0s autopkgtest [19:02:05]: starting date and time: 2024-03-20 19:02:05+0000 0s autopkgtest [19:02:05]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:02:05]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0689l1rp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:perl --apt-upgrade proteinortho --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-16.secgroup --name adt-noble-s390x-proteinortho-20240320-190205-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 79s autopkgtest [19:03:24]: testbed dpkg architecture: s390x 79s autopkgtest [19:03:24]: testbed apt version: 2.7.12 79s autopkgtest [19:03:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 80s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 80s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3809 kB] 81s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 81s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [501 kB] 81s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 81s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [679 kB] 81s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 81s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 81s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 81s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4058 kB] 82s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 82s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [45.3 kB] 82s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 84s Fetched 9282 kB in 3s (3193 kB/s) 84s Reading package lists... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Calculating upgrade... 87s The following packages were automatically installed and are no longer required: 87s fuse3 libfuse3-3 libgdbm-compat4t64 libperl5.38 lto-disabled-list make 87s perl-modules-5.38 s390-tools-data s390-tools-signed 87s Use 'sudo apt autoremove' to remove them. 87s The following packages will be REMOVED: 87s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl s390-tools 87s sysconfig-hardware 87s The following NEW packages will be installed: 87s libgdbm-compat4t64 libgdbm6t64 87s The following packages will be upgraded: 87s perl-base perl-modules-5.38 87s 2 upgraded, 2 newly installed, 7 to remove and 0 not upgraded. 87s Need to get 5114 kB of archives. 87s After this operation, 15.7 MB disk space will be freed. 87s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-base s390x 5.38.2-3.2 [1961 kB] 88s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm6t64 s390x 1.23-5.1 [36.4 kB] 88s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm-compat4t64 s390x 1.23-5.1 [6880 B] 88s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 89s Fetched 5114 kB in 2s (2820 kB/s) 89s (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 ... 52171 files and directories currently installed.) 89s Removing sysconfig-hardware (0.0.14ubuntu2) ... 89s Removing s390-tools (2.31.0-0ubuntu1) ... 89s Removing dpkg-dev (1.22.4ubuntu5) ... 89s Removing libdpkg-perl (1.22.4ubuntu5) ... 89s Removing perl (5.38.2-3) ... 89s (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 ... 51332 files and directories currently installed.) 89s Preparing to unpack .../perl-base_5.38.2-3.2_s390x.deb ... 89s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 89s Setting up perl-base (5.38.2-3.2) ... 89s dpkg: libgdbm6:s390x: dependency problems, but removing anyway as you requested: 89s python3-gdbm:s390x depends on libgdbm6 (>= 1.16). 89s man-db depends on libgdbm6 (>= 1.16). 89s libperl5.38:s390x depends on libgdbm6 (>= 1.21). 89s libgdbm-compat4:s390x depends on libgdbm6 (>= 1.16). 89s 90s (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 ... 51332 files and directories currently installed.) 90s Removing libgdbm6:s390x (1.23-5) ... 90s Selecting previously unselected package libgdbm6t64:s390x. 90s (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 ... 51327 files and directories currently installed.) 90s Preparing to unpack .../libgdbm6t64_1.23-5.1_s390x.deb ... 90s Unpacking libgdbm6t64:s390x (1.23-5.1) ... 90s dpkg: libgdbm-compat4:s390x: dependency problems, but removing anyway as you requested: 90s libperl5.38:s390x depends on libgdbm-compat4 (>= 1.18-3). 90s 90s (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 ... 51333 files and directories currently installed.) 90s Removing libgdbm-compat4:s390x (1.23-5) ... 90s Selecting previously unselected package libgdbm-compat4t64:s390x. 90s (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 ... 51328 files and directories currently installed.) 90s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_s390x.deb ... 90s Unpacking libgdbm-compat4t64:s390x (1.23-5.1) ... 90s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 90s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 90s Setting up libgdbm6t64:s390x (1.23-5.1) ... 