0s autopkgtest [14:35:09]: starting date and time: 2025-03-15 14:35:09+0000 0s autopkgtest [14:35:09]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:35:09]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.felpd0uz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade proteinortho --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-arm64-27.secgroup --name adt-plucky-arm64-proteinortho-20250315-143509-juju-7f2275-prod-proposed-migration-environment-15-be8ae5a7-3aaa-4293-a531-dca0065cfc28 --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/ 177s autopkgtest [14:38:06]: testbed dpkg architecture: arm64 177s autopkgtest [14:38:06]: testbed apt version: 2.9.33 177s autopkgtest [14:38:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 178s autopkgtest [14:38:07]: testbed release detected to be: None 178s autopkgtest [14:38:07]: updating testbed package index (apt update) 179s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 179s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 179s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 179s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 179s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 179s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 179s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 180s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 180s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 180s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 180s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 180s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 180s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 180s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 180s Fetched 1094 kB in 1s (736 kB/s) 181s Reading package lists... 182s + lsb_release --codename --short 182s + RELEASE=plucky 182s + cat 182s + [ plucky != trusty ] 182s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 182s Reading package lists... 182s Building dependency tree... 182s Reading state information... 183s Calculating upgrade... 183s Calculating upgrade... 183s The following packages will be upgraded: 183s python3-jinja2 strace 184s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 184s Need to get 608 kB of archives. 184s After this operation, 11.3 kB of additional disk space will be used. 184s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 184s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 185s Fetched 608 kB in 1s (673 kB/s) 185s (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.) 185s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 185s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 185s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 185s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 185s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 186s Setting up strace (6.13+ds-1ubuntu1) ... 186s Processing triggers for man-db (2.13.0-1) ... 187s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 187s + /usr/lib/apt/apt-helper analyze-pattern ?true 187s + uname -r 187s + sed s/\./\\./g 187s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 187s + apt list ?obsolete 187s + tail -n+2 187s + cut -d/ -f1+ grep -v ^linux-.*6\.14\.0-10-generic.* 187s 187s + obsolete_pkgs=linux-headers-6.11.0-8-generic 187s linux-headers-6.11.0-8 187s linux-image-6.11.0-8-generic 187s linux-modules-6.11.0-8-generic 187s linux-tools-6.11.0-8-generic 187s linux-tools-6.11.0-8 187s + 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 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s Solving dependencies... 188s The following packages will be REMOVED: 188s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 188s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 188s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 188s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 188s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 188s After this operation, 267 MB disk space will be freed. 189s (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.) 189s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 189s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 189s Removing libpython3.12t64:arm64 (3.12.9-1) ... 189s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 189s Removing libnsl2:arm64 (1.3.0-3build3) ... 189s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 189s Removing libunwind8:arm64 (1.6.2-3.1) ... 189s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 189s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 191s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 191s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 191s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 191s /etc/kernel/postrm.d/initramfs-tools: 191s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 191s /etc/kernel/postrm.d/zz-flash-kernel: 191s flash-kernel: Kernel 6.11.0-8-generic has been removed. 