0s autopkgtest [11:56:41]: starting date: 2024-03-13 0s autopkgtest [11:56:41]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [11:56:41]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u5b60brz/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@bos01-ppc64el-6.secgroup --name adt-noble-ppc64el-proteinortho-20240313-115641-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-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://us.ports.ubuntu.com/ubuntu-ports/ 112s autopkgtest [11:58:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 112s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 113s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 113s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [448 kB] 113s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2754 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [40.4 kB] 113s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [594 kB] 113s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 113s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 113s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 113s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3111 kB] 114s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 114s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [39.1 kB] 114s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 116s Fetched 7121 kB in 2s (3235 kB/s) 116s Reading package lists... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 122s Calculating upgrade... 122s The following packages were automatically installed and are no longer required: 122s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 122s Use 'sudo apt autoremove' to remove them. 122s The following packages will be REMOVED: 122s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 122s The following NEW packages will be installed: 122s libgdbm-compat4t64 libgdbm6t64 122s The following packages have been kept back: 122s libperl5.38 122s The following packages will be upgraded: 122s cloud-init gdisk perl-base perl-modules-5.38 122s 4 upgraded, 2 newly installed, 5 to remove and 1 not upgraded. 122s Need to get 5932 kB of archives. 122s After this operation, 4151 kB disk space will be freed. 122s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-base ppc64el 5.38.2-3.2 [1916 kB] 122s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm6t64 ppc64el 1.23-5.1 [41.9 kB] 122s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm-compat4t64 ppc64el 1.23-5.1 [6972 B] 122s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 123s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.1-0ubuntu1 [597 kB] 123s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el gdisk ppc64el 1.0.10-1 [260 kB] 123s Preconfiguring packages ... 123s Fetched 5932 kB in 1s (7257 kB/s) 123s (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 ... 70112 files and directories currently installed.) 123s Removing dpkg-dev (1.22.4ubuntu5) ... 123s Removing libdpkg-perl (1.22.4ubuntu5) ... 123s Removing perl (5.38.2-3) ... 123s (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 ... 69531 files and directories currently installed.) 123s Preparing to unpack .../perl-base_5.38.2-3.2_ppc64el.deb ... 123s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 123s Setting up perl-base (5.38.2-3.2) ... 123s dpkg: libgdbm6:ppc64el: dependency problems, but removing anyway as you requested: 123s python3-gdbm:ppc64el depends on libgdbm6 (>= 1.16). 123s man-db depends on libgdbm6 (>= 1.16). 123s libperl5.38:ppc64el depends on libgdbm6 (>= 1.21). 123s libgdbm-compat4:ppc64el depends on libgdbm6 (>= 1.16). 123s 124s (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 ... 69531 files and directories currently installed.) 124s Removing libgdbm6:ppc64el (1.23-5) ... 124s Selecting previously unselected package libgdbm6t64:ppc64el. 124s (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 ... 69526 files and directories currently installed.) 124s Preparing to unpack .../libgdbm6t64_1.23-5.1_ppc64el.deb ... 124s Unpacking libgdbm6t64:ppc64el (1.23-5.1) ... 124s dpkg: libgdbm-compat4:ppc64el: dependency problems, but removing anyway as you requested: 124s libperl5.38:ppc64el depends on libgdbm-compat4 (>= 1.18-3). 124s 124s (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 ... 69532 files and directories currently installed.) 124s Removing libgdbm-compat4:ppc64el (1.23-5) ... 124s Selecting previously unselected package libgdbm-compat4t64:ppc64el. 124s (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 ... 69527 files and directories currently installed.) 124s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_ppc64el.deb ... 124s Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1) ... 