0s autopkgtest [15:07:26]: starting date and time: 2025-03-15 15:07:26+0000 0s autopkgtest [15:07:26]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:07:26]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j4oy26xn/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-8.secgroup --name adt-plucky-s390x-proteinortho-20250315-150725-juju-7f2275-prod-proposed-migration-environment-15-b37d1179-5e69-47d6-bb75-1745d458132b --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 162s autopkgtest [15:10:08]: testbed dpkg architecture: s390x 162s autopkgtest [15:10:08]: testbed apt version: 2.9.33 162s autopkgtest [15:10:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 162s autopkgtest [15:10:08]: testbed release detected to be: None 163s autopkgtest [15:10:09]: updating testbed package index (apt update) 163s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 164s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 164s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 164s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 164s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 164s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 164s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 164s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [80.6 kB] 165s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1940 B] 165s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 165s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [342 kB] 165s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [14.4 kB] 165s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 165s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [328 B] 165s Fetched 1090 kB in 2s (599 kB/s) 166s Reading package lists... 166s + lsb_release --codename --short 166s + RELEASE=plucky 166s + cat 166s + [ plucky != trusty ] 166s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 167s Calculating upgrade... 167s Calculating upgrade... 167s The following packages were automatically installed and are no longer required: 167s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 167s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 167s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 167s linux-tools-6.11.0-8-generic 167s Use 'sudo apt autoremove' to remove them. 167s The following packages will be upgraded: 167s python3-jinja2 strace 167s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Need to get 609 kB of archives. 167s After this operation, 27.6 kB of additional disk space will be used. 167s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 168s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 168s Fetched 609 kB in 1s (586 kB/s) 168s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 168s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 168s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 168s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 168s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 168s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 168s Setting up strace (6.13+ds-1ubuntu1) ... 168s Processing triggers for man-db (2.13.0-1) ... 169s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 169s + /usr/lib/apt/apt-helper analyze-pattern ?true 169s + uname -r 169s + sed s/\./\\./g 169s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 169s + apt list ?obsolete 169s + tail -n+2 169s + cut+ -d/ -f1 169s grep -v ^linux-.*6\.14\.0-10-generic.* 169s + obsolete_pkgs=linux-headers-6.11.0-8-generic 169s linux-headers-6.11.0-8 169s linux-modules-6.11.0-8-generic 169s linux-tools-6.11.0-8-generic 169s linux-tools-6.11.0-8 169s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 169s Solving dependencies... 169s The following packages will be REMOVED: 169s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 169s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 169s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 169s linux-tools-6.11.0-8-generic* 169s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 169s After this operation, 167 MB disk space will be freed. 169s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 169s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 169s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 169s Removing libpython3.12t64:s390x (3.12.9-1) ... 169s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 170s Removing libnsl2:s390x (1.3.0-3build3) ... 170s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 170s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 170s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 170s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 170s Processing triggers for libc-bin (2.41-1ubuntu1) ... 170s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56328 files and directories currently installed.) 170s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 170s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 171s + grep -q trusty /etc/lsb-release 171s + [ ! -d /usr/share/doc/unattended-upgrades ] 171s + [ ! -d /usr/share/doc/lxd ] 171s + [ ! -d /usr/share/doc/lxd-client ] 171s + [ ! -d /usr/share/doc/snapd ] 171s + type iptables 171s + cat 171s + chmod 755 /etc/rc.local 171s + . /etc/rc.local 171s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 171s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 171s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 171s + uname -m 171s + [ s390x = ppc64le ] 171s + [ -d /run/systemd/system ] 171s + systemd-detect-virt --quiet --vm 171s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 171s + cat 171s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 171s + echo COMPRESS=lz4 171s autopkgtest [15:10:17]: upgrading testbed (apt dist-upgrade and autopurge) 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 171s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 171s Starting 2 pkgProblemResolver with broken count: 0 171s Done 171s Entering ResolveByKeep 171s 172s Calculating upgrade... 