191s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 191s /etc/kernel/postrm.d/zz-update-grub: 191s Sourcing file `/etc/default/grub' 191s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 191s Generating grub configuration file ... 192s Found linux image: /boot/vmlinuz-6.14.0-10-generic 192s Found initrd image: /boot/initrd.img-6.14.0-10-generic 192s Warning: os-prober will not be executed to detect other bootable partitions. 192s Systems on them will not be added to the GRUB boot configuration. 192s Check GRUB_DISABLE_OS_PROBER documentation entry. 192s Adding boot menu entry for UEFI Firmware Settings ... 192s done 192s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 192s Processing triggers for libc-bin (2.41-1ubuntu1) ... 192s (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.) 192s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 192s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 192s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 193s + grep -q trusty /etc/lsb-release 193s + [ ! -d /usr/share/doc/unattended-upgrades ] 193s + [ ! -d /usr/share/doc/lxd ] 193s + [ ! -d /usr/share/doc/lxd-client ] 193s + [ ! -d /usr/share/doc/snapd ] 193s + type iptables 193s + cat 193s + chmod 755 /etc/rc.local 193s + . /etc/rc.local 193s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 193s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 193s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 193s + uname -m 193s + [ aarch64 = ppc64le ] 193s + [ -d /run/systemd/system ] 193s + systemd-detect-virt --quiet --vm 193s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 193s + cat 193s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 193s + echo COMPRESS=lz4 193s autopkgtest [14:38:22]: upgrading testbed (apt dist-upgrade and autopurge) 193s Reading package lists... 193s Building dependency tree... 193s Reading state information... 194s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 194s Starting 2 pkgProblemResolver with broken count: 0 194s Done 195s Entering ResolveByKeep 195s 196s Calculating upgrade... 196s The following packages will be upgraded: 196s libc-bin libc-dev-bin libc6 libc6-dev locales 196s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 196s Need to get 9530 kB of archives. 196s After this operation, 0 B of additional disk space will be used. 196s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 197s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 197s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 200s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 200s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 205s Preconfiguring packages ... 205s Fetched 9530 kB in 9s (1065 kB/s) 206s (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.) 206s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 206s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 206s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 206s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 206s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 206s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 206s Setting up libc6:arm64 (2.41-1ubuntu2) ... 206s (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.) 206s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 206s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 206s Setting up libc-bin (2.41-1ubuntu2) ... 206s (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.) 206s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 207s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 207s Setting up locales (2.41-1ubuntu2) ... 207s Generating locales (this might take a while)... 209s en_US.UTF-8... done 209s Generation complete. 209s Setting up libc-dev-bin (2.41-1ubuntu2) ... 209s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 209s Processing triggers for man-db (2.13.0-1) ... 210s Processing triggers for systemd (257.3-1ubuntu3) ... 211s Reading package lists... 211s Building dependency tree... 211s Reading state information... 212s Starting pkgProblemResolver with broken count: 0 212s Starting 2 pkgProblemResolver with broken count: 0 212s Done 212s Solving dependencies... 213s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 213s autopkgtest [14:38:42]: rebooting testbed after setup commands that affected boot 237s autopkgtest [14:39:06]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 239s autopkgtest [14:39:08]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 242s Get:1 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 242s Get:2 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 242s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 242s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 242s gpgv: issuer "tille@debian.org" 242s gpgv: Can't check signature: No public key 242s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 242s autopkgtest [14:39:11]: testing package proteinortho version 6.3.1+dfsg-1 242s autopkgtest [14:39:11]: build not needed 243s autopkgtest [14:39:12]: test run-unit-test: preparing testbed 243s Reading package lists... 