124s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 124s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 124s Preparing to unpack .../cloud-init_24.1.1-0ubuntu1_all.deb ... 124s Unpacking cloud-init (24.1.1-0ubuntu1) over (24.1-0ubuntu1) ... 124s Preparing to unpack .../gdisk_1.0.10-1_ppc64el.deb ... 124s Unpacking gdisk (1.0.10-1) over (1.0.9-2.1) ... 124s Setting up cloud-init (24.1.1-0ubuntu1) ... 126s Setting up libgdbm6t64:ppc64el (1.23-5.1) ... 126s Setting up libgdbm-compat4t64:ppc64el (1.23-5.1) ... 126s Setting up gdisk (1.0.10-1) ... 126s Setting up perl-modules-5.38 (5.38.2-3.2) ... 126s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 126s Processing triggers for man-db (2.12.0-3) ... 127s Processing triggers for libc-bin (2.39-0ubuntu2) ... 127s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 127s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 127s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s The following packages will be REMOVED: 128s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 128s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. 128s After this operation, 53.0 MB disk space will be freed. 128s (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 ... 69533 files and directories currently installed.) 128s Removing libperl5.38:ppc64el (5.38.2-3) ... 128s Removing libgdbm-compat4t64:ppc64el (1.23-5.1) ... 128s Removing lto-disabled-list (47) ... 128s Removing make (4.3-4.1build1) ... 128s Removing perl-modules-5.38 (5.38.2-3.2) ... 128s Processing triggers for man-db (2.12.0-3) ... 128s Processing triggers for libc-bin (2.39-0ubuntu2) ... 129s sh: Attempting to set up Debian/Ubuntu apt sources automatically 129s sh: Distribution appears to be Ubuntu 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s eatmydata is already the newest version (131-1). 130s dbus is already the newest version (1.14.10-4ubuntu1). 130s dbus set to manually installed. 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s rng-tools-debian is already the newest version (2.4). 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s haveged is already the newest version (1.9.14-1ubuntu1). 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s The following additional packages will be installed: 131s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 131s make perl perl-modules-5.38 131s Suggested packages: 131s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 131s libterm-readline-gnu-perl | libterm-readline-perl-perl 131s libtap-harness-archive-perl 131s Recommended packages: 131s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 131s libfile-fcntllock-perl 131s The following packages will be REMOVED: 131s libdb5.3 131s The following NEW packages will be installed: 131s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 131s lto-disabled-list make perl perl-modules-5.38 131s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 131s Need to get 7626 kB/10.7 MB of archives. 131s After this operation, 57.2 MB of additional disk space will be used. 131s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdb5.3t64 ppc64el 5.3.28+dfsg2-5build1 [868 kB] 132s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libperl5.38t64 ppc64el 5.38.2-3.2 [4957 kB] 132s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl ppc64el 5.38.2-3.2 [231 kB] 132s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdpkg-perl all 1.22.4ubuntu5 [268 kB] 132s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el make ppc64el 4.3-4.1build1 [211 kB] 132s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el lto-disabled-list all 47 [12.4 kB] 132s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el dpkg-dev all 1.22.4ubuntu5 [1078 kB] 133s Fetched 7626 kB in 1s (7285 kB/s) 133s dpkg: libdb5.3:ppc64el: dependency problems, but removing anyway as you requested: 133s libsasl2-modules-db:ppc64el depends on libdb5.3. 133s libpython3.12-stdlib:ppc64el depends on libdb5.3. 133s libpython3.11-stdlib:ppc64el depends on libdb5.3. 133s libpam-modules:ppc64el depends on libdb5.3. 133s iproute2 depends on libdb5.3. 133s apt-utils depends on libdb5.3. 133s 133s (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 ... 67568 files and directories currently installed.) 133s Removing libdb5.3:ppc64el (5.3.28+dfsg2-4) ... 133s Selecting previously unselected package libdb5.3t64:ppc64el. 133s (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 ... 67562 files and directories currently installed.) 133s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5build1_ppc64el.deb ... 133s Unpacking libdb5.3t64:ppc64el (5.3.28+dfsg2-5build1) ... 133s Setting up libdb5.3t64:ppc64el (5.3.28+dfsg2-5build1) ... 133s Selecting previously unselected package perl-modules-5.38. 