172s The following packages will be upgraded: 172s libc-bin libc-dev-bin libc6 libc6-dev locales 172s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 9512 kB of archives. 172s After this operation, 8192 B of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 174s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 177s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 178s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 182s Preconfiguring packages ... 182s Fetched 9512 kB in 10s (957 kB/s) 182s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 182s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 182s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 182s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 182s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Setting up libc6:s390x (2.41-1ubuntu2) ... 182s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 182s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 182s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Setting up libc-bin (2.41-1ubuntu2) ... 182s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 182s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 182s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Setting up locales (2.41-1ubuntu2) ... 183s Generating locales (this might take a while)... 184s en_US.UTF-8... done 184s Generation complete. 184s Setting up libc-dev-bin (2.41-1ubuntu2) ... 184s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 184s Processing triggers for man-db (2.13.0-1) ... 184s Processing triggers for systemd (257.3-1ubuntu3) ... 185s Reading package lists... 185s Building dependency tree... 185s Reading state information... 185s Starting pkgProblemResolver with broken count: 0 185s Starting 2 pkgProblemResolver with broken count: 0 185s Done 186s Solving dependencies... 186s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s autopkgtest [15:10:32]: rebooting testbed after setup commands that affected boot 207s autopkgtest [15:10:53]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 209s autopkgtest [15:10:55]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 211s Get:1 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 211s Get:2 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 211s Get:3 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 211s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 211s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 211s gpgv: issuer "tille@debian.org" 211s gpgv: Can't check signature: No public key 211s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 212s autopkgtest [15:10:58]: testing package proteinortho version 6.3.1+dfsg-1 212s autopkgtest [15:10:58]: build not needed 213s autopkgtest [15:10:59]: test run-unit-test: preparing testbed 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 213s Starting pkgProblemResolver with broken count: 0 213s Starting 2 pkgProblemResolver with broken count: 0 213s Done 213s The following NEW packages will be installed: 213s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto16 213s libmbedtls21 libmbedx509-7 ncbi-blast+ ncbi-data proteinortho 213s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 213s Need to get 26.2 MB of archives. 213s After this operation, 105 MB of additional disk space will be used. 213s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x diamond-aligner s390x 2.1.11-2 [2296 kB] 216s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 216s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 217s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 217s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 220s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedcrypto16 s390x 3.6.2-3ubuntu1 [261 kB] 220s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedx509-7 s390x 3.6.2-3ubuntu1 [34.9 kB] 220s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedtls21 s390x 3.6.2-3ubuntu1 [122 kB] 221s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 224s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x ncbi-blast+ s390x 2.16.0+ds-6build1 [15.2 MB] 242s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x proteinortho s390x 6.3.1+dfsg-1 [333 kB] 242s Fetched 26.2 MB in 29s (908 kB/s) 242s Selecting previously unselected package diamond-aligner. 242s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 242s Preparing to unpack .../00-diamond-aligner_2.1.11-2_s390x.deb ... 242s Unpacking diamond-aligner (2.1.11-2) ... 242s Selecting previously unselected package libblas3:s390x. 242s Preparing to unpack .../01-libblas3_3.12.1-2_s390x.deb ... 242s Unpacking libblas3:s390x (3.12.1-2) ... 243s Selecting previously unselected package libgfortran5:s390x. 243s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 243s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 243s Selecting previously unselected package libgomp1:s390x. 243s Preparing to unpack .../03-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 243s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 243s Selecting previously unselected package liblapack3:s390x. 243s Preparing to unpack .../04-liblapack3_3.12.1-2_s390x.deb ... 