244s Building dependency tree... 244s Reading state information... 244s Starting pkgProblemResolver with broken count: 0 244s Starting 2 pkgProblemResolver with broken count: 0 244s Done 245s The following NEW packages will be installed: 245s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto16 245s libmbedtls21 libmbedx509-7 ncbi-blast+ ncbi-data proteinortho 245s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 245s Need to get 24.6 MB of archives. 245s After this operation, 107 MB of additional disk space will be used. 245s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 diamond-aligner arm64 2.1.11-2 [2027 kB] 247s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 247s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 248s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 248s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 250s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB] 251s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB] 251s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB] 251s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 256s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6build1 [14.8 MB] 272s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 proteinortho arm64 6.3.1+dfsg-1 [340 kB] 272s Fetched 24.6 MB in 27s (896 kB/s) 272s Selecting previously unselected package diamond-aligner. 273s (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.) 273s Preparing to unpack .../00-diamond-aligner_2.1.11-2_arm64.deb ... 273s Unpacking diamond-aligner (2.1.11-2) ... 273s Selecting previously unselected package libblas3:arm64. 273s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 273s Unpacking libblas3:arm64 (3.12.1-2) ... 273s Selecting previously unselected package libgfortran5:arm64. 273s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 273s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 273s Selecting previously unselected package libgomp1:arm64. 273s Preparing to unpack .../03-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 273s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 273s Selecting previously unselected package liblapack3:arm64. 273s Preparing to unpack .../04-liblapack3_3.12.1-2_arm64.deb ... 273s Unpacking liblapack3:arm64 (3.12.1-2) ... 273s Selecting previously unselected package libmbedcrypto16:arm64. 273s Preparing to unpack .../05-libmbedcrypto16_3.6.2-3ubuntu1_arm64.deb ... 273s Unpacking libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 273s Selecting previously unselected package libmbedx509-7:arm64. 273s Preparing to unpack .../06-libmbedx509-7_3.6.2-3ubuntu1_arm64.deb ... 273s Unpacking libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 273s Selecting previously unselected package libmbedtls21:arm64. 273s Preparing to unpack .../07-libmbedtls21_3.6.2-3ubuntu1_arm64.deb ... 273s Unpacking libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 273s Selecting previously unselected package ncbi-data. 273s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 273s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 273s Selecting previously unselected package ncbi-blast+. 273s Preparing to unpack .../09-ncbi-blast+_2.16.0+ds-6build1_arm64.deb ... 273s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 274s Selecting previously unselected package proteinortho. 274s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_arm64.deb ... 274s Unpacking proteinortho (6.3.1+dfsg-1) ... 274s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 274s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 274s Setting up diamond-aligner (2.1.11-2) ... 274s Setting up libblas3:arm64 (3.12.1-2) ... 274s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 274s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 274s Setting up libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 274s Setting up liblapack3:arm64 (3.12.1-2) ... 274s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 274s Setting up libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 274s Setting up libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 274s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 274s Setting up proteinortho (6.3.1+dfsg-1) ... 274s Processing triggers for man-db (2.13.0-1) ... 274s Processing triggers for libc-bin (2.41-1ubuntu2) ... 275s autopkgtest [14:39:44]: test run-unit-test: [----------------------- 276s ***************************************************************** 276s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 276s ***************************************************************** 276s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 276s Checking input files. 276s Checking input files. 276s Checking test/C_clean.faa... ok 276s Checking test/C2.faa... ok 276s Checking test/E.faa... ok 276s Checking test/L.faa... ok 276s Checking test/M.faa... ok 276s Checking test/C.faa... 276s  [WARNING] input 'test/C.faa' contains a gene-name with a comma, this causes problems with the proteinortho.tsv output, I will clean the file ('test/C_clean.faa') and restart the analysis !!! 