0s autopkgtest [03:38:38]: starting date: 2024-03-11 0s autopkgtest [03:38:38]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [03:38:38]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.29cpnq4e/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:perl,src:db5.3,src:gdbm,src:mmdebstrap --apt-upgrade proteinortho --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 db5.3/5.3.28+dfsg2-5 gdbm/1.23-5.1 mmdebstrap/1.4.3-6' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-25.secgroup --name adt-noble-arm64-proteinortho-20240311-033838-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 90s autopkgtest [03:40:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 91s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 91s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 91s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 91s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [434 kB] 92s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2615 kB] 92s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [581 kB] 92s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 92s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 92s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 92s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2990 kB] 92s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 92s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 92s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 94s Fetched 6850 kB in 2s (4420 kB/s) 94s Reading package lists... 97s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s Calculating upgrade... 100s The following packages were automatically installed and are no longer required: 100s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 100s Use 'sudo apt autoremove' to remove them. 100s The following packages will be REMOVED: 100s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 100s The following NEW packages will be installed: 100s libgdbm-compat4t64 libgdbm6t64 100s The following packages have been kept back: 100s libperl5.38 100s The following packages will be upgraded: 100s perl-base perl-modules-5.38 100s 2 upgraded, 2 newly installed, 5 to remove and 1 not upgraded. 100s Need to get 4928 kB of archives. 100s After this operation, 4158 kB disk space will be freed. 100s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB] 100s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB] 100s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B] 100s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 101s Fetched 4928 kB in 1s (6635 kB/s) 102s (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 ... 74748 files and directories currently installed.) 102s Removing dpkg-dev (1.22.4ubuntu5) ... 102s Removing libdpkg-perl (1.22.4ubuntu5) ... 102s Removing perl (5.38.2-3) ... 102s (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 ... 74167 files and directories currently installed.) 102s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ... 102s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 102s Setting up perl-base (5.38.2-3.2) ... 102s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested: 102s python3-gdbm:arm64 depends on libgdbm6 (>= 1.16). 102s man-db depends on libgdbm6 (>= 1.16). 102s libperl5.38:arm64 depends on libgdbm6 (>= 1.21). 102s libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16). 102s 102s (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 ... 74167 files and directories currently installed.) 102s Removing libgdbm6:arm64 (1.23-5) ... 102s Selecting previously unselected package libgdbm6t64:arm64. 102s (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 ... 74162 files and directories currently installed.) 102s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ... 102s Unpacking libgdbm6t64:arm64 (1.23-5.1) ... 102s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested: 102s libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3). 102s 102s (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 ... 74168 files and directories currently installed.) 102s Removing libgdbm-compat4:arm64 (1.23-5) ... 102s Selecting previously unselected package libgdbm-compat4t64:arm64. 102s (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 ... 74163 files and directories currently installed.) 102s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_arm64.deb ... 102s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 102s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 102s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 103s Setting up libgdbm6t64:arm64 (1.23-5.1) ... 103s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 103s Setting up perl-modules-5.38 (5.38.2-3.2) ... 103s Processing triggers for man-db (2.12.0-3) ... 104s Processing triggers for libc-bin (2.39-0ubuntu2) ... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s The following packages will be REMOVED: 105s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 105s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. 105s After this operation, 52.0 MB disk space will be freed. 105s (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 ... 74169 files and directories currently installed.) 105s Removing libperl5.38:arm64 (5.38.2-3) ... 