243s Unpacking liblapack3:s390x (3.12.1-2) ... 243s Selecting previously unselected package libmbedcrypto16:s390x. 243s Preparing to unpack .../05-libmbedcrypto16_3.6.2-3ubuntu1_s390x.deb ... 243s Unpacking libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 243s Selecting previously unselected package libmbedx509-7:s390x. 243s Preparing to unpack .../06-libmbedx509-7_3.6.2-3ubuntu1_s390x.deb ... 243s Unpacking libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 243s Selecting previously unselected package libmbedtls21:s390x. 243s Preparing to unpack .../07-libmbedtls21_3.6.2-3ubuntu1_s390x.deb ... 243s Unpacking libmbedtls21:s390x (3.6.2-3ubuntu1) ... 243s Selecting previously unselected package ncbi-data. 243s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 243s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 243s Selecting previously unselected package ncbi-blast+. 243s Preparing to unpack .../09-ncbi-blast+_2.16.0+ds-6build1_s390x.deb ... 243s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 243s Selecting previously unselected package proteinortho. 243s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_s390x.deb ... 243s Unpacking proteinortho (6.3.1+dfsg-1) ... 243s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 243s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 243s Setting up diamond-aligner (2.1.11-2) ... 243s Setting up libblas3:s390x (3.12.1-2) ... 243s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 243s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 243s Setting up libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 243s Setting up liblapack3:s390x (3.12.1-2) ... 243s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 243s Setting up libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 243s Setting up libmbedtls21:s390x (3.6.2-3ubuntu1) ... 243s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 243s Setting up proteinortho (6.3.1+dfsg-1) ... 243s Processing triggers for man-db (2.13.0-1) ... 243s Processing triggers for libc-bin (2.41-1ubuntu2) ... 244s autopkgtest [15:11:30]: test run-unit-test: [----------------------- 245s ***************************************************************** 245s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 245s ***************************************************************** 245s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 245s Checking input files. 245s Checking input files. 245s Checking test/C_clean.faa... ok 245s Checking test/C2.faa... ok 245s Checking test/E.faa... ok 245s Checking test/L.faa... ok 245s Checking test/M.faa... ok 245s Checking test/C.faa... 245s  [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 !!! 245s The line is: 245s C_10,test 245s ok 245s Checking test/E.faa... ok 245s Checking test/L.faa... ok 245s Checking test/C_clean.faa... ok 245s Checking test/C2.faa... ok 245s 245s **Step 1** 245s Generating indices anyway (forced). 245s Building database for 'test/C_clean.faa' (218 sequences) 245s Generating indices anyway (forced). 245s Building database for 'test/E.faa' (144 sequences) 245s Generating indices anyway (forced). 245s Building database for 'test/C2.faa' (4 sequences) 245s Generating indices anyway (forced). 245s Building database for 'test/L.faa' (80 sequences) 245s Generating indices anyway (forced). 245s Building database for 'test/M.faa' (40 sequences) 245s 245s **Step 2** using blastp+ 249s 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) 249s [OUTPUT] -> written to test_blastp.blast-graph 249s 249s **Step 3** 249s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 249s Reading test_blastp.blast-graph 249s 5 species 249s 112 paired proteins 249s 147 bidirectional edges 250s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@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* + 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 (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 250s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 250s You can extract the fasta files of each orthology group with 250s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/C_clean.faa' 'test/E.faa' 'test/C2.faa' 'test/L.faa' 'test/M.faa' 250s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 250s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 250s # test_blastp.proteinortho.tsv statistics: 250s # number of groups that contains at least p% species: 250s # p species groups genes in groups 250s 0% 0 32 (100%) 112 (100%) 250s 20% 1 32 (100%) 112 (100%) 250s 40% 2 32 (100%) 112 (100%) 250s 60% 3 17 (53.12%) 74 (66.07%) 250s 80% 4 11 (34.37%) 51 (45.53%) 250s 100% 5 1 (3.12%) 5 (4.46%) 250s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 250s # number of groups for each input species: 250s L.faa 32 100% 250s M.faa 32 100% 250s E.faa 15 46.87% 250s C_clean.faa 13 40.62% 250s C2.faa 1 3.12% 250s 250s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 250s 250s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 250s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 250s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 250s 250s All finished. 250s ***************************************************************** 250s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 250s ***************************************************************** 250s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 250s Checking input files. 