133s (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 ... 67568 files and directories currently installed.) 133s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 133s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 133s Selecting previously unselected package libgdbm-compat4t64:ppc64el. 133s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_ppc64el.deb ... 133s Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1) ... 133s Selecting previously unselected package libperl5.38t64:ppc64el. 133s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_ppc64el.deb ... 133s Unpacking libperl5.38t64:ppc64el (5.38.2-3.2) ... 134s Selecting previously unselected package perl. 134s Preparing to unpack .../3-perl_5.38.2-3.2_ppc64el.deb ... 134s Unpacking perl (5.38.2-3.2) ... 134s Selecting previously unselected package libdpkg-perl. 134s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 134s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 134s Selecting previously unselected package make. 134s Preparing to unpack .../5-make_4.3-4.1build1_ppc64el.deb ... 134s Unpacking make (4.3-4.1build1) ... 134s Selecting previously unselected package lto-disabled-list. 134s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 134s Unpacking lto-disabled-list (47) ... 134s Selecting previously unselected package dpkg-dev. 134s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 134s Unpacking dpkg-dev (1.22.4ubuntu5) ... 134s Setting up lto-disabled-list (47) ... 134s Setting up libgdbm-compat4t64:ppc64el (1.23-5.1) ... 134s Setting up make (4.3-4.1build1) ... 134s Setting up perl-modules-5.38 (5.38.2-3.2) ... 134s Setting up libperl5.38t64:ppc64el (5.38.2-3.2) ... 134s Setting up perl (5.38.2-3.2) ... 134s Setting up libdpkg-perl (1.22.4ubuntu5) ... 134s Setting up dpkg-dev (1.22.4ubuntu5) ... 134s Processing triggers for man-db (2.12.0-3) ... 135s Processing triggers for libc-bin (2.39-0ubuntu2) ... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s The following packages will be REMOVED: 139s cloud-init* python3-configobj* python3-debconf* 139s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 139s After this operation, 3252 kB disk space will be freed. 139s (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 ... 70114 files and directories currently installed.) 139s Removing cloud-init (24.1.1-0ubuntu1) ... 139s Removing python3-configobj (5.0.8-3) ... 139s Removing python3-debconf (1.5.86) ... 139s Processing triggers for man-db (2.12.0-3) ... 140s (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 ... 69725 files and directories currently installed.) 140s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 140s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 140s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s linux-generic is already the newest version (6.8.0-11.11+1). 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 142s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 142s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 142s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 142s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 146s Reading package lists... 146s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 146s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Calculating upgrade... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s autopkgtest [11:59:08]: rebooting testbed after setup commands that affected boot 306s autopkgtest [12:01:47]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 306s autopkgtest [12:01:47]: testbed dpkg architecture: ppc64el 307s autopkgtest [12:01:48]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 308s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 308s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 308s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 309s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 309s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 309s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 309s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 309s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 309s gpgv: issuer "tille@debian.org" 309s gpgv: Can't check signature: No public key 309s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 309s autopkgtest [12:01:50]: testing package proteinortho version 6.3.1+dfsg-1 309s autopkgtest [12:01:50]: build not needed 310s autopkgtest [12:01:51]: test run-unit-test: preparing testbed 314s Reading package lists... 314s Building dependency tree... 314s Reading state information... 