90s Setting up libgdbm-compat4t64:s390x (1.23-5.1) ... 90s Setting up perl-modules-5.38 (5.38.2-3.2) ... 90s Processing triggers for libc-bin (2.39-0ubuntu2) ... 90s Processing triggers for man-db (2.12.0-3) ... 91s Processing triggers for initramfs-tools (0.142ubuntu20) ... 91s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 91s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s The following packages will be REMOVED: 94s fuse3* libfuse3-3* libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* 94s perl-modules-5.38* s390-tools-data* s390-tools-signed* 94s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 94s After this operation, 50.6 MB disk space will be freed. 94s (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 ... 51334 files and directories currently installed.) 94s Removing fuse3 (3.14.0-5) ... 94s update-initramfs: deferring update (trigger activated) 94s Removing libfuse3-3:s390x (3.14.0-5) ... 94s Removing libperl5.38:s390x (5.38.2-3) ... 94s Removing libgdbm-compat4t64:s390x (1.23-5.1) ... 94s Removing lto-disabled-list (47) ... 94s Removing make (4.3-4.1build1) ... 94s Removing perl-modules-5.38 (5.38.2-3.2) ... 94s Removing s390-tools-data (2.31.0-0ubuntu1) ... 94s Removing s390-tools-signed (2.31.0-0ubuntu1) ... 94s Processing triggers for libc-bin (2.39-0ubuntu2) ... 94s Processing triggers for man-db (2.12.0-3) ... 95s Processing triggers for initramfs-tools (0.142ubuntu20) ... 95s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 95s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 98s (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 ... 49337 files and directories currently installed.) 98s Purging configuration files for fuse3 (3.14.0-5) ... 98s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 98s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 98s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 98s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 100s Reading package lists... 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s autopkgtest [19:03:46]: rebooting testbed after setup commands that affected boot 126s autopkgtest [19:04:11]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 128s autopkgtest [19:04:13]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Starting pkgProblemResolver with broken count: 0 132s Starting 2 pkgProblemResolver with broken count: 0 132s Done 133s The following additional packages will be installed: 133s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 133s lto-disabled-list make perl perl-modules-5.38 133s Suggested packages: 133s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 133s libterm-readline-gnu-perl | libterm-readline-perl-perl 133s libtap-harness-archive-perl 133s Recommended packages: 133s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 133s libfile-fcntllock-perl 133s The following packages will be REMOVED: 133s libdb5.3 133s The following NEW packages will be installed: 133s autopkgtest-satdep dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 133s libperl5.38t64 lto-disabled-list make perl perl-modules-5.38 133s 0 upgraded, 10 newly installed, 1 to remove and 0 not upgraded. 133s Need to get 7542 kB/10.7 MB of archives. 133s After this operation, 54.4 MB of additional disk space will be used. 133s Get:1 /tmp/autopkgtest.zaccph/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 133s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-5build1 [763 kB] 133s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libperl5.38t64 s390x 5.38.2-3.2 [5007 kB] 135s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl s390x 5.38.2-3.2 [231 kB] 135s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libdpkg-perl all 1.22.4ubuntu5 [268 kB] 135s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x make s390x 4.3-4.1build1 [182 kB] 135s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 47 [12.4 kB] 135s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x dpkg-dev all 1.22.4ubuntu5 [1078 kB] 135s Fetched 7542 kB in 3s (2959 kB/s) 136s dpkg: libdb5.3:s390x: dependency problems, but removing anyway as you requested: 136s libsasl2-modules-db:s390x depends on libdb5.3. 136s libpython3.12-stdlib:s390x depends on libdb5.3. 136s libpython3.11-stdlib:s390x depends on libdb5.3. 136s libpam-modules:s390x depends on libdb5.3. 136s iproute2 depends on libdb5.3. 136s apt-utils depends on libdb5.3. 136s 136s (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 ... 49336 files and directories currently installed.) 136s Removing libdb5.3:s390x (5.3.28+dfsg2-4) ... 136s Selecting previously unselected package libdb5.3t64:s390x. 136s (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 ... 49330 files and directories currently installed.) 136s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5build1_s390x.deb ... 