250s Checking test/C_clean.faa... ok 250s Checking test/C2.faa... ok 250s Checking test/E.faa... ok 250s Checking test/L.faa... ok 250s Checking test/M.faa... ok 250s 250s **Step 1** 250s Generating indices anyway (forced). 250s Building database for 'test/L.faa' (40 sequences) 250s Generating indices anyway (forced). 250s Building database for 'test/E.faa' (72 sequences) 250s Generating indices anyway (forced). 250s Building database for 'test/C_clean.faa' (109 sequences) 250s Generating indices anyway (forced). 250s Building database for 'test/M.faa' (40 sequences) 250s Generating indices anyway (forced). 250s Building database for 'test/C2.faa' (2 sequences) 250s 250s **Step 2** using blastp+ with : synteny 254s 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) 254s [OUTPUT] -> written to test_synteny.blast-graph 254s 254s **Step 3** 254s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 254s Reading test_synteny.blast-graph 254s 5 species 254s 112 paired proteins 254s 149 bidirectional edges 255s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@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 (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 (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 (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 255s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 255s You can extract the fasta files of each orthology group with 255s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/L.faa' 'test/E.faa' 'test/C_clean.faa' 'test/M.faa' 'test/C2.faa' 255s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 255s Adding singles... 255s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 255s # test_synteny.proteinortho.tsv statistics: 255s # number of groups that contains at least p% species: 255s # p species groups genes in groups 255s 0% 0 182 (100%) 262 (100%) 255s 20% 1 182 (100%) 262 (100%) 255s 40% 2 32 (17.58%) 112 (42.74%) 255s 60% 3 17 (9.34%) 74 (28.24%) 255s 80% 4 11 (6.04%) 51 (19.46%) 255s 100% 5 1 (0.54%) 5 (1.9%) 255s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 255s # groups that contains only one species: 255s single 5 150 (82.41%) 150 (57.25%) 255s # number of groups for each input species: 255s L.faa 32 100% 255s M.faa 32 100% 255s E.faa 15 46.87% 255s C_clean.faa 13 40.62% 255s C2.faa 1 3.12% 255s 255s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 255s 255s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 255s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 255s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 255s 255s 255s Clustering by gene-order (POFF mode) 255s Reading test_synteny.ffadj-graph 255s 5 species 255s 106 paired proteins 255s 106 bidirectional edges 256s 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 (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 (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 (3@lapack* + 0@power) connected components Reading test_synteny.ffadj-graph 256s 5 species 256s 106 paired proteins 256s 106 bidirectional edges 257s Clustering: working on (2@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 (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 (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 (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 (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 (3@lapack* + 0@power) connected components 257s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 257s You can extract the fasta files of each orthology group with 257s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/L.faa' 'test/E.faa' 'test/C_clean.faa' 'test/M.faa' 'test/C2.faa' 257s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 257s Adding singles... 257s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 257s # test_synteny.poff.tsv statistics: 257s # number of groups that contains at least p% species: 257s # p species groups genes in groups 257s 0% 0 195 (100%) 262 (100%) 257s 20% 1 195 (100%) 262 (100%) 257s 40% 2 38 (19.48%) 105 (40.07%) 257s 60% 3 17 (8.71%) 63 (24.04%) 257s 80% 4 10 (5.12%) 42 (16.03%) 257s 100% 5 1 (0.51%) 5 (1.9%) 257s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 257s # groups that contains only one species: 257s single 5 157 (80.51%) 157 (59.92%) 257s # number of groups for each input species: 257s L.faa 37 97.36% 257s M.faa 37 97.36% 257s E.faa 15 39.47% 257s C_clean.faa 14 36.84% 257s C2.faa 1 2.63% 257s 257s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 257s 257s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 257s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 257s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 257s 257s All finished. 257s ***************************************************************** 257s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 257s ***************************************************************** 257s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.11 257s Checking input files. 257s Checking test/C_clean.faa... ok 257s Checking test/C2.faa... ok 257s Checking test/E.faa... ok 257s Checking test/L.faa... ok 257s Checking test/M.faa... ok 257s 257s **Step 1** 257s Generating indices anyway (forced). 257s Building database for 'test/E.faa' (72 sequences) 257s Generating indices anyway (forced). 257s Building database for 'test/C2.faa' (2 sequences) 257s Generating indices anyway (forced). 257s Building database for 'test/M.faa' (40 sequences) 257s Generating indices anyway (forced). 257s Building database for 'test/L.faa' (40 sequences) 257s Generating indices anyway (forced). 