105s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ... 105s Removing lto-disabled-list (47) ... 105s Removing make (4.3-4.1build1) ... 105s Removing perl-modules-5.38 (5.38.2-3.2) ... 106s Processing triggers for man-db (2.12.0-3) ... 106s Processing triggers for libc-bin (2.39-0ubuntu2) ... 107s sh: Attempting to set up Debian/Ubuntu apt sources automatically 107s sh: Distribution appears to be Ubuntu 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s eatmydata is already the newest version (131-1). 109s dbus is already the newest version (1.14.10-4ubuntu1). 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s rng-tools-debian is already the newest version (2.4). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s haveged is already the newest version (1.9.14-1ubuntu1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s The following additional packages will be installed: 112s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 112s make perl perl-modules-5.38 112s Suggested packages: 112s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 112s libterm-readline-gnu-perl | libterm-readline-perl-perl 112s libtap-harness-archive-perl 112s Recommended packages: 112s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 112s libfile-fcntllock-perl 112s The following packages will be REMOVED: 112s libdb5.3 112s The following NEW packages will be installed: 112s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 112s lto-disabled-list make perl perl-modules-5.38 112s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 112s Need to get 7257 kB/10.4 MB of archives. 112s After this operation, 56.1 MB of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB] 113s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB] 113s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB] 113s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB] 113s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] 113s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB] 114s Fetched 7257 kB in 1s (8607 kB/s) 114s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: 114s libsasl2-modules-db:arm64 depends on libdb5.3. 114s libpython3.12-stdlib:arm64 depends on libdb5.3. 114s libpam-modules:arm64 depends on libdb5.3. 114s iproute2 depends on libdb5.3. 114s apt-utils depends on libdb5.3. 114s 114s (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 ... 72198 files and directories currently installed.) 114s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ... 114s Selecting previously unselected package libdb5.3t64:arm64. 114s (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 ... 72192 files and directories currently installed.) 114s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ... 114s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 114s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 114s Selecting previously unselected package perl-modules-5.38. 115s (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 ... 72198 files and directories currently installed.) 115s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 115s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 115s Selecting previously unselected package libgdbm-compat4t64:arm64. 115s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ... 115s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 115s Selecting previously unselected package libperl5.38t64:arm64. 115s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ... 115s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ... 115s Selecting previously unselected package perl. 115s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ... 115s Unpacking perl (5.38.2-3.2) ... 116s Selecting previously unselected package libdpkg-perl. 116s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 116s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 116s Selecting previously unselected package make. 116s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ... 116s Unpacking make (4.3-4.1build1) ... 116s Selecting previously unselected package lto-disabled-list. 116s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 116s Unpacking lto-disabled-list (47) ... 116s Selecting previously unselected package dpkg-dev. 116s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 116s Unpacking dpkg-dev (1.22.4ubuntu5) ... 116s Setting up lto-disabled-list (47) ... 116s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 116s Setting up make (4.3-4.1build1) ... 116s Setting up perl-modules-5.38 (5.38.2-3.2) ... 116s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ... 116s Setting up perl (5.38.2-3.2) ... 116s Setting up libdpkg-perl (1.22.4ubuntu5) ... 116s Setting up dpkg-dev (1.22.4ubuntu5) ... 116s Processing triggers for man-db (2.12.0-3) ... 117s Processing triggers for libc-bin (2.39-0ubuntu2) ... 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 118s The following packages will be REMOVED: 118s cloud-init* python3-configobj* python3-debconf* 119s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 119s After this operation, 3248 kB disk space will be freed. 119s (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 ... 74750 files and directories currently installed.) 119s Removing cloud-init (24.1-0ubuntu1) ... 