314s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 314s Starting 2 pkgProblemResolver with broken count: 0 314s Done 314s Done 314s Starting pkgProblemResolver with broken count: 0 314s Starting 2 pkgProblemResolver with broken count: 0 314s Done 315s The following additional packages will be installed: 315s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 315s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 315s Recommended packages: 315s med-config 315s The following NEW packages will be installed: 315s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 315s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 315s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 315s 1 not fully installed or removed. 315s Need to get 24.3 MB of archives. 315s After this operation, 103 MB of additional disk space will be used. 315s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 315s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 315s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 315s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 316s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 316s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedcrypto7 ppc64el 2.28.7-1ubuntu1 [262 kB] 316s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedx509-1 ppc64el 2.28.7-1ubuntu1 [51.4 kB] 316s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedtls14 ppc64el 2.28.7-1ubuntu1 [89.7 kB] 316s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-blast+ ppc64el 2.12.0+ds-4 [13.4 MB] 316s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el diamond-aligner ppc64el 2.1.9-1 [1959 kB] 317s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el proteinortho ppc64el 6.3.1+dfsg-1 [374 kB] 317s Fetched 24.3 MB in 2s (13.8 MB/s) 317s Selecting previously unselected package libgomp1:ppc64el. 317s (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 ... 69670 files and directories currently installed.) 317s Preparing to unpack .../00-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 317s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 317s Selecting previously unselected package libblas3:ppc64el. 317s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ... 317s Unpacking libblas3:ppc64el (3.12.0-3) ... 317s Selecting previously unselected package libgfortran5:ppc64el. 317s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 317s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 317s Selecting previously unselected package liblapack3:ppc64el. 317s Preparing to unpack .../03-liblapack3_3.12.0-3_ppc64el.deb ... 317s Unpacking liblapack3:ppc64el (3.12.0-3) ... 317s Selecting previously unselected package ncbi-data. 317s Preparing to unpack .../04-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 317s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 317s Selecting previously unselected package libmbedcrypto7:ppc64el. 317s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_ppc64el.deb ... 317s Unpacking libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 317s Selecting previously unselected package libmbedx509-1:ppc64el. 317s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_ppc64el.deb ... 317s Unpacking libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 317s Selecting previously unselected package libmbedtls14:ppc64el. 317s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_ppc64el.deb ... 317s Unpacking libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 317s Selecting previously unselected package ncbi-blast+. 317s Preparing to unpack .../08-ncbi-blast+_2.12.0+ds-4_ppc64el.deb ... 317s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 318s Selecting previously unselected package diamond-aligner. 318s Preparing to unpack .../09-diamond-aligner_2.1.9-1_ppc64el.deb ... 318s Unpacking diamond-aligner (2.1.9-1) ... 318s Selecting previously unselected package proteinortho. 318s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_ppc64el.deb ... 318s Unpacking proteinortho (6.3.1+dfsg-1) ... 318s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 318s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 318s Setting up diamond-aligner (2.1.9-1) ... 318s Setting up libblas3:ppc64el (3.12.0-3) ... 318s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 318s Setting up libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 318s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 318s Setting up liblapack3:ppc64el (3.12.0-3) ... 318s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 318s Setting up libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 318s Setting up libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 318s Setting up ncbi-blast+ (2.12.0+ds-4) ... 318s Setting up proteinortho (6.3.1+dfsg-1) ... 318s Setting up autopkgtest-satdep (0) ... 318s Processing triggers for man-db (2.12.0-3) ... 