136s Unpacking libdb5.3t64:s390x (5.3.28+dfsg2-5build1) ... 136s Setting up libdb5.3t64:s390x (5.3.28+dfsg2-5build1) ... 136s Selecting previously unselected package perl-modules-5.38. 136s (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 ... 49336 files and directories currently installed.) 136s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 136s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 136s Selecting previously unselected package libgdbm-compat4t64:s390x. 136s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_s390x.deb ... 136s Unpacking libgdbm-compat4t64:s390x (1.23-5.1) ... 136s Selecting previously unselected package libperl5.38t64:s390x. 136s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_s390x.deb ... 136s Unpacking libperl5.38t64:s390x (5.38.2-3.2) ... 137s Selecting previously unselected package perl. 137s Preparing to unpack .../3-perl_5.38.2-3.2_s390x.deb ... 137s Unpacking perl (5.38.2-3.2) ... 137s Selecting previously unselected package libdpkg-perl. 137s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 137s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 137s Selecting previously unselected package make. 137s Preparing to unpack .../5-make_4.3-4.1build1_s390x.deb ... 137s Unpacking make (4.3-4.1build1) ... 137s Selecting previously unselected package lto-disabled-list. 137s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 137s Unpacking lto-disabled-list (47) ... 137s Selecting previously unselected package dpkg-dev. 137s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 137s Unpacking dpkg-dev (1.22.4ubuntu5) ... 137s Selecting previously unselected package autopkgtest-satdep. 137s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 137s Unpacking autopkgtest-satdep (0) ... 137s Setting up lto-disabled-list (47) ... 137s Setting up libgdbm-compat4t64:s390x (1.23-5.1) ... 137s Setting up make (4.3-4.1build1) ... 137s Setting up perl-modules-5.38 (5.38.2-3.2) ... 137s Setting up libperl5.38t64:s390x (5.38.2-3.2) ... 137s Setting up perl (5.38.2-3.2) ... 137s Setting up libdpkg-perl (1.22.4ubuntu5) ... 137s Setting up dpkg-dev (1.22.4ubuntu5) ... 137s Setting up autopkgtest-satdep (0) ... 137s Processing triggers for man-db (2.12.0-3) ... 137s Processing triggers for libc-bin (2.39-0ubuntu2) ... 139s (Reading database ... 51881 files and directories currently installed.) 139s Removing autopkgtest-satdep (0) ... 139s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 139s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 139s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 140s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 140s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 140s gpgv: issuer "tille@debian.org" 140s gpgv: Can't check signature: No public key 140s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 140s autopkgtest [19:04:25]: testing package proteinortho version 6.3.1+dfsg-1 140s autopkgtest [19:04:25]: build not needed 142s autopkgtest [19:04:27]: test run-unit-test: preparing testbed 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 146s The following additional packages will be installed: 146s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 146s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 146s Recommended packages: 146s med-config 146s The following NEW packages will be installed: 146s autopkgtest-satdep diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 146s libmbedcrypto7 libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 146s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 23.9 MB/23.9 MB of archives. 146s After this operation, 91.0 MB of additional disk space will be used. 146s Get:1 /tmp/autopkgtest.zaccph/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 146s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x diamond-aligner s390x 2.1.9-1 [2266 kB] 147s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 147s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 147s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 147s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 147s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedcrypto7 s390x 2.28.7-1ubuntu1 [216 kB] 147s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedx509-1 s390x 2.28.7-1ubuntu1 [46.0 kB] 147s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedtls14 s390x 2.28.7-1ubuntu1 [84.5 kB] 147s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 148s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-blast+ s390x 2.12.0+ds-4 [12.6 MB] 149s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x proteinortho s390x 6.3.1+dfsg-1 [333 kB] 149s Fetched 23.9 MB in 3s (8220 kB/s) 149s Selecting previously unselected package diamond-aligner. 