120s Removing python3-configobj (5.0.8-3) ... 120s Removing python3-debconf (1.5.86) ... 120s Processing triggers for man-db (2.12.0-3) ... 120s (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 ... 74361 files and directories currently installed.) 120s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 121s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 121s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s linux-generic is already the newest version (6.8.0-11.11+1). 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 124s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 124s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 125s Reading package lists... 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s autopkgtest [03:40:46]: rebooting testbed after setup commands that affected boot 166s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 172s autopkgtest [03:41:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 172s autopkgtest [03:41:30]: testbed dpkg architecture: arm64 173s autopkgtest [03:41:31]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 176s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 176s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 176s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 176s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 176s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 176s gpgv: issuer "tille@debian.org" 176s gpgv: Can't check signature: No public key 176s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 177s autopkgtest [03:41:35]: testing package proteinortho version 6.3.1+dfsg-1 177s autopkgtest [03:41:35]: build not needed 177s autopkgtest [03:41:35]: test run-unit-test: preparing testbed 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 181s Done 181s Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 182s The following additional packages will be installed: 182s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 182s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 182s Recommended packages: 182s med-config 182s The following NEW packages will be installed: 182s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 182s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 182s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 182s 1 not fully installed or removed. 182s Need to get 22.0 MB of archives. 182s After this operation, 92.0 MB of additional disk space will be used. 182s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 182s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 182s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 183s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 183s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 183s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 183s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 183s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 183s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] 183s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 diamond-aligner arm64 2.1.9-1 [1905 kB] 183s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 proteinortho arm64 6.3.1+dfsg-1 [340 kB] 184s Fetched 22.0 MB in 1s (20.3 MB/s) 184s Selecting previously unselected package libgomp1:arm64. 184s (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 ... 74306 files and directories currently installed.) 184s Preparing to unpack .../00-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 184s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 184s Selecting previously unselected package libblas3:arm64. 184s Preparing to unpack .../01-libblas3_3.12.0-3_arm64.deb ... 184s Unpacking libblas3:arm64 (3.12.0-3) ... 184s Selecting previously unselected package libgfortran5:arm64. 184s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 184s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 184s Selecting previously unselected package liblapack3:arm64. 184s Preparing to unpack .../03-liblapack3_3.12.0-3_arm64.deb ... 184s Unpacking liblapack3:arm64 (3.12.0-3) ... 184s Selecting previously unselected package ncbi-data. 184s Preparing to unpack .../04-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 184s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 184s Selecting previously unselected package libmbedcrypto7:arm64. 184s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 184s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 184s Selecting previously unselected package libmbedx509-1:arm64. 184s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 184s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 184s Selecting previously unselected package libmbedtls14:arm64. 184s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 184s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 184s Selecting previously unselected package ncbi-blast+. 184s Preparing to unpack .../08-ncbi-blast+_2.12.0+ds-4_arm64.deb ... 184s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 184s Selecting previously unselected package diamond-aligner. 184s Preparing to unpack .../09-diamond-aligner_2.1.9-1_arm64.deb ... 184s Unpacking diamond-aligner (2.1.9-1) ... 184s Selecting previously unselected package proteinortho. 