318s Processing triggers for libc-bin (2.39-0ubuntu2) ... 321s (Reading database ... 70004 files and directories currently installed.) 321s Removing autopkgtest-satdep (0) ... 322s autopkgtest [12:02:03]: test run-unit-test: [----------------------- 322s ***************************************************************** 322s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 322s ***************************************************************** 322s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 322s Checking input files. 322s Checking input files. 322s Checking test/C_clean.faa... ok 322s Checking test/C2.faa... ok 322s Checking test/E.faa... ok 322s Checking test/L.faa... ok 322s Checking test/M.faa... ok 322s Checking test/C.faa... 322s  [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 !!! 322s The line is: 322s C_10,test 322s ok 322s Checking test/C_clean.faa... ok 322s Checking test/E.faa... ok 322s Checking test/M.faa... ok 322s Checking test/L.faa... ok 322s 322s **Step 1** 322s Generating indices anyway (forced). 322s Building database for 'test/E.faa' (144 sequences) 322s Generating indices anyway (forced). 322s Building database for 'test/C_clean.faa' (218 sequences) 322s Generating indices anyway (forced). 322s Building database for 'test/L.faa' (80 sequences) 322s Generating indices anyway (forced). 322s Building database for 'test/M.faa' (80 sequences) 322s Generating indices anyway (forced). 322s Building database for 'test/C2.faa' (2 sequences) 322s 322s **Step 2** using blastp+ 328s 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) 328s [OUTPUT] -> written to test_blastp.blast-graph 328s 328s **Step 3** 328s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 328s Reading test_blastp.blast-graph 328s 5 species 328s 112 paired proteins 328s 149 bidirectional edges 329s 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 329s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 329s You can extract the fasta files of each orthology group with 329s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/E.faa' 'test/C_clean.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa' 329s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 329s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 329s # test_blastp.proteinortho.tsv statistics: 329s # number of groups that contains at least p% species: 329s # p species groups genes in groups 329s 0% 0 32 (100%) 112 (100%) 329s 20% 1 32 (100%) 112 (100%) 329s 40% 2 32 (100%) 112 (100%) 329s 60% 3 17 (53.12%) 74 (66.07%) 329s 80% 4 11 (34.37%) 51 (45.53%) 329s 100% 5 1 (3.12%) 5 (4.46%) 329s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 329s # number of groups for each input species: 329s L.faa 32 100% 329s M.faa 32 100% 329s E.faa 15 46.87% 329s C_clean.faa 13 40.62% 329s C2.faa 1 3.12% 329s 329s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 329s 329s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 329s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 329s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 329s 329s All finished. 329s ***************************************************************** 329s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 329s ***************************************************************** 329s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 329s Checking input files. 329s Checking test/C_clean.faa... ok 329s Checking test/C2.faa... ok 329s Checking test/E.faa... ok 329s Checking test/L.faa... ok 329s Checking test/M.faa... ok 329s 329s **Step 1** 329s Generating indices anyway (forced). 329s Building database for 'test/L.faa' (40 sequences) 329s Generating indices anyway (forced). 329s Building database for 'test/E.faa' (72 sequences) 329s Generating indices anyway (forced). 329s Building database for 'test/C2.faa' (2 sequences) 329s Generating indices anyway (forced). 329s Building database for 'test/C_clean.faa' (109 sequences) 329s Generating indices anyway (forced). 329s Building database for 'test/M.faa' (40 sequences) 329s 329s **Step 2** using blastp+ with : synteny 337s 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) 337s [OUTPUT] -> written to test_synteny.blast-graph 337s 337s **Step 3** 337s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 337s Reading test_synteny.blast-graph 337s 5 species 337s 112 paired proteins 337s 149 bidirectional edges 338s 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 338s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 338s You can extract the fasta files of each orthology group with 338s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/L.faa' 'test/E.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/M.faa' 338s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 338s Adding singles... 