257s Building database for 'test/C_clean.faa' (109 sequences) 257s 257s **Step 2** using diamond 263s 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) 263s [OUTPUT] -> written to test_diamond.blast-graph 263s 263s **Step 3** 263s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 263s Reading test_diamond.blast-graph 263s 5 species 263s 112 paired proteins 263s 145 bidirectional edges 264s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@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 (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 (5@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 264s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 264s You can extract the fasta files of each orthology group with 264s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/E.faa' 'test/C2.faa' 'test/M.faa' 'test/L.faa' 'test/C_clean.faa' 264s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 264s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 264s # test_diamond.proteinortho.tsv statistics: 264s # number of groups that contains at least p% species: 264s # p species groups genes in groups 264s 0% 0 32 (100%) 111 (100%) 264s 20% 1 32 (100%) 111 (100%) 264s 40% 2 32 (100%) 111 (100%) 264s 60% 3 17 (53.12%) 75 (67.56%) 264s 80% 4 11 (34.37%) 52 (46.84%) 264s 100% 5 1 (3.12%) 5 (4.5%) 264s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 264s # number of groups for each input species: 264s L.faa 32 100% 264s M.faa 32 100% 264s E.faa 15 46.87% 264s C_clean.faa 13 40.62% 264s C2.faa 1 3.12% 264s 264s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 264s 264s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 264s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 264s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 264s 264s All finished. 264s ***************************************************************** 264s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 264s ***************************************************************** 264s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.11 264s Checking input files. 264s Checking test/C_clean.faa... ok 264s Checking test/C2.faa... ok 264s Checking test/E.faa... ok 264s Checking test/L.faa... ok 264s Checking test/M.faa... ok 264s 264s **Step 1** 264s Generating indices anyway (forced). 264s Building database for 'test/E.faa' (72 sequences) 264s Generating indices anyway (forced). 264s Building database for 'test/C_clean.faa' (109 sequences) 264s Generating indices anyway (forced). 264s Building database for 'test/L.faa' (40 sequences) 264s Generating indices anyway (forced). 264s Building database for 'test/M.faa' (40 sequences) 264s Generating indices anyway (forced). 264s Building database for 'test/C2.faa' (2 sequences) 264s 264s **Step 2** using diamond 271s 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) 271s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 271s 271s **Step 3** 271s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 271s Reading test_diamondmoresensitive.blast-graph 271s 5 species 271s 112 paired proteins 271s 145 bidirectional edges 272s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@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 (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 (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 (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 272s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 272s You can extract the fasta files of each orthology group with 272s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/E.faa' 'test/C_clean.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa' 272s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 272s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 272s # test_diamondmoresensitive.proteinortho.tsv statistics: 272s # number of groups that contains at least p% species: 272s # p species groups genes in groups 272s 0% 0 32 (100%) 111 (100%) 272s 20% 1 32 (100%) 111 (100%) 272s 40% 2 32 (100%) 111 (100%) 272s 60% 3 17 (53.12%) 75 (67.56%) 272s 80% 4 11 (34.37%) 52 (46.84%) 272s 100% 5 1 (3.12%) 5 (4.5%) 272s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 272s # number of groups for each input species: 272s L.faa 32 100% 272s M.faa 32 100% 272s E.faa 15 46.87% 272s C_clean.faa 13 40.62% 272s C2.faa 1 3.12% 272s 272s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 272s 272s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 272s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 272s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 272s 272s All finished. 272s ***************************************************************** 272s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 272s ***************************************************************** 272s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 272s Checking input files. 272s Checking test/C_clean.faa... ok 272s Checking test/C2.faa... ok 272s Checking test/E.faa... ok 272s Checking test/L.faa... ok 272s Checking test/M.faa... ok 272s 272s **Step 1** 272s Generating indices anyway (forced). 272s Building database for 'test/M.faa' (40 sequences) 272s Generating indices anyway (forced). 272s Building database for 'test/L.faa' (40 sequences) 272s Generating indices anyway (forced). 272s Building database for 'test/C2.faa' (2 sequences) 272s Generating indices anyway (forced). 272s Building database for 'test/C_clean.faa' (109 sequences) 272s Generating indices anyway (forced). 