149s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51881 files and directories currently installed.) 149s Preparing to unpack .../00-diamond-aligner_2.1.9-1_s390x.deb ... 149s Unpacking diamond-aligner (2.1.9-1) ... 149s Selecting previously unselected package libblas3:s390x. 149s Preparing to unpack .../01-libblas3_3.12.0-3_s390x.deb ... 149s Unpacking libblas3:s390x (3.12.0-3) ... 149s Selecting previously unselected package libgfortran5:s390x. 149s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 149s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 149s Selecting previously unselected package libgomp1:s390x. 149s Preparing to unpack .../03-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 149s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 149s Selecting previously unselected package liblapack3:s390x. 149s Preparing to unpack .../04-liblapack3_3.12.0-3_s390x.deb ... 149s Unpacking liblapack3:s390x (3.12.0-3) ... 149s Selecting previously unselected package libmbedcrypto7:s390x. 149s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_s390x.deb ... 149s Unpacking libmbedcrypto7:s390x (2.28.7-1ubuntu1) ... 149s Selecting previously unselected package libmbedx509-1:s390x. 149s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_s390x.deb ... 149s Unpacking libmbedx509-1:s390x (2.28.7-1ubuntu1) ... 149s Selecting previously unselected package libmbedtls14:s390x. 149s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_s390x.deb ... 149s Unpacking libmbedtls14:s390x (2.28.7-1ubuntu1) ... 149s Selecting previously unselected package ncbi-data. 149s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 149s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 149s Selecting previously unselected package ncbi-blast+. 149s Preparing to unpack .../09-ncbi-blast+_2.12.0+ds-4_s390x.deb ... 149s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 150s Selecting previously unselected package proteinortho. 150s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_s390x.deb ... 150s Unpacking proteinortho (6.3.1+dfsg-1) ... 150s Selecting previously unselected package autopkgtest-satdep. 150s Preparing to unpack .../11-2-autopkgtest-satdep.deb ... 150s Unpacking autopkgtest-satdep (0) ... 150s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 150s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 150s Setting up diamond-aligner (2.1.9-1) ... 150s Setting up libblas3:s390x (3.12.0-3) ... 150s 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 150s Setting up libmbedcrypto7:s390x (2.28.7-1ubuntu1) ... 150s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 150s Setting up liblapack3:s390x (3.12.0-3) ... 150s 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 150s Setting up libmbedx509-1:s390x (2.28.7-1ubuntu1) ... 150s Setting up libmbedtls14:s390x (2.28.7-1ubuntu1) ... 150s Setting up ncbi-blast+ (2.12.0+ds-4) ... 150s Setting up proteinortho (6.3.1+dfsg-1) ... 150s Setting up autopkgtest-satdep (0) ... 150s Processing triggers for man-db (2.12.0-3) ... 150s Processing triggers for libc-bin (2.39-0ubuntu2) ... 152s (Reading database ... 52215 files and directories currently installed.) 152s Removing autopkgtest-satdep (0) ... 153s autopkgtest [19:04:38]: test run-unit-test: [----------------------- 153s ***************************************************************** 153s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 153s ***************************************************************** 153s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 153s Checking input files. 153s Checking input files. 153s Checking test/C_clean.faa... ok 153s Checking test/C2.faa... ok 153s Checking test/E.faa... ok 153s Checking test/L.faa... ok 153s Checking test/M.faa... ok 153s Checking test/C.faa... 153s  [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 !!! 153s The line is: 153s C_10,test 153s ok 153s Checking test/L.faa... ok 153s Checking test/C2.faa... ok 153s Checking test/C_clean.faa... ok 153s Checking test/E.faa... ok 153s 153s **Step 1** 153s Generating indices anyway (forced). 153s Building database for 'test/C_clean.faa' (218 sequences) 153s Generating indices anyway (forced). 153s Building database for 'test/L.faa' (80 sequences) 153s Generating indices anyway (forced). 153s Building database for 'test/C2.faa' (4 sequences) 153s Generating indices anyway (forced). 153s Building database for 'test/E.faa' (144 sequences) 153s Generating indices anyway (forced). 