185s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_arm64.deb ... 185s Unpacking proteinortho (6.3.1+dfsg-1) ... 185s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 185s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 185s Setting up diamond-aligner (2.1.9-1) ... 185s Setting up libblas3:arm64 (3.12.0-3) ... 185s 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 185s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 185s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 185s Setting up liblapack3:arm64 (3.12.0-3) ... 185s 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 185s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 185s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 185s Setting up ncbi-blast+ (2.12.0+ds-4) ... 185s Setting up proteinortho (6.3.1+dfsg-1) ... 185s Setting up autopkgtest-satdep (0) ... 185s Processing triggers for man-db (2.12.0-3) ... 185s Processing triggers for libc-bin (2.39-0ubuntu2) ... 189s (Reading database ... 74640 files and directories currently installed.) 189s Removing autopkgtest-satdep (0) ... 190s autopkgtest [03:41:48]: test run-unit-test: [----------------------- 191s ***************************************************************** 191s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 191s ***************************************************************** 192s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 192s Checking input files. 192s Checking input files. 192s Checking test/C_clean.faa... ok 192s Checking test/C2.faa... ok 192s Checking test/E.faa... ok 192s Checking test/L.faa... ok 192s Checking test/M.faa... ok 192s Checking test/C.faa... 192s  [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 !!! 192s The line is: 192s C_10,test 192s ok 192s Checking test/L.faa... ok 192s Checking test/E.faa... ok 192s Checking test/C2.faa... ok 192s Checking test/M.faa... ok 192s 192s **Step 1** 192s Generating indices anyway (forced). 192s Building database for 'test/E.faa' (144 sequences) 192s Generating indices anyway (forced). 192s Building database for 'test/M.faa' (80 sequences) 193s Generating indices anyway (forced). 193s Building database for 'test/C_clean.faa' (109 sequences) 193s Generating indices anyway (forced). 193s Building database for 'test/C2.faa' (4 sequences) 193s Generating indices anyway (forced). 193s Building database for 'test/L.faa' (80 sequences) 193s 193s **Step 2** using blastp+ 198s 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) 198s [OUTPUT] -> written to test_blastp.blast-graph 198s 198s **Step 3** 198s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 198s Reading test_blastp.blast-graph 198s 5 species 198s 112 paired proteins 198s 149 bidirectional edges 199s 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 (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 (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 (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 (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 199s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 199s You can extract the fasta files of each orthology group with 199s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/E.faa' 'test/M.faa' 'test/C_clean.faa' 'test/C2.faa' 'test/L.faa' 199s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 199s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 199s # test_blastp.proteinortho.tsv statistics: 199s # number of groups that contains at least p% species: 199s # p species groups genes in groups 199s 0% 0 32 (100%) 112 (100%) 199s 20% 1 32 (100%) 112 (100%) 199s 40% 2 32 (100%) 112 (100%) 199s 60% 3 17 (53.12%) 74 (66.07%) 199s 80% 4 11 (34.37%) 51 (45.53%) 199s 100% 5 1 (3.12%) 5 (4.46%) 199s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 199s # number of groups for each input species: 199s L.faa 32 100% 199s M.faa 32 100% 199s E.faa 15 46.87% 199s C_clean.faa 13 40.62% 199s C2.faa 1 3.12% 199s 199s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 199s 199s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 199s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 199s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 199s 199s All finished. 199s ***************************************************************** 199s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 199s ***************************************************************** 199s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 199s Checking input files. 199s Checking test/C_clean.faa... ok 199s Checking test/C2.faa... ok 199s Checking test/E.faa... ok 199s Checking test/L.faa... ok 199s Checking test/M.faa... ok 199s 199s **Step 1** 199s Generating indices anyway (forced). 199s Building database for 'test/M.faa' (40 sequences) 199s Generating indices anyway (forced). 199s Building database for 'test/C2.faa' (2 sequences) 199s Generating indices anyway (forced). 199s Building database for 'test/E.faa' (72 sequences) 199s Generating indices anyway (forced). 199s Building database for 'test/C_clean.faa' (109 sequences) 199s Generating indices anyway (forced). 