338s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 338s # test_synteny.proteinortho.tsv statistics: 338s # number of groups that contains at least p% species: 338s # p species groups genes in groups 338s 0% 0 182 (100%) 262 (100%) 338s 20% 1 182 (100%) 262 (100%) 338s 40% 2 32 (17.58%) 112 (42.74%) 338s 60% 3 17 (9.34%) 74 (28.24%) 338s 80% 4 11 (6.04%) 51 (19.46%) 338s 100% 5 1 (0.54%) 5 (1.9%) 338s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 338s # groups that contains only one species: 338s single 5 150 (82.41%) 150 (57.25%) 338s # number of groups for each input species: 338s L.faa 32 100% 338s M.faa 32 100% 338s E.faa 15 46.87% 338s C_clean.faa 13 40.62% 338s C2.faa 1 3.12% 338s 338s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 338s 338s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 338s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 338s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 338s 338s 338s Clustering by gene-order (POFF mode) 338s Reading test_synteny.ffadj-graph 338s 5 species 338s 106 paired proteins 338s 106 bidirectional edges 339s 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 (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (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 339s 5 species 339s 106 paired proteins 339s 106 bidirectional edges 340s 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 (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (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 340s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 340s You can extract the fasta files of each orthology group with 340s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/L.faa' 'test/E.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/M.faa' 340s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 340s Adding singles... 340s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 340s # test_synteny.poff.tsv statistics: 340s # number of groups that contains at least p% species: 340s # p species groups genes in groups 340s 0% 0 195 (100%) 262 (100%) 340s 20% 1 195 (100%) 262 (100%) 340s 40% 2 38 (19.48%) 105 (40.07%) 340s 60% 3 17 (8.71%) 63 (24.04%) 340s 80% 4 10 (5.12%) 42 (16.03%) 340s 100% 5 1 (0.51%) 5 (1.9%) 340s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 340s # groups that contains only one species: 340s single 5 157 (80.51%) 157 (59.92%) 340s # number of groups for each input species: 340s L.faa 37 97.36% 340s M.faa 37 97.36% 340s E.faa 15 39.47% 340s C_clean.faa 14 36.84% 340s C2.faa 1 2.63% 340s 340s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 340s 340s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 340s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 340s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 340s 340s All finished. 340s ***************************************************************** 340s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 340s ***************************************************************** 340s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 340s Checking input files. 340s Checking test/C_clean.faa... ok 340s Checking test/C2.faa... ok 340s Checking test/E.faa... ok 340s Checking test/L.faa... ok 340s Checking test/M.faa... ok 340s 340s **Step 1** 340s Generating indices anyway (forced). 340s Building database for 'test/L.faa' (40 sequences) 340s Generating indices anyway (forced). 340s Building database for 'test/C_clean.faa' (109 sequences) 340s Generating indices anyway (forced). 340s Building database for 'test/E.faa' (72 sequences) 340s Generating indices anyway (forced). 340s Building database for 'test/M.faa' (40 sequences) 340s Generating indices anyway (forced). 340s Building database for 'test/C2.faa' (2 sequences) 340s 340s **Step 2** using diamond 348s 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) 348s [OUTPUT] -> written to test_diamond.blast-graph 348s 348s **Step 3** 348s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 348s Reading test_diamond.blast-graph 349s 5 species 349s 113 paired proteins 349s 147 bidirectional edges 350s 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 (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 350s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 350s You can extract the fasta files of each orthology group with 350s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 'test/M.faa' 'test/C2.faa' 350s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 350s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 350s # test_diamond.proteinortho.tsv statistics: 350s # number of groups that contains at least p% species: 350s # p species groups genes in groups 350s 0% 0 32 (100%) 112 (100%) 350s 20% 1 32 (100%) 112 (100%) 350s 40% 2 32 (100%) 112 (100%) 350s 60% 3 17 (53.12%) 76 (67.85%) 350s 80% 4 11 (34.37%) 53 (47.32%) 350s 100% 5 1 (3.12%) 5 (4.46%) 350s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 350s # number of groups for each input species: 350s L.faa 32 100% 350s M.faa 32 100% 350s E.faa 15 46.87% 350s C_clean.faa 13 40.62% 350s C2.faa 1 3.12% 350s 350s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 350s 350s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 350s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 350s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 350s 350s All finished. 