272s Building database for 'test/E.faa' (72 sequences) 272s 272s **Step 2** using blastp+ 276s 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) 276s [OUTPUT] -> written to test_blastall.blast-graph 276s 276s **Step 3** 276s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 276s Reading test_blastall.blast-graph 276s 5 species 276s 112 paired proteins 276s 147 bidirectional edges 277s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@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 (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 (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 277s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 277s You can extract the fasta files of each orthology group with 277s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/M.faa' 'test/L.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/E.faa' 277s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 277s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 277s # test_blastall.proteinortho.tsv statistics: 277s # number of groups that contains at least p% species: 277s # p species groups genes in groups 277s 0% 0 32 (100%) 112 (100%) 277s 20% 1 32 (100%) 112 (100%) 277s 40% 2 32 (100%) 112 (100%) 277s 60% 3 17 (53.12%) 74 (66.07%) 277s 80% 4 11 (34.37%) 51 (45.53%) 277s 100% 5 1 (3.12%) 5 (4.46%) 277s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 277s # number of groups for each input species: 277s L.faa 32 100% 277s M.faa 32 100% 277s E.faa 15 46.87% 277s C_clean.faa 13 40.62% 277s C2.faa 1 3.12% 277s 277s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 277s 277s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 277s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 277s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 277s 277s All finished. 277s - test max_of_diag() : OK 277s - test generate_random_vector() : OK 277s - test get_new_x() : OK 277s - test makeOrthogonal() : OK 277s - test normalize() : OK 277s - test getY() : OK 277s - test lapack() : OK 277s - test power() : OK 277s - test smirnov-grubb() : OK 277s All test passed. 277s Reading test_blastp.blast-graph 277s 5 species 277s 112 paired proteins 277s 147 bidirectional edges 277s Clustering: working on (2@lapack* + 0# Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 278s @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 5 5 1 C_10 C_10;test E_10 L_10 M_10 278s 4 4 1 * C_11 E_11 L_11 M_11 278s 4 6 0.149 * C_12,C_21 E_313,E_315 L_313 M_313 278s 4 4 1 * C_14 E_14 L_14 M_14 278s 4 4 1 * C_15 E_15 L_15 M_15 278s 4 4 1 * C_16 E_16 L_16 M_16 278s 4 4 1 * C_17 E_17 L_17 M_17 278s 4 4 1 * C_64 E_18 L_18 M_18 278s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 278s 2 2 1 * * * L_619 M_619 278s 3 3 0.33 * * E_367 L_319 M_319 278s 2 2 1 * * * L_617 M_617 278s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 278s 2 4 0.5 * * * L_645,L_647 M_644,M_646 278s 3 3 0.33 * * E_432 L_328 M_328 278s 2 2 1 * * * L_333 M_333 278s 3 3 1 * C_20 * L_20 M_20 278s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 278s 2 2 1 * * * L_3 M_3 278s 2 2 1 * * * L_4 M_4 278s 2 2 1 * * * L_5 M_5 278s 2 2 1 * * * L_6 M_6 278s 2 2 1 * * * L_8 M_8 278s 2 2 1 * * * L_9 M_9 278s 2 2 1 * * * L_623 M_623 278s 4 4 1 * C_13 E_13 L_621 M_621 278s 2 4 0.146 * * * L_637,L_639 M_636,M_638 278s 3 3 0.33 * * E_437 L_317 M_317 278s 2 3 0.33 * * * L_631,L_633 M_632 278s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 278s 2 2 1 * * * L_331 M_331 278s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 278s Reading test_blastp.blast-graph 278s 5 species 278s 112 paired proteins 278s 147# Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 278s bidirectional edges 279s 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 2 2 1 * * * L_619 M_619 279s 3 3 0.33 * * E_367 L_319 M_319 279s 2 2 1 * * * L_617 M_617 279s 3 3 0.33 * * E_432 L_328 M_328 279s 2 2 1 * * * L_333 M_333 279s 3 3 1 * C_20 * L_20 M_20 279s 2 2 1 * * * L_3 M_3 279s 2 2 1 * * * L_4 M_4 279s 2 2 1 * * * L_5 M_5 279s 2 2 1 * * * L_6 M_6 279s 2 2 1 * * * L_8 M_8 279s 2 2 1 * * * L_9 M_9 279s 5 5 0.687 C_10 C_10;test E_10 L_10 M_10 279s 4 4 0.727 * C_11 E_11 L_11 M_11 279s 4 6 0.137 * C_12,C_21 E_313,E_315 L_313 M_313 279s 2 2 1 * * * L_623 M_623 279s 4 4 0.74 * C_14 E_14 L_14 M_14 279s 4 4 0.814 * C_15 E_15 L_15 M_15 279s 4 4 0.815 * C_16 E_16 L_16 M_16 279s 4 4 0.824 * C_17 E_17 L_17 M_17 279s 4 4 0.779 * C_64 E_18 L_18 M_18 279s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 279s 3 3 0.33 * * E_437 L_317 M_317 279s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 279s 2 4 0.478 * * * L_645,L_647 M_644,M_646 279s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 279s 4 4 0.717 * C_13 E_13 L_621 M_621 279s 2 4 0.145 * * * L_637,L_639 M_636,M_638 279s 2 2 1 * * * L_331 M_331 279s 2 3 0.33 * * * L_631,L_633 M_632 279s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 279s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 279s Test okay 280s autopkgtest [15:12:06]: test run-unit-test: -----------------------] 280s autopkgtest [15:12:06]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 280s run-unit-test PASS 280s autopkgtest [15:12:06]: @@@@@@@@@@@@@@@@@@@@ summary 280s run-unit-test PASS 298s nova [W] Using flock in prodstack6-s390x 298s Creating nova instance adt-plucky-s390x-proteinortho-20250315-150725-juju-7f2275-prod-proposed-migration-environment-15-b37d1179-5e69-47d6-bb75-1745d458132b from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 298s nova [W] Timed out waiting for 71961826-6f9b-4c37-8abe-db3165ec32a2 to get deleted.