199s Building database for 'test/L.faa' (40 sequences) 199s 199s **Step 2** using blastp+ with : synteny 204s 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) 204s [OUTPUT] -> written to test_synteny.blast-graph 204s 204s **Step 3** 204s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 204s Reading test_synteny.blast-graph 204s 5 species 204s 112 paired proteins 204s 149 bidirectional edges 205s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (20@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 (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 (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 (5@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 205s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 205s You can extract the fasta files of each orthology group with 205s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/M.faa' 'test/C2.faa' 'test/E.faa' 'test/C_clean.faa' 'test/L.faa' 205s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 205s Adding singles... 205s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 205s # test_synteny.proteinortho.tsv statistics: 205s # number of groups that contains at least p% species: 205s # p species groups genes in groups 205s 0% 0 182 (100%) 262 (100%) 205s 20% 1 182 (100%) 262 (100%) 205s 40% 2 32 (17.58%) 112 (42.74%) 205s 60% 3 17 (9.34%) 74 (28.24%) 205s 80% 4 11 (6.04%) 51 (19.46%) 205s 100% 5 1 (0.54%) 5 (1.9%) 205s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 205s # groups that contains only one species: 205s single 5 150 (82.41%) 150 (57.25%) 205s # number of groups for each input species: 205s L.faa 32 100% 205s M.faa 32 100% 205s E.faa 15 46.87% 205s C_clean.faa 13 40.62% 205s C2.faa 1 3.12% 205s 205s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 205s 205s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 205s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 205s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 205s 205s 205s Clustering by gene-order (POFF mode) 205s Reading test_synteny.ffadj-graph 205s 5 species 205s 106 paired proteins 205s 106 bidirectional edges 206s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (6@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 (18@lapack* + 0@power) connected components Clustering: working on (17@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 (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 (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 (3@lapack* + 0@power) connected components Reading test_synteny.ffadj-graph 206s 5 species 206s 106 paired proteins 206s 106 bidirectional edges 207s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (12@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 (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 (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 (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 (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 (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 207s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 207s You can extract the fasta files of each orthology group with 207s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/M.faa' 'test/C2.faa' 'test/E.faa' 'test/C_clean.faa' 'test/L.faa' 207s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 207s Adding singles... 207s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 207s # test_synteny.poff.tsv statistics: 207s # number of groups that contains at least p% species: 207s # p species groups genes in groups 207s 0% 0 195 (100%) 262 (100%) 207s 20% 1 195 (100%) 262 (100%) 207s 40% 2 38 (19.48%) 105 (40.07%) 207s 60% 3 17 (8.71%) 63 (24.04%) 207s 80% 4 10 (5.12%) 42 (16.03%) 207s 100% 5 1 (0.51%) 5 (1.9%) 207s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 207s # groups that contains only one species: 207s single 5 157 (80.51%) 157 (59.92%) 207s # number of groups for each input species: 207s L.faa 37 97.36% 207s M.faa 37 97.36% 207s E.faa 15 39.47% 207s C_clean.faa 14 36.84% 207s C2.faa 1 2.63% 207s 207s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 207s 207s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 207s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 207s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 207s 207s All finished. 207s ***************************************************************** 207s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 207s ***************************************************************** 207s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 207s Checking input files. 207s Checking test/C_clean.faa... ok 207s Checking test/C2.faa... ok 207s Checking test/E.faa... ok 207s Checking test/L.faa... ok 207s Checking test/M.faa... ok 207s 207s **Step 1** 207s Generating indices anyway (forced). 207s Building database for 'test/L.faa' (40 sequences) 207s Generating indices anyway (forced). 207s Building database for 'test/C_clean.faa' (109 sequences) 207s Generating indices anyway (forced). 207s Building database for 'test/E.faa' (72 sequences) 207s Generating indices anyway (forced). 207s Building database for 'test/C2.faa' (2 sequences) 207s Generating indices anyway (forced). 