350s ***************************************************************** 350s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 350s ***************************************************************** 350s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 350s Checking input files. 350s Checking test/C_clean.faa... ok 350s Checking test/C2.faa... ok 350s Checking test/E.faa... ok 350s Checking test/L.faa... ok 350s Checking test/M.faa... ok 350s 350s **Step 1** 350s Generating indices anyway (forced). 350s Building database for 'test/C2.faa' (2 sequences) 350s Generating indices anyway (forced). 350s Building database for 'test/E.faa' (72 sequences) 350s Generating indices anyway (forced). 350s Building database for 'test/L.faa' (40 sequences) 350s Generating indices anyway (forced). 350s Building database for 'test/C_clean.faa' (109 sequences) 350s Generating indices anyway (forced). 350s Building database for 'test/M.faa' (40 sequences) 350s 350s **Step 2** using diamond 360s 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) 360s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 360s 360s **Step 3** 360s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 360s Reading test_diamondmoresensitive.blast-graph 360s 5 species 360s 112 paired proteins 360s 145 bidirectional edges 361s 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 (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 361s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 361s You can extract the fasta files of each orthology group with 361s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/C2.faa' 'test/E.faa' 'test/L.faa' 'test/C_clean.faa' 'test/M.faa' 361s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 361s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 361s # test_diamondmoresensitive.proteinortho.tsv statistics: 361s # number of groups that contains at least p% species: 361s # p species groups genes in groups 361s 0% 0 32 (100%) 111 (100%) 361s 20% 1 32 (100%) 111 (100%) 361s 40% 2 32 (100%) 111 (100%) 361s 60% 3 17 (53.12%) 75 (67.56%) 361s 80% 4 11 (34.37%) 52 (46.84%) 361s 100% 5 1 (3.12%) 5 (4.5%) 361s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 361s # number of groups for each input species: 361s L.faa 32 100% 361s M.faa 32 100% 361s E.faa 15 46.87% 361s C_clean.faa 13 40.62% 361s C2.faa 1 3.12% 361s 361s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 361s 361s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 361s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 361s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 361s 361s All finished. 362s ***************************************************************** 362s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 362s ***************************************************************** 362s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 362s Checking input files. 362s Checking test/C_clean.faa... ok 362s Checking test/C2.faa... ok 362s Checking test/E.faa... ok 362s Checking test/L.faa... ok 362s Checking test/M.faa... ok 362s 362s **Step 1** 362s Generating indices anyway (forced). 362s Building database for 'test/C2.faa' (2 sequences) 362s Generating indices anyway (forced). 362s Building database for 'test/M.faa' (40 sequences) 362s Generating indices anyway (forced). 362s Building database for 'test/L.faa' (40 sequences) 362s Generating indices anyway (forced). 362s Building database for 'test/C_clean.faa' (109 sequences) 362s Generating indices anyway (forced). 362s Building database for 'test/E.faa' (72 sequences) 362s 362s **Step 2** using blastp+ 368s 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) 368s [OUTPUT] -> written to test_blastall.blast-graph 368s 368s **Step 3** 368s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 368s Reading test_blastall.blast-graph 368s 5 species 368s 112 paired proteins 368s 147 bidirectional edges 369s 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 (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 369s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 369s You can extract the fasta files of each orthology group with 369s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C2.faa' 'test/M.