276s The line is: 276s C_10,test 276s ok 276s Checking test/L.faa... ok 276s Checking test/C_clean.faa... ok 276s Checking test/C2.faa... ok 276s Checking test/E.faa... ok 276s 276s **Step 1** 276s Generating indices anyway (forced). 276s Building database for 'test/E.faa' (144 sequences) 276s Generating indices anyway (forced). 276s Building database for 'test/C2.faa' (4 sequences) 276s Generating indices anyway (forced). 276s Building database for 'test/C_clean.faa' (218 sequences) 276s Generating indices anyway (forced). 276s Building database for 'test/L.faa' (80 sequences) 276s Generating indices anyway (forced). 276s Building database for 'test/M.faa' (40 sequences) 276s 276s **Step 2** using blastp+ 280s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 280s [OUTPUT] -> written to test_blastp.blast-graph 280s 280s **Step 3** 280s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 280s Reading test_blastp.blast-graph 280s 5 species 280s 112 paired proteins 280s 149 bidirectional edges 281s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 281s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 281s You can extract the fasta files of each orthology group with 281s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/E.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/L.faa' 'test/M.faa' 281s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 281s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 281s # test_blastp.proteinortho.tsv statistics: 281s # number of groups that contains at least p% species: 281s # p species groups genes in groups 281s 0% 0 32 (100%) 112 (100%) 281s 20% 1 32 (100%) 112 (100%) 281s 40% 2 32 (100%) 112 (100%) 281s 60% 3 17 (53.12%) 74 (66.07%) 281s 80% 4 11 (34.37%) 51 (45.53%) 281s 100% 5 1 (3.12%) 5 (4.46%) 281s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 281s # number of groups for each input species: 281s L.faa 32 100% 281s M.faa 32 100% 281s E.faa 15 46.87% 281s C_clean.faa 13 40.62% 281s C2.faa 1 3.12% 281s 281s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 281s 281s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 281s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 281s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 281s 281s All finished. 281s ***************************************************************** 281s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 281s ***************************************************************** 282s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 282s Checking input files. 282s Checking test/C_clean.faa... ok 282s Checking test/C2.faa... ok 282s Checking test/E.faa... ok 282s Checking test/L.faa... ok 282s Checking test/M.faa... ok 282s 282s **Step 1** 282s Generating indices anyway (forced). 282s Building database for 'test/L.faa' (40 sequences) 282s Generating indices anyway (forced). 282s Building database for 'test/C2.faa' (2 sequences) 282s Generating indices anyway (forced). 282s Building database for 'test/E.faa' (72 sequences) 282s Generating indices anyway (forced). 282s Building database for 'test/M.faa' (40 sequences) 282s Generating indices anyway (forced). 282s Building database for 'test/C_clean.faa' (109 sequences) 282s 282s **Step 2** using blastp+ with : synteny 286s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 286s [OUTPUT] -> written to test_synteny.blast-graph 286s 286s **Step 3** 286s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 286s Reading test_synteny.blast-graph 286s 5 species 286s 112 paired proteins 286s 149 bidirectional edges 287s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 287s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 287s You can extract the fasta files of each orthology group with 287s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/L.faa' 'test/C2.faa' 'test/E.faa' 'test/M.faa' 'test/C_clean.faa' 287s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 287s Adding singles... 287s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 287s # test_synteny.proteinortho.tsv statistics: 287s # number of groups that contains at least p% species: 287s # p species groups genes in groups 287s 0% 0 182 (100%) 262 (100%) 287s 20% 1 182 (100%) 262 (100%) 287s 40% 2 32 (17.58%) 112 (42.74%) 287s 60% 3 17 (9.34%) 74 (28.24%) 287s 80% 4 11 (6.04%) 51 (19.46%) 287s 100% 5 1 (0.54%) 5 (1.9%) 287s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 287s # groups that contains only one species: 287s single 5 150 (82.41%) 150 (57.25%) 287s # number of groups for each input species: 287s L.faa 32 100% 287s M.faa 32 100% 287s E.faa 15 46.87% 287s C_clean.faa 13 40.62% 287s C2.faa 1 3.12% 287s 287s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 287s 287s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 287s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 287s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 287s 287s 287s Clustering by gene-order (POFF mode) 