153s Building database for 'test/M.faa' (40 sequences) 153s 153s **Step 2** using blastp+ 158s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 158s [OUTPUT] -> written to test_blastp.blast-graph 158s 158s **Step 3** 158s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 158s Reading test_blastp.blast-graph 158s 5 species 158s 112 paired proteins 158s 147 bidirectional edges 159s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 159s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 159s You can extract the fasta files of each orthology group with 159s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/C_clean.faa' 'test/L.faa' 'test/C2.faa' 'test/E.faa' 'test/M.faa' 159s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 159s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 159s # test_blastp.proteinortho.tsv statistics: 159s # number of groups that contains at least p% species: 159s # p species groups genes in groups 159s 0% 0 32 (100%) 112 (100%) 159s 20% 1 32 (100%) 112 (100%) 159s 40% 2 32 (100%) 112 (100%) 159s 60% 3 17 (53.12%) 74 (66.07%) 159s 80% 4 11 (34.37%) 51 (45.53%) 159s 100% 5 1 (3.12%) 5 (4.46%) 159s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 159s # number of groups for each input species: 159s L.faa 32 100% 159s M.faa 32 100% 159s E.faa 15 46.87% 159s C_clean.faa 13 40.62% 159s C2.faa 1 3.12% 159s 159s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 159s 159s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 159s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 159s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 159s 159s All finished. 159s ***************************************************************** 159s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 159s ***************************************************************** 159s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 159s Checking input files. 159s Checking test/C_clean.faa... ok 159s Checking test/C2.faa... ok 159s Checking test/E.faa... ok 159s Checking test/L.faa... ok 159s Checking test/M.faa... ok 159s 159s **Step 1** 159s Generating indices anyway (forced). 159s Building database for 'test/E.faa' (72 sequences) 159s Generating indices anyway (forced). 159s Building database for 'test/C_clean.faa' (109 sequences) 160s Generating indices anyway (forced). 160s Building database for 'test/M.faa' (40 sequences) 160s Generating indices anyway (forced). 160s Building database for 'test/C2.faa' (2 sequences) 160s Generating indices anyway (forced). 160s Building database for 'test/L.faa' (40 sequences) 160s 160s **Step 2** using blastp+ with : synteny 165s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 165s [OUTPUT] -> written to test_synteny.blast-graph 165s 165s **Step 3** 165s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 165s Reading test_synteny.blast-graph 165s 5 species 165s 112 paired proteins 165s 149 bidirectional edges 166s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 166s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 166s You can extract the fasta files of each orthology group with 166s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/E.faa' 'test/C_clean.faa' 'test/M.faa' 'test/C2.faa' 'test/L.faa' 166s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 166s Adding singles... 166s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 166s # test_synteny.proteinortho.tsv statistics: 166s # number of groups that contains at least p% species: 166s # p species groups genes in groups 166s 0% 0 182 (100%) 262 (100%) 166s 20% 1 182 (100%) 262 (100%) 166s 40% 2 32 (17.58%) 112 (42.74%) 166s 60% 3 17 (9.34%) 74 (28.24%) 166s 80% 4 11 (6.04%) 51 (19.46%) 166s 100% 5 1 (0.54%) 5 (1.9%) 166s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 166s # groups that contains only one species: 166s single 5 150 (82.41%) 150 (57.25%) 166s # number of groups for each input species: 166s L.faa 32 100% 166s M.faa 32 100% 166s E.faa 15 46.87% 166s C_clean.faa 13 40.62% 166s C2.faa 1 3.12% 166s 166s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 166s 166s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 166s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 166s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 166s 166s 166s Clustering by gene-order (POFF mode) 166s Reading test_synteny.ffadj-graph 166s 5 species 166s 106 paired proteins 166s 106 bidirectional edges 167s 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 (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 (28@lapack* + 0@power) connected components Clustering: working on (27@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 (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 Reading test_synteny.ffadj-graph 167s 5 species 167s 106 paired proteins 167s 106 bidirectional edges 168s 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 (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 (28@lapack* + 0@power) connected components Clustering: working on (27@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 (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 168s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 168s You can extract the fasta files of each orthology group with 168s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/E.faa' 'test/C_clean.faa' 'test/M.faa' 'test/C2.faa' 'test/L.faa' 168s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 168s Adding singles... 