% 837s [16:21:02] INFO: "gambia" synteny blocks coverage: 80.04% 837s [16:21:02] INFO: "puno" synteny blocks coverage: 80.58% 837s [16:21:02] INFO: "sjm180" synteny blocks coverage: 83.86% 837s [16:21:02] INFO: Reading H.Pylori/out/sibelia-workdir/500/blocks_coords.txt 837s [16:21:02] INFO: "els" synteny blocks coverage: 96.82% 837s [16:21:02] INFO: "g27" synteny blocks coverage: 94.8% 837s [16:21:02] INFO: "gambia" synteny blocks coverage: 94.9% 837s [16:21:02] INFO: "puno" synteny blocks coverage: 92.43% 837s [16:21:02] INFO: "sjm180" synteny blocks coverage: 96.75% 837s [16:21:02] INFO: Reading H.Pylori/out/sibelia-workdir/100/blocks_coords.txt 837s [16:21:02] INFO: "els" synteny blocks coverage: 97.08% 837s [16:21:02] INFO: "g27" synteny blocks coverage: 95.16% 837s [16:21:02] INFO: "gambia" synteny blocks coverage: 95.13% 837s [16:21:02] INFO: "puno" synteny blocks coverage: 92.78% 837s [16:21:02] INFO: "sjm180" synteny blocks coverage: 96.5% 837s [16:21:02] INFO: Reading H.Pylori/out/sibelia-workdir/100/blocks_coords.txt 837s [16:21:02] INFO: "els" synteny blocks coverage: 97.08% 837s [16:21:02] INFO: "g27" synteny blocks coverage: 95.16% 837s [16:21:02] INFO: "gambia" synteny blocks coverage: 95.13% 837s [16:21:02] INFO: "puno" synteny blocks coverage: 92.78% 837s [16:21:02] INFO: "sjm180" synteny blocks coverage: 96.5% 837s [16:21:02] INFO: Reading contigs file 837s [16:21:02] INFO: Detecting chimeric adjacencies 837s [16:21:02] INFO: Stage "5000" 837s [16:21:02] INFO: Removing chimeric adjacencies 837s [16:21:02] INFO: Inferring missing adjacencies 837s [16:21:02] INFO: Stage "500" 837s [16:21:02] INFO: Removing chimeric adjacencies 837s [16:21:02] INFO: Inferring missing adjacencies 837s [16:21:02] INFO: Removing chimeric adjacencies 837s [16:21:02] INFO: Merging two iterations 837s [16:21:02] INFO: Stage "100" 837s [16:21:02] INFO: Removing chimeric adjacencies 837s [16:21:02] INFO: Inferring missing adjacencies 837s [16:21:02] INFO: Removing chimeric adjacencies 837s [16:21:02] INFO: Merging two iterations 837s [16:21:02] INFO: Stage "refine" 837s [16:21:02] INFO: Removing chimeric adjacencies 837s [16:21:02] INFO: Inferring missing adjacencies 837s [16:21:02] INFO: Removing chimeric adjacencies 837s [16:21:02] INFO: Merging two iterations 837s [16:21:02] INFO: Building assembly graph 837s Reading FASTA 837s Building FM-index 837s Overapping 837s Kmer size is set to 54 837s [16:21:02] INFO: Refining with assembly graph 837s [16:21:02] INFO: Generating FASTA output 837s [16:21:02] INFO: Assembly statistics: 837s 837s Scaffolds: 1 837s Used fragments: 133 837s Scaffolds length: 1654315 837s 837s Unplaced fragments: 78 837s Unplaced length: 18234 (1.10%) 837s Introduced Ns length: 11306 (0.68%) 837s 837s Fragments N50: 75870 837s Assembly N50: 1654315 837s 837s [16:21:02] INFO: Done! 837s + ragout S.Aureus/aureus.rcp --outdir S.Aureus/out/ --refine 837s [16:21:02] INFO: Starting Ragout v2.3 837s [16:21:02] INFO: Running withs synteny block sizes '[5000, 500, 100]' 838s [16:21:02] INFO: Running Sibelia with block size 5000 975s [16:23:20] INFO: Running Sibelia with block size 500 1105s [16:25:30] INFO: Running Sibelia with block size 100 1205s [16:27:10] INFO: Inferring phylogeny from synteny blocks data 1205s [16:27:10] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 1205s [16:27:10] INFO: "col" synteny blocks coverage: 98.34% 1205s [16:27:10] INFO: "jkd" synteny blocks coverage: 94.31% 1205s [16:27:10] INFO: "rf122" synteny blocks coverage: 93.71% 1205s [16:27:10] INFO: "n315" synteny blocks coverage: 97.19% 1205s [16:27:10] INFO: "usa" synteny blocks coverage: 96.35% 1205s [16:27:10] INFO: Inferred tree: (('jkd' : 47.625, ('col' : 5.375, 'usa' : 40.625) : 14.375) : 11.4375, ('n315' : 35.333333333333336, 'rf122' : 61.666666666666664) : 11.4375) 1205s [16:27:10] INFO: 'col' is chosen as a naming reference 1205s [16:27:10] INFO: Processing permutation files 1205s [16:27:10] INFO: Reading S.Aureus/out/sibelia-workdir/5000/blocks_coords.txt 1205s [16:27:10] INFO: "col" synteny blocks coverage: 84.15% 1205s [16:27:10] INFO: "jkd" synteny blocks coverage: 80.65% 1205s [16:27:10] INFO: "rf122" synteny blocks coverage: 83.55% 1205s [16:27:10] INFO: "n315" synteny blocks coverage: 83.81% 1205s [16:27:10] INFO: "usa" synteny blocks coverage: 89.64% 1205s [16:27:10] INFO: Reading S.Aureus/out/sibelia-workdir/500/blocks_coords.txt 1205s [16:27:10] INFO: "col" synteny blocks coverage: 97.78% 1205s [16:27:10] INFO: "jkd" synteny blocks coverage: 93.69% 1205s [16:27:10] INFO: "rf122" synteny blocks coverage: 93.63% 1205s [16:27:10] INFO: "n315" synteny blocks coverage: 96.93% 1205s [16:27:10] INFO: "usa" synteny blocks coverage: 97.32% 1205s [16:27:10] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 1205s [16:27:10] INFO: "col" synteny blocks coverage: 98.34% 1205s [16:27:10] INFO: "jkd" synteny blocks coverage: 94.31% 1205s [16:27:10] INFO: "rf122" synteny blocks coverage: 93.71% 1205s [16:27:10] INFO: "n315" synteny blocks coverage: 97.19% 1205s [16:27:10] INFO: "usa" synteny blocks coverage: 96.35% 1205s [16:27:10] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 1205s [16:27:10] INFO: "col" synteny blocks coverage: 98.34% 1205s [16:27:10] INFO: "jkd" synteny blocks coverage: 94.31% 1205s [16:27:10] INFO: "rf122" synteny blocks coverage: 93.71% 1205s [16:27:10] INFO: "n315" synteny blocks coverage: 97.19% 1205s [16:27:10] INFO: "usa" synteny blocks coverage: 96.35% 1205s [16:27:10] INFO: Reading contigs file 1205s [16:27:10] INFO: Detecting chimeric adjacencies 1205s [16:27:10] INFO: Stage "5000" 1205s [16:27:10] INFO: Removing chimeric adjacencies 1205s [16:27:10] INFO: Inferring missing adjacencies 1205s [16:27:10] INFO: Stage "500" 1205s [16:27:10] INFO: Removing chimeric adjacencies 1205s [16:27:10] INFO: Inferring missing adjacencies 1205s [16:27:10] INFO: Removing chimeric adjacencies 1205s [16:27:10] INFO: Merging two iterations 1205s [16:27:10] INFO: Stage "100" 1205s [16:27:10] INFO: Removing chimeric adjacencies 1205s [16:27:10] INFO: Inferring missing adjacencies 1206s [16:27:10] INFO: Removing chimeric adjacencies 1206s [16:27:10] INFO: Merging two iterations 1206s [16:27:10] INFO: Stage "refine" 1206s [16:27:10] INFO: Removing chimeric adjacencies 1206s [16:27:11] INFO: Inferring missing adjacencies 1206s [16:27:11] INFO: Removing chimeric adjacencies 1206s [16:27:11] INFO: Merging two iterations 1206s [16:27:11] INFO: Building assembly graph 1206s Reading FASTA 1206s Building FM-index 1206s Overapping 1206s Kmer size is set to 55 1206s [16:27:11] INFO: Refining with assembly graph 1206s [16:27:11] INFO: Generating FASTA output 1206s [16:27:11] INFO: Assembly statistics: 1206s 1206s Scaffolds: 1 1206s Used fragments: 169 1206s Scaffolds length: 2828340 1206s 1206s Unplaced fragments: 633 1206s Unplaced length: 441368 (13.88%) 1206s Introduced Ns length: 83415 (2.95%) 1206s 1206s Fragments N50: 45930 1206s Assembly N50: 2828340 1206s 1206s [16:27:11] INFO: Done! 1206s + ragout V.Cholerae/cholerae.rcp --outdir V.Cholerae/out/ --refine 1206s [16:27:11] INFO: Starting Ragout v2.3 1206s [16:27:11] INFO: Running withs synteny block sizes '[5000, 500, 100]' 1206s [16:27:11] INFO: Running Sibelia with block size 5000 1299s [16:28:44] INFO: Running Sibelia with block size 500 1389s [16:30:14] INFO: Running Sibelia with block size 100 1482s [16:31:47] INFO: Inferring phylogeny from synteny blocks data 1482s [16:31:47] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 1482s [16:31:47] INFO: "biovar" synteny blocks coverage: 99.26% 1482s [16:31:47] INFO: "inaba" synteny blocks coverage: 97.98% 1482s [16:31:47] INFO: "o395" synteny blocks coverage: 97.85% 1482s [16:31:47] INFO: "h1" synteny blocks coverage: 99.19% 1482s [16:31:47] INFO: Inferred tree: (('biovar' : 4.75, 'o395' : 13.25) : 4.625, ('h1' : 1e-06, 'inaba' : 6.75) : 4.625) 1482s [16:31:47] INFO: 'inaba' is chosen as a naming reference 1482s [16:31:47] INFO: Processing permutation files 1482s [16:31:47] INFO: Reading V.Cholerae/out/sibelia-workdir/5000/blocks_coords.txt 1482s [16:31:47] INFO: "biovar" synteny blocks coverage: 92.08% 1482s [16:31:47] INFO: "inaba" synteny blocks coverage: 91.94% 1482s [16:31:47] INFO: "o395" synteny blocks coverage: 91.08% 1482s [16:31:47] INFO: "h1" synteny blocks coverage: 98.87% 1482s [16:31:47] INFO: Reading V.Cholerae/out/sibelia-workdir/500/blocks_coords.txt 1482s [16:31:47] INFO: "biovar" synteny blocks coverage: 99.0% 1482s [16:31:47] INFO: "inaba" synteny blocks coverage: 97.68% 1482s [16:31:47] INFO: "o395" synteny blocks coverage: 97.52% 1482s [16:31:47] INFO: "h1" synteny blocks coverage: 99.3% 1482s [16:31:47] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 1482s [16:31:47] INFO: "biovar" synteny blocks coverage: 99.26% 1482s [16:31:47] INFO: "inaba" synteny blocks coverage: 97.98% 1482s [16:31:47] INFO: "o395" synteny blocks coverage: 97.85% 1482s [16:31:47] INFO: "h1" synteny blocks coverage: 99.19% 1482s [16:31:47] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 1482s [16:31:47] INFO: "biovar" synteny blocks coverage: 99.26% 1482s [16:31:47] INFO: "inaba" synteny blocks coverage: 97.98% 1482s [16:31:47] INFO: "o395" synteny blocks coverage: 97.85% 1482s [16:31:47] INFO: "h1" synteny blocks coverage: 99.19% 1482s [16:31:47] INFO: Reading contigs file 1482s [16:31:47] INFO: Detecting chimeric adjacencies 1482s [16:31:47] INFO: Stage "5000" 1482s [16:31:47] INFO: Removing chimeric adjacencies 1482s [16:31:47] INFO: Inferring missing adjacencies 1482s [16:31:47] INFO: Stage "500" 1482s [16:31:47] INFO: Removing chimeric adjacencies 1482s [16:31:47] INFO: Inferring missing adjacencies 1482s [16:31:47] INFO: Removing chimeric adjacencies 1482s [16:31:47] INFO: Merging two iterations 1482s [16:31:47] INFO: Stage "100" 1482s [16:31:47] INFO: Removing chimeric adjacencies 1482s [16:31:47] INFO: Inferring missing adjacencies 1482s [16:31:47] INFO: Removing chimeric adjacencies 1482s [16:31:47] INFO: Merging two iterations 1482s [16:31:47] INFO: Stage "refine" 1482s [16:31:47] INFO: Removing chimeric adjacencies 1482s [16:31:47] INFO: Inferring missing adjacencies 1482s [16:31:47] INFO: Removing chimeric adjacencies 1482s [16:31:47] INFO: Merging two iterations 1482s [16:31:47] INFO: Building assembly graph 1482s Reading FASTA 1482s Building FM-index 1482s Overapping 1482s Kmer size is set to 33 1482s [16:31:47] INFO: Refining with assembly graph 1483s [16:31:48] INFO: Generating FASTA output 1483s [16:31:48] INFO: Assembly statistics: 1483s 1483s Scaffolds: 4 1483s Used fragments: 816 1483s Scaffolds length: 4062392 1483s 1483s Unplaced fragments: 885 1483s Unplaced length: 76312 (1.89%) 1483s Introduced Ns length: 76706 (1.89%) 1483s 1483s Fragments N50: 38091 1483s Assembly N50: 2150683 1483s 1483s [16:31:48] INFO: Done! 1484s autopkgtest [16:31:49]: test run-unit-test: -----------------------] 1484s autopkgtest [16:31:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1484s run-unit-test PASS 1485s autopkgtest [16:31:50]: @@@@@@@@@@@@@@@@@@@@ summary 1485s run-unit-test PASS 1506s nova [W] Using flock in prodstack6-arm64 1506s flock: timeout while waiting to get lock 1506s Creating nova instance adt-plucky-arm64-ragout-20250315-160704-juju-7f2275-prod-proposed-migration-environment-15-206f6e06-077a-4ce1-800e-68971d4ff2c8 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1506s nova [W] Timed out waiting for 9690408f-a995-472c-bacf-57be054c3617 to get deleted.