287s Reading test_synteny.ffadj-graph 287s 5 species 287s 106 paired proteins 287s 106 bidirectional edges 288s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (35@lapack* + 0@power) connected components Clustering: working on (34@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Reading test_synteny.ffadj-graph 288s 5 species 288s 106 paired proteins 288s 106 bidirectional edges 289s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (35@lapack* + 0@power) connected components Clustering: working on (34@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 289s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 289s You can extract the fasta files of each orthology group with 289s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/L.faa' 'test/C2.faa' 'test/E.faa' 'test/M.faa' 'test/C_clean.faa' 289s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 289s Adding singles... 289s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 289s # test_synteny.poff.tsv statistics: 289s # number of groups that contains at least p% species: 289s # p species groups genes in groups 289s 0% 0 195 (100%) 262 (100%) 289s 20% 1 195 (100%) 262 (100%) 289s 40% 2 38 (19.48%) 105 (40.07%) 289s 60% 3 17 (8.71%) 63 (24.04%) 289s 80% 4 10 (5.12%) 42 (16.03%) 289s 100% 5 1 (0.51%) 5 (1.9%) 289s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 289s # groups that contains only one species: 289s single 5 157 (80.51%) 157 (59.92%) 289s # number of groups for each input species: 289s L.faa 37 97.36% 289s M.faa 37 97.36% 289s E.faa 15 39.47% 289s C_clean.faa 14 36.84% 289s C2.faa 1 2.63% 289s 289s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 289s 289s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 289s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 289s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 289s 289s All finished. 289s ***************************************************************** 289s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 289s ***************************************************************** 289s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.11 289s Checking input files. 289s Checking test/C_clean.faa... ok 289s Checking test/C2.faa... ok 289s Checking test/E.faa... ok 289s Checking test/L.faa... ok 289s Checking test/M.faa... ok 289s 289s **Step 1** 289s Generating indices anyway (forced). 289s Building database for 'test/L.faa' (40 sequences) 289s Generating indices anyway (forced). 289s Building database for 'test/C_clean.faa' (109 sequences) 289s Generating indices anyway (forced). 289s Building database for 'test/M.faa' (40 sequences) 289s Generating indices anyway (forced). 289s Building database for 'test/E.faa' (72 sequences) 290s Generating indices anyway (forced). 290s Building database for 'test/C2.faa' (2 sequences) 290s 290s **Step 2** using diamond 294s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 294s [OUTPUT] -> written to test_diamond.blast-graph 294s 294s **Step 3** 294s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 294s Reading test_diamond.blast-graph 294s 5 species 294s 113 paired proteins 294s 147 bidirectional edges 295s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 295s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 295s You can extract the fasta files of each orthology group with 295s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/L.faa' 'test/C_clean.faa' 'test/M.faa' 'test/E.faa' 'test/C2.faa' 295s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 295s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 295s # test_diamond.proteinortho.tsv statistics: 295s # number of groups that contains at least p% species: 295s # p species groups genes in groups 295s 0% 0 32 (100%) 112 (100%) 295s 20% 1 32 (100%) 112 (100%) 295s 40% 2 32 (100%) 112 (100%) 295s 60% 3 17 (53.12%) 76 (67.85%) 295s 80% 4 11 (34.37%) 53 (47.32%) 295s 100% 5 1 (3.12%) 5 (4.46%) 295s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 295s # number of groups for each input species: 295s L.faa 32 100% 295s M.faa 32 100% 295s E.faa 15 46.87% 295s C_clean.faa 13 40.62% 295s C2.faa 1 3.12% 295s 295s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 295s 295s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 295s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 295s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 295s 295s All finished. 295s ***************************************************************** 295s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 295s ***************************************************************** 295s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.11 295s Checking input files. 295s Checking test/C_clean.faa... ok 295s Checking test/C2.faa... ok 295s Checking test/E.faa... ok 295s Checking test/L.faa... ok 295s Checking test/M.faa... ok 295s 295s **Step 1** 295s Generating indices anyway (forced). 295s Building database for 'test/C_clean.faa' (109 sequences) 295s Generating indices anyway (forced). 