168s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 168s # test_synteny.poff.tsv statistics: 168s # number of groups that contains at least p% species: 168s # p species groups genes in groups 168s 0% 0 195 (100%) 262 (100%) 168s 20% 1 195 (100%) 262 (100%) 168s 40% 2 38 (19.48%) 105 (40.07%) 168s 60% 3 17 (8.71%) 63 (24.04%) 168s 80% 4 10 (5.12%) 42 (16.03%) 168s 100% 5 1 (0.51%) 5 (1.9%) 168s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 168s # groups that contains only one species: 168s single 5 157 (80.51%) 157 (59.92%) 168s # number of groups for each input species: 168s L.faa 37 97.36% 168s M.faa 37 97.36% 168s E.faa 15 39.47% 168s C_clean.faa 14 36.84% 168s C2.faa 1 2.63% 168s 168s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 168s 168s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 168s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 168s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 168s 168s All finished. 168s ***************************************************************** 168s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 168s ***************************************************************** 168s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 168s Checking input files. 168s Checking test/C_clean.faa... ok 168s Checking test/C2.faa... ok 168s Checking test/E.faa... ok 168s Checking test/L.faa... ok 168s Checking test/M.faa... ok 168s 168s **Step 1** 168s Generating indices anyway (forced). 168s Building database for 'test/M.faa' (40 sequences) 168s Generating indices anyway (forced). 168s Building database for 'test/C2.faa' (2 sequences) 168s Generating indices anyway (forced). 168s Building database for 'test/L.faa' (40 sequences) 168s Generating indices anyway (forced). 168s Building database for 'test/C_clean.faa' (109 sequences) 168s Generating indices anyway (forced). 168s Building database for 'test/E.faa' (72 sequences) 168s 168s **Step 2** using diamond 177s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 177s [OUTPUT] -> written to test_diamond.blast-graph 177s 177s **Step 3** 177s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 177s Reading test_diamond.blast-graph 177s 5 species 177s 113 paired proteins 177s 147 bidirectional edges 178s 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 (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 (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 178s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 178s You can extract the fasta files of each orthology group with 178s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/M.faa' 'test/C2.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 178s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 178s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 178s # test_diamond.proteinortho.tsv statistics: 178s # number of groups that contains at least p% species: 178s # p species groups genes in groups 178s 0% 0 32 (100%) 112 (100%) 178s 20% 1 32 (100%) 112 (100%) 178s 40% 2 32 (100%) 112 (100%) 178s 60% 3 17 (53.12%) 76 (67.85%) 178s 80% 4 11 (34.37%) 53 (47.32%) 178s 100% 5 1 (3.12%) 5 (4.46%) 178s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 178s # number of groups for each input species: 178s L.faa 32 100% 178s M.faa 32 100% 178s E.faa 15 46.87% 178s C_clean.faa 13 40.62% 178s C2.faa 1 3.12% 178s 178s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 178s 178s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 178s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 178s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 178s 178s All finished. 178s ***************************************************************** 178s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 178s ***************************************************************** 178s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 178s Checking input files. 178s Checking test/C_clean.faa... ok 178s Checking test/C2.faa... ok 178s Checking test/E.faa... ok 178s Checking test/L.faa... ok 178s Checking test/M.faa... ok 178s 178s **Step 1** 178s Generating indices anyway (forced). 178s Building database for 'test/C2.faa' (2 sequences) 178s Generating indices anyway (forced). 178s Building database for 'test/E.faa' (72 sequences) 178s Generating indices anyway (forced). 178s Building database for 'test/M.faa' (40 sequences) 178s Generating indices anyway (forced). 178s Building database for 'test/C_clean.faa' (109 sequences) 178s Generating indices anyway (forced). 