207s Building database for 'test/M.faa' (40 sequences) 207s 207s **Step 2** using diamond 211s 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) 211s [OUTPUT] -> written to test_diamond.blast-graph 211s 211s **Step 3** 211s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 211s Reading test_diamond.blast-graph 211s 5 species 211s 113 paired proteins 211s 147 bidirectional edges 212s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (8@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 (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 212s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 212s You can extract the fasta files of each orthology group with 212s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 'test/C2.faa' 'test/M.faa' 212s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 213s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 213s # test_diamond.proteinortho.tsv statistics: 213s # number of groups that contains at least p% species: 213s # p species groups genes in groups 213s 0% 0 32 (100%) 112 (100%) 213s 20% 1 32 (100%) 112 (100%) 213s 40% 2 32 (100%) 112 (100%) 213s 60% 3 17 (53.12%) 76 (67.85%) 213s 80% 4 11 (34.37%) 53 (47.32%) 213s 100% 5 1 (3.12%) 5 (4.46%) 213s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 213s # number of groups for each input species: 213s L.faa 32 100% 213s M.faa 32 100% 213s E.faa 15 46.87% 213s C_clean.faa 13 40.62% 213s C2.faa 1 3.12% 213s 213s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 213s 213s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 213s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 213s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 213s 213s All finished. 213s ***************************************************************** 213s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 213s ***************************************************************** 213s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 213s Checking input files. 213s Checking test/C_clean.faa... ok 213s Checking test/C2.faa... ok 213s Checking test/E.faa... ok 213s Checking test/L.faa... ok 213s Checking test/M.faa... ok 213s 213s **Step 1** 213s Generating indices anyway (forced). 213s Building database for 'test/E.faa' (72 sequences) 213s Generating indices anyway (forced). 213s Building database for 'test/C2.faa' (2 sequences) 213s Generating indices anyway (forced). 213s Building database for 'test/C_clean.faa' (109 sequences) 213s Generating indices anyway (forced). 213s Building database for 'test/L.faa' (40 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/M.faa' (40 sequences) 214s 214s **Step 2** using diamond 218s 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) 218s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 218s 218s **Step 3** 218s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 218s Reading test_diamondmoresensitive.blast-graph 218s 5 species 218s 112 paired proteins 218s 145 bidirectional edges 219s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@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 (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 Clustering: working on (3@lapack* + 0@power) connected components 219s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 219s You can extract the fasta files of each orthology group with 219s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/E.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/L.faa' 'test/M.faa' 219s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 219s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 219s # test_diamondmoresensitive.proteinortho.tsv statistics: 219s # number of groups that contains at least p% species: 219s # p species groups genes in groups 219s 0% 0 32 (100%) 111 (100%) 219s 20% 1 32 (100%) 111 (100%) 219s 40% 2 32 (100%) 111 (100%) 219s 60% 3 17 (53.12%) 75 (67.56%) 219s 80% 4 11 (34.37%) 52 (46.84%) 219s 100% 5 1 (3.12%) 5 (4.5%) 219s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 219s # number of groups for each input species: 219s L.faa 32 100% 219s M.faa 32 100% 219s E.faa 15 46.87% 219s C_clean.faa 13 40.62% 219s C2.faa 1 3.12% 219s 219s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 219s 219s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 219s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 219s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 219s 219s All finished. 219s ***************************************************************** 219s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 219s ***************************************************************** 220s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 220s Checking input files. 220s Checking test/C_clean.faa... ok 220s Checking test/C2.faa... ok 220s Checking test/E.faa... ok 220s Checking test/L.faa... ok 220s Checking test/M.faa... ok 220s 220s **Step 1** 220s Generating indices anyway (forced). 220s Building database for 'test/C2.faa' (2 sequences) 220s Generating indices anyway (forced). 220s Building database for 'test/E.faa' (72 sequences) 220s Generating indices anyway (forced). 220s Building database for 'test/C_clean.faa' (109 sequences) 220s Generating indices anyway (forced). 220s Building database for 'test/L.faa' (40 sequences) 220s Generating indices anyway (forced). 