295s Building database for 'test/L.faa' (40 sequences) 295s Generating indices anyway (forced). 295s Building database for 'test/E.faa' (72 sequences) 295s Generating indices anyway (forced). 295s Building database for 'test/M.faa' (40 sequences) 295s Generating indices anyway (forced). 295s Building database for 'test/C2.faa' (2 sequences) 295s 295s **Step 2** using diamond 299s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 299s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 299s 299s **Step 3** 299s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 299s Reading test_diamondmoresensitive.blast-graph 299s 5 species 299s 113 paired proteins 299s 147 bidirectional edges 300s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 300s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 300s You can extract the fasta files of each orthology group with 300s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/C_clean.faa' 'test/L.faa' 'test/E.faa' 'test/M.faa' 'test/C2.faa' 300s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 300s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 300s # test_diamondmoresensitive.proteinortho.tsv statistics: 300s # number of groups that contains at least p% species: 300s # p species groups genes in groups 300s 0% 0 32 (100%) 112 (100%) 300s 20% 1 32 (100%) 112 (100%) 300s 40% 2 32 (100%) 112 (100%) 300s 60% 3 17 (53.12%) 76 (67.85%) 300s 80% 4 11 (34.37%) 53 (47.32%) 300s 100% 5 1 (3.12%) 5 (4.46%) 300s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 300s # number of groups for each input species: 300s L.faa 32 100% 300s M.faa 32 100% 300s E.faa 15 46.87% 300s C_clean.faa 13 40.62% 300s C2.faa 1 3.12% 300s 300s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 300s 300s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 300s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 300s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 300s 300s All finished. 300s ***************************************************************** 300s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 300s ***************************************************************** 300s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 300s Checking input files. 300s Checking test/C_clean.faa... ok 300s Checking test/C2.faa... ok 300s Checking test/E.faa... ok 300s Checking test/L.faa... ok 300s Checking test/M.faa... ok 300s 300s **Step 1** 300s Generating indices anyway (forced). 300s Building database for 'test/C_clean.faa' (109 sequences) 300s Generating indices anyway (forced). 300s Building database for 'test/L.faa' (40 sequences) 301s Generating indices anyway (forced). 301s Building database for 'test/C2.faa' (2 sequences) 301s Generating indices anyway (forced). 301s Building database for 'test/E.faa' (72 sequences) 301s Generating indices anyway (forced). 301s Building database for 'test/M.faa' (40 sequences) 301s 301s **Step 2** using blastp+ 305s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 305s [OUTPUT] -> written to test_blastall.blast-graph 305s 305s **Step 3** 305s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 305s Reading test_blastall.blast-graph 305s 5 species 305s 112 paired proteins 305s 147 bidirectional edges 306s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 306s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 306s You can extract the fasta files of each orthology group with 306s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C_clean.faa' 'test/L.faa' 'test/C2.faa' 'test/E.faa' 'test/M.faa' 306s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 306s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 306s # test_blastall.proteinortho.tsv statistics: 306s # number of groups that contains at least p% species: 306s # p species groups genes in groups 306s 0% 0 32 (100%) 112 (100%) 306s 20% 1 32 (100%) 112 (100%) 306s 40% 2 32 (100%) 112 (100%) 306s 60% 3 17 (53.12%) 74 (66.07%) 306s 80% 4 11 (34.37%) 51 (45.53%) 306s 100% 5 1 (3.12%) 5 (4.46%) 306s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 306s # number of groups for each input species: 306s L.faa 32 100% 306s M.faa 32 100% 306s E.faa 15 46.87% 306s C_clean.faa 13 40.62% 306s C2.faa 1 3.12% 306s 306s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 306s 306s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 306s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 306s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 306s 306s All finished. 306s - test max_of_diag() : OK 306s - test generate_random_vector() : OK 306s - test get_new_x() : OK 306s - test makeOrthogonal() : OK 306s - test normalize() : OK 306s - test getY() : OK 306s - test lapack() : OK 306s - test power() : OK 306s - test smirnov-grubb() : OK 306s All test passed. 