178s Building database for 'test/L.faa' (40 sequences) 178s 178s **Step 2** using diamond 188s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 188s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 188s 188s **Step 3** 188s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 188s Reading test_diamondmoresensitive.blast-graph 188s 5 species 188s 112 paired proteins 188s 145 bidirectional edges 189s 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 (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 189s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 189s You can extract the fasta files of each orthology group with 189s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/C2.faa' 'test/E.faa' 'test/M.faa' 'test/C_clean.faa' 'test/L.faa' 189s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 189s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 189s # test_diamondmoresensitive.proteinortho.tsv statistics: 189s # number of groups that contains at least p% species: 189s # p species groups genes in groups 189s 0% 0 32 (100%) 111 (100%) 189s 20% 1 32 (100%) 111 (100%) 189s 40% 2 32 (100%) 111 (100%) 189s 60% 3 17 (53.12%) 75 (67.56%) 189s 80% 4 11 (34.37%) 52 (46.84%) 189s 100% 5 1 (3.12%) 5 (4.5%) 189s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 189s # number of groups for each input species: 189s L.faa 32 100% 189s M.faa 32 100% 189s E.faa 15 46.87% 189s C_clean.faa 13 40.62% 189s C2.faa 1 3.12% 189s 189s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 189s 189s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 189s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 189s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 189s 189s All finished. 189s ***************************************************************** 189s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 189s ***************************************************************** 189s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 189s Checking input files. 189s Checking test/C_clean.faa... ok 189s Checking test/C2.faa... ok 189s Checking test/E.faa... ok 189s Checking test/L.faa... ok 189s Checking test/M.faa... ok 189s 189s **Step 1** 189s Generating indices anyway (forced). 189s Building database for 'test/C_clean.faa' (109 sequences) 189s Generating indices anyway (forced). 189s Building database for 'test/M.faa' (40 sequences) 189s Generating indices anyway (forced). 189s Building database for 'test/L.faa' (40 sequences) 189s Generating indices anyway (forced). 189s Building database for 'test/E.faa' (72 sequences) 189s Generating indices anyway (forced). 189s Building database for 'test/C2.faa' (2 sequences) 189s 189s **Step 2** using blastp+ 194s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 194s [OUTPUT] -> written to test_blastall.blast-graph 194s 194s **Step 3** 194s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 194s Reading test_blastall.blast-graph 194s 5 species 194s 112 paired proteins 194s 147 bidirectional edges 195s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 195s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 195s You can extract the fasta files of each orthology group with 195s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C_clean.faa' 'test/M.faa' 'test/L.faa' 'test/E.faa' 'test/C2.faa' 195s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 195s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 195s # test_blastall.proteinortho.tsv statistics: 195s # number of groups that contains at least p% species: 195s # p species groups genes in groups 195s 0% 0 32 (100%) 112 (100%) 195s 20% 1 32 (100%) 112 (100%) 195s 40% 2 32 (100%) 112 (100%) 195s 60% 3 17 (53.12%) 74 (66.07%) 195s 80% 4 11 (34.37%) 51 (45.53%) 195s 100% 5 1 (3.12%) 5 (4.46%) 195s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 195s # number of groups for each input species: 195s L.faa 32 100% 195s M.faa 32 100% 195s E.faa 15 46.87% 195s C_clean.faa 13 40.62% 195s C2.faa 1 3.12% 195s 195s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 195s 195s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 195s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 195s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 195s 195s All finished. 195s - test max_of_diag() : OK 195s - test generate_random_vector() : OK 195s - test get_new_x() : OK 195s - test makeOrthogonal() : OK 195s - test normalize() : OK 195s - test getY() : OK 195s - test lapack() : OK 195s - test power() : OK 195s - test smirnov-grubb() : OK 195s All test passed. 