220s Building database for 'test/M.faa' (40 sequences) 220s 220s **Step 2** using blastp+ 224s 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) 224s [OUTPUT] -> written to test_blastall.blast-graph 224s 224s **Step 3** 224s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 224s Reading test_blastall.blast-graph 224s 5 species 224s 112 paired proteins 225s 149 bidirectional edges 225s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (11@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 (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 225s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 225s You can extract the fasta files of each orthology group with 225s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C2.faa' 'test/E.faa' 'test/C_clean.faa' 'test/L.faa' 'test/M.faa' 225s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 226s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 226s # test_blastall.proteinortho.tsv statistics: 226s # number of groups that contains at least p% species: 226s # p species groups genes in groups 226s 0% 0 32 (100%) 112 (100%) 226s 20% 1 32 (100%) 112 (100%) 226s 40% 2 32 (100%) 112 (100%) 226s 60% 3 17 (53.12%) 74 (66.07%) 226s 80% 4 11 (34.37%) 51 (45.53%) 226s 100% 5 1 (3.12%) 5 (4.46%) 226s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 226s # number of groups for each input species: 226s L.faa 32 100% 226s M.faa 32 100% 226s E.faa 15 46.87% 226s C_clean.faa 13 40.62% 226s C2.faa 1 3.12% 226s 226s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 226s 226s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 226s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 226s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 226s 226s All finished. 226s - test max_of_diag() : OK 226s - test generate_random_vector() : OK 226s - test get_new_x() : OK 226s - test makeOrthogonal() : OK 226s - test normalize() : OK 226s - test getY() : OK 226s - test lapack() : OK 226s - test power() : OK 226s - test smirnov-grubb() : OK 226s All test passed. 226s Reading test_blastp.blast-graph 226s 5 species 226s 112 paired proteins 226s 149 bidirectional edges 226s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 227s 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 (18@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 227s 4 4 1 * C_11 E_11 L_11 M_11 227s 4 6 0.333 * C_12,C_21 E_313,E_315 L_313 M_313 227s 4 4 1 * C_14 E_14 L_14 M_14 227s 4 4 1 * C_15 E_15 L_15 M_15 227s 4 4 1 * C_16 E_16 L_16 M_16 227s 4 4 1 * C_17 E_17 L_17 M_17 227s 4 4 1 * C_64 E_18 L_18 M_18 227s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 227s 3 3 0.33 * * E_367 L_319 M_319 227s 3 3 0.33 * * E_432 L_328 M_328 227s 3 3 1 * C_20 * L_20 M_20 227s 3 6 0.333 * C_167,C_2,C_164,C_166 * L_2 M_2 227s 2 2 1 * * * L_619 M_619 227s 2 2 1 * * * L_617 M_617 227s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 227s 2 4 0.5 * * * L_645,L_647 M_644,M_646 227s 2 2 1 * * * L_333 M_333 227s 2 2 1 * * * L_3 M_3 227s 2 2 1 * * * L_4 M_4 227s 2 2 1 * * * L_5 M_5 227s 2 2 1 * * * L_6 M_6 227s 2 2 1 * * * L_8 M_8 227s 2 2 1 * * * L_9 M_9 227s 2 2 1 * * * L_623 M_623 227s 4 4 1 * C_13 E_13 L_621 M_621 227s 2 4 0.146 * * * L_637,L_639 M_636,M_638 227s 3 3 0.33 * * E_437 L_317 M_317 227s 2 3 0.33 * * * L_631,L_633 M_632 227s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 227s 2 2 1 * * * L_331 M_331 227s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 227s Reading test_blastp.blast-graph 227s 5 species 227s 112 paired proteins 227s 149 bidirectional edges 227s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 228s 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 0.33 * * E_367 L_319 M_319 228s 3 3 0.33 * * E_432 L_328 M_328 228s 3 3 1 * C_20 * L_20 M_20 228s 2 2 1 * * * L_619 M_619 228s 2 2 1 * * * L_617 M_617 228s 2 2 1 * * * L_333 M_333 228s 2 2 1 * * * L_3 M_3 228s 2 2 1 * * * L_4 M_4 228s 2 2 1 * * * L_5 M_5 228s 2 2 1 * * * L_6 M_6 228s 2 2 1 * * * L_8 M_8 228s 2 2 1 * * * L_9 M_9 228s 5 5 0.694 C_10 C_10;test E_10 L_10 M_10 228s 4 4 0.727 * C_11 E_11 L_11 M_11 228s 4 6 0.297 * C_12,C_21 E_313,E_315 L_313 M_313 228s 2 2 1 * * * L_623 M_623 228s 4 4 0.743 * C_14 E_14 L_14 M_14 228s 4 4 0.818 * C_15 E_15 L_15 M_15 228s 4 4 0.815 * C_16 E_16 L_16 M_16 228s 4 4 0.824 * C_17 E_17 L_17 M_17 228s 4 4 0.777 * C_64 E_18 L_18 M_18 228s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 228s 3 3 0.33 * * E_437 L_317 M_317 228s 3 6 0.314 * C_167,C_2,C_164,C_166 * L_2 M_2 228s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 228s 2 4 0.478 * * * L_645,L_647 M_644,M_646 228s 4 4 0.702 * C_13 E_13 L_621 M_621 228s 2 4 0.145 * * * L_637,L_639 M_636,M_638 228s 2 2 1 * * * L_331 M_331 228s 2 3 0.33 * * * L_631,L_633 M_632 228s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 228s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 228s Test okay 228s autopkgtest [03:42:26]: test run-unit-test: -----------------------] 229s run-unit-test PASS 229s autopkgtest [03:42:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 229s autopkgtest [03:42:27]: @@@@@@@@@@@@@@@@@@@@ summary 229s run-unit-test PASS 240s Creating nova instance adt-noble-arm64-proteinortho-20240311-033838-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240311.img (UUID 900cfff9-7f1a-42c7-81a7-22635cd2a5f9)...