306s Reading test_blastp.blast-graph 306s 5 species 306s 112 paired proteins 306s 149 bidirectional edges 306s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 307s 5 5 1 C_10 C_10;test E_10 L_10 M_10 307s 4 4 1 * C_11 E_11 L_11 M_11 307s 4 6 0.333 * C_12,C_21 E_313,E_315 L_313 M_313 307s 4 4 1 * C_14 E_14 L_14 M_14 307s 4 4 1 * C_15 E_15 L_15 M_15 307s 4 4 1 * C_16 E_16 L_16 M_16 307s 4 4 1 * C_17 E_17 L_17 M_17 307s 4 4 1 * C_64 E_18 L_18 M_18 307s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 307s 3 3 1 * C_20 * L_20 M_20 307s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 307s 2 2 1 * * * L_619 M_619 307s 3 3 0.33 * * E_367 L_319 M_319 307s 2 2 1 * * * L_617 M_617 307s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 307s 2 4 0.5 * * * L_645,L_647 M_644,M_646 307s 3 3 0.33 * * E_432 L_328 M_328 307s 2 2 1 * * * L_333 M_333 307s 2 2 1 * * * L_3 M_3 307s 2 2 1 * * * L_4 M_4 307s 2 2 1 * * * L_5 M_5 307s 2 2 1 * * * L_6 M_6 307s 2 2 1 * * * L_8 M_8 307s 2 2 1 * * * L_9 M_9 307s 2 2 1 * * * L_623 M_623 307s 4 4 1 * C_13 E_13 L_621 M_621 307s 2 4 0.146 * * * L_637,L_639 M_636,M_638 307s 3 3 0.33 * * E_437 L_317 M_317 307s 2 3 0.33 * * * L_631,L_633 M_632 307s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 307s 2 2 1 * * * L_331 M_331 307s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 307s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 307s Reading test_blastp.blast-graph 307s 5 species 307s 112 paired proteins 307s 149 bidirectional edges 308s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 1@power) connected components Clustering: working on (13@lapack* + 2@power) connected components Clustering: working on (12@lapack* + 3@power) connected components Clustering: working on (11@lapack* + 4@power) connected components Clustering: working on (10@lapack* + 5@power) connected components Clustering: working on (9@lapack* + 6@power) connected components Clustering: working on (8@lapack* + 7@power) connected components Clustering: working on (7@lapack* + 8@power) connected components Clustering: working on (6@lapack* + 9@power) connected components Clustering: working on (5@lapack* + 10@power) connected components Clustering: working on (4@lapack* + 11@power) connected components Clustering: working on (3@lapack* + 12@power) connected components Clustering: working on (2@lapack* + 13@power) connected components Clustering: working on (0@lapack + 15@power*) connected components Clustering: working on (0@lapack + 14@power*) connected components Clustering: working on (0@lapack + 13@power*) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (3@lapack* + 10@power) connected components Clustering: working on (2@lapack* + 10@power) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (0@lapack + 11@power*) connected components Clustering: working on (0@lapack + 10@power*) connected components Clustering: working on (0@lapack + 9@power*) connected components Clustering: working on (0@lapack + 8@power*) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (4@lapack* + 4@power) connected components Clustering: working on (3@lapack* + 4@power) connected components Clustering: working on (2@lapack* + 5@power) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (0@lapack + 5@power*) connected components Clustering: working on (0@lapack + 4@power*) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components 3 3 1 * C_20 * L_20 M_20 308s 2 2 1 * * * L_619 M_619 308s 3 3 0.33 * * E_367 L_319 M_319 308s 2 2 1 * * * L_617 M_617 308s 3 3 0.33 * * E_432 L_328 M_328 308s 2 2 1 * * * L_333 M_333 308s 2 2 1 * * * L_3 M_3 308s 2 2 1 * * * L_4 M_4 308s 2 2 1 * * * L_5 M_5 308s 2 2 1 * * * L_6 M_6 308s 2 2 1 * * * L_8 M_8 308s 2 2 1 * * * L_9 M_9 308s 5 5 0.694 C_10 C_10;test E_10 L_10 M_10 308s 4 4 0.727 * C_11 E_11 L_11 M_11 308s 4 6 0.297 * C_12,C_21 E_313,E_315 L_313 M_313 308s 2 2 1 * * * L_623 M_623 308s 4 4 0.743 * C_14 E_14 L_14 M_14 308s 4 4 0.818 * C_15 E_15 L_15 M_15 308s 4 4 0.815 * C_16 E_16 L_16 M_16 308s 4 4 0.824 * C_17 E_17 L_17 M_17 308s 4 4 0.777 * C_64 E_18 L_18 M_18 308s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 308s 3 3 0.33 * * E_437 L_317 M_317 308s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 308s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 308s 2 4 0.478 * * * L_645,L_647 M_644,M_646 308s 4 4 0.702 * C_13 E_13 L_621 M_621 308s 2 4 0.145 * * * L_637,L_639 M_636,M_638 308s 2 2 1 * * * L_331 M_331 308s 2 3 0.33 * * * L_631,L_633 M_632 308s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 308s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 308s Test okay 308s autopkgtest [14:40:17]: test run-unit-test: -----------------------] 309s autopkgtest [14:40:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 309s run-unit-test PASS 309s autopkgtest [14:40:18]: @@@@@@@@@@@@@@@@@@@@ summary 309s run-unit-test PASS 315s nova [W] Using flock in prodstack6-arm64 315s flock: timeout while waiting to get lock 315s Creating nova instance adt-plucky-arm64-proteinortho-20250315-143509-juju-7f2275-prod-proposed-migration-environment-15-be8ae5a7-3aaa-4293-a531-dca0065cfc28 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 315s nova [W] Timed out waiting for db53e0f8-72e2-4960-80e4-c28663e083bb to get deleted.