195s Reading test_blastp.blast-graph 195s 5 species 195s 112 paired proteins 195s 147 bidirectional edges 195s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 195s 5 5 1 C_10 C_10;test E_10 L_10 M_10 195s 4 4 1 * C_11 E_11 L_11 M_11 195s 4 6 0.149 * C_12,C_21 E_313,E_315 L_313 M_313 195s 4 4 1 * C_14 E_14 L_14 M_14 195s 4 4 1 * C_15 E_15 L_15 M_15 195s 4 4 1 * C_16 E_16 L_16 M_16 195s 4 4 1 * C_17 E_17 L_17 M_17 195s 4 4 1 * C_64 E_18 L_18 M_18 195s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 195s 3 3 1 * C_20 * L_20 M_20 195s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 195s 2 2 1 * * * L_619 M_619 195s 3 3 0.33 * * E_367 L_319 M_319 195s 2 2 1 * * * L_617 M_617 195s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 195s 2 4 0.5 * * * L_645,L_647 M_644,M_646 195s 3 3 0.33 * * E_432 L_328 M_328 195s 2 2 1 * * * L_333 M_333 195s 2 2 1 * * * L_3 M_3 195s 2 2 1 * * * L_4 M_4 195s 2 2 1 * * * L_5 M_5 195s 2 2 1 * * * L_6 M_6 195s 2 2 1 * * * L_8 M_8 195s 2 2 1 * * * L_9 M_9 195s 2 2 1 * * * L_623 M_623 195s 4 4 1 * C_13 E_13 L_621 M_621 195s 2 4 0.146 * * * L_637,L_639 M_636,M_638 195s 3 3 0.33 * * E_437 L_317 M_317 195s 2 3 0.33 * * * L_631,L_633 M_632 195s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 195s 2 2 1 * * * L_331 M_331 195s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 195s Reading test_blastp.blast-graph 196s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 196s 5 species 196s 112 paired proteins 196s 147 bidirectional edges 197s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 1@power) connected components Clustering: working on (13@lapack* + 2@power) connected components Clustering: working on (12@lapack* + 3@power) connected components Clustering: working on (11@lapack* + 4@power) connected components Clustering: working on (10@lapack* + 5@power) connected components Clustering: working on (9@lapack* + 6@power) connected components Clustering: working on (8@lapack* + 7@power) connected components Clustering: working on (7@lapack* + 8@power) connected components Clustering: working on (6@lapack* + 9@power) connected components Clustering: working on (5@lapack* + 10@power) connected components Clustering: working on (4@lapack* + 11@power) connected components Clustering: working on (3@lapack* + 12@power) connected components Clustering: working on (2@lapack* + 13@power) connected components Clustering: working on (0@lapack + 15@power*) connected components Clustering: working on (0@lapack + 14@power*) connected components Clustering: working on (0@lapack + 13@power*) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (3@lapack* + 10@power) connected components Clustering: working on (2@lapack* + 10@power) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (0@lapack + 11@power*) connected components Clustering: working on (0@lapack + 10@power*) connected components Clustering: working on (0@lapack + 9@power*) connected components Clustering: working on (0@lapack + 8@power*) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (4@lapack* + 4@power) connected components Clustering: working on (3@lapack* + 4@power) connected components Clustering: working on (2@lapack* + 5@power) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (0@lapack + 5@power*) connected components Clustering: working on (0@lapack + 4@power*) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components 3 3 1 * C_20 * L_20 M_20 197s 2 2 1 * * * L_619 M_619 197s 3 3 0.33 * * E_367 L_319 M_319 197s 2 2 1 * * * L_617 M_617 197s 3 3 0.33 * * E_432 L_328 M_328 197s 2 2 1 * * * L_333 M_333 197s 2 2 1 * * * L_3 M_3 197s 2 2 1 * * * L_4 M_4 197s 2 2 1 * * * L_5 M_5 197s 2 2 1 * * * L_6 M_6 197s 2 2 1 * * * L_8 M_8 197s 2 2 1 * * * L_9 M_9 197s 5 5 0.687 C_10 C_10;test E_10 L_10 M_10 197s 4 4 0.727 * C_11 E_11 L_11 M_11 197s 4 6 0.137 * C_12,C_21 E_313,E_315 L_313 M_313 197s 2 2 1 * * * L_623 M_623 197s 4 4 0.74 * C_14 E_14 L_14 M_14 197s 4 4 0.814 * C_15 E_15 L_15 M_15 197s 4 4 0.815 * C_16 E_16 L_16 M_16 197s 4 4 0.824 * C_17 E_17 L_17 M_17 197s 4 4 0.779 * C_64 E_18 L_18 M_18 197s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 197s 3 3 0.33 * * E_437 L_317 M_317 197s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 197s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 197s 2 4 0.478 * * * L_645,L_647 M_644,M_646 197s 4 4 0.717 * C_13 E_13 L_621 M_621 197s 2 4 0.145 * * * L_637,L_639 M_636,M_638 197s 2 2 1 * * * L_331 M_331 197s 2 3 0.33 * * * L_631,L_633 M_632 197s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 197s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 197s Test okay 197s autopkgtest [19:05:22]: test run-unit-test: -----------------------] 197s autopkgtest [19:05:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 197s run-unit-test PASS 198s autopkgtest [19:05:23]: @@@@@@@@@@@@@@@@@@@@ summary 198s run-unit-test PASS 209s Creating nova instance adt-noble-s390x-proteinortho-20240320-190205-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240320.img (UUID 6569a0ff-4984-4a4c-a4d0-b93f21cb5de9)...