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 369s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 369s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 369s # test_blastall.proteinortho.tsv statistics: 369s # number of groups that contains at least p% species: 369s # p species groups genes in groups 369s 0% 0 32 (100%) 112 (100%) 369s 20% 1 32 (100%) 112 (100%) 369s 40% 2 32 (100%) 112 (100%) 369s 60% 3 17 (53.12%) 74 (66.07%) 369s 80% 4 11 (34.37%) 51 (45.53%) 369s 100% 5 1 (3.12%) 5 (4.46%) 369s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 369s # number of groups for each input species: 369s L.faa 32 100% 369s M.faa 32 100% 369s E.faa 15 46.87% 369s C_clean.faa 13 40.62% 369s C2.faa 1 3.12% 369s 369s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 369s 369s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 369s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 369s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 369s 369s All finished. 369s - test max_of_diag() : OK 369s - test generate_random_vector() : OK 369s - test get_new_x() : OK 369s - test makeOrthogonal() : OK 369s - test normalize() : OK 369s - test getY() : OK 369s - test lapack() : OK 369s - test power() : OK 369s - test smirnov-grubb() : OK 369s All test passed. 369s Reading test_blastp.blast-graph 369s 5 species 369s 112 paired proteins 369s 149 bidirectional edges 369s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 370s 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 5 5 1 C_10 C_10;test E_10 L_10 M_10 370s 4 4 1 * C_11 E_11 L_11 M_11 370s 4 6 0.333 * C_12,C_21 E_313,E_315 L_313 M_313 370s 4 4 1 * C_14 E_14 L_14 M_14 370s 4 4 1 * C_15 E_15 L_15 M_15 370s 4 4 1 * C_16 E_16 L_16 M_16 370s 4 4 1 * C_17 E_17 L_17 M_17 370s 4 4 1 * C_64 E_18 L_18 M_18 370s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 370s 3 3 0.33 * * E_367 L_319 M_319 370s 3 3 0.33 * * E_432 L_328 M_328 370s 3 3 1 * C_20 * L_20 M_20 370s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 370s 2 2 1 * * * L_619 M_619 370s 2 2 1 * * * L_617 M_617 370s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 370s 2 4 0.5 * * * L_645,L_647 M_644,M_646 370s 2 2 1 * * * L_333 M_333 370s 2 2 1 * * * L_3 M_3 370s 2 2 1 * * * L_4 M_4 370s 2 2 1 * * * L_5 M_5 370s 2 2 1 * * * L_6 M_6 370s 2 2 1 * * * L_8 M_8 370s 2 2 1 * * * L_9 M_9 370s 2 2 1 * * * L_623 M_623 370s 4 4 1 * C_13 E_13 L_621 M_621 370s 2 4 0.146 * * * L_637,L_639 M_636,M_638 370s 3 3 0.33 * * E_437 L_317 M_317 370s 2 3 0.33 * * * L_631,L_633 M_632 370s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 370s 2 2 1 * * * L_331 M_331 370s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 370s Reading test_blastp.blast-graph 370s 5 species 370s 112 paired proteins 370s 149 bidirectional edges 370s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 371s 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 371s 3 3 0.33 * * E_432 L_328 M_328 371s 3 3 1 * C_20 * L_20 M_20 371s 2 2 1 * * * L_619 M_619 371s 2 2 1 * * * L_617 M_617 371s 2 2 1 * * * L_333 M_333 371s 2 2 1 * * * L_3 M_3 371s 2 2 1 * * * L_4 M_4 371s 2 2 1 * * * L_5 M_5 371s 2 2 1 * * * L_6 M_6 371s 2 2 1 * * * L_8 M_8 371s 2 2 1 * * * L_9 M_9 371s 5 5 0.694 C_10 C_10;test E_10 L_10 M_10 371s 4 4 0.727 * C_11 E_11 L_11 M_11 371s 4 6 0.297 * C_12,C_21 E_313,E_315 L_313 M_313 371s 2 2 1 * * * L_623 M_623 371s 4 4 0.743 * C_14 E_14 L_14 M_14 371s 4 4 0.818 * C_15 E_15 L_15 M_15 371s 4 4 0.815 * C_16 E_16 L_16 M_16 371s 4 4 0.824 * C_17 E_17 L_17 M_17 371s 4 4 0.777 * C_64 E_18 L_18 M_18 371s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 371s 3 3 0.33 * * E_437 L_317 M_317 371s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 371s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 371s 2 4 0.478 * * * L_645,L_647 M_644,M_646 371s 4 4 0.702 * C_13 E_13 L_621 M_621 371s 2 4 0.145 * * * L_637,L_639 M_636,M_638 371s 2 2 1 * * * L_331 M_331 371s 2 3 0.33 * * * L_631,L_633 M_632 371s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 371s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 371s Test okay 371s autopkgtest [12:02:52]: test run-unit-test: -----------------------] 371s run-unit-test PASS 371s autopkgtest [12:02:52]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 372s autopkgtest [12:02:53]: @@@@@@@@@@@@@@@@@@@@ summary 372s run-unit-test PASS 385s Creating nova instance adt-noble-ppc64el-proteinortho-20240313-115641-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240312.img (UUID 2068c266-b1f4-4468-a3e5-e52b1c42dc85)...