0s autopkgtest [12:14:53]: starting date: 2024-03-13 0s autopkgtest [12:14:53]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [12:14:53]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9h9pzx_h/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 trim-galore --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-2@bos01-ppc64el-9.secgroup --name adt-noble-ppc64el-trim-galore-20240313-121453-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 111s autopkgtest [12:16:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 112s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 112s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2754 kB] 113s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [40.4 kB] 113s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [448 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 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] 113s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 113s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [39.1 kB] 113s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 115s Fetched 7121 kB in 2s (3208 kB/s) 115s Reading package lists... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s The following packages were automatically installed and are no longer required: 121s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 121s Use 'sudo apt autoremove' to remove them. 121s The following packages will be REMOVED: 121s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 121s The following NEW packages will be installed: 121s libgdbm-compat4t64 libgdbm6t64 121s The following packages have been kept back: 121s libperl5.38 121s The following packages will be upgraded: 121s 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] 122s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.1-0ubuntu1 [597 kB] 122s 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 (6950 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 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 Removing libgdbm6:ppc64el (1.23-5) ... 123s Selecting previously unselected package libgdbm6t64:ppc64el. 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 ... 69526 files and directories currently installed.) 123s Preparing to unpack .../libgdbm6t64_1.23-5.1_ppc64el.deb ... 123s Unpacking libgdbm6t64:ppc64el (1.23-5.1) ... 123s dpkg: libgdbm-compat4:ppc64el: dependency problems, but removing anyway as you requested: 123s libperl5.38:ppc64el depends on libgdbm-compat4 (>= 1.18-3). 123s 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 ... 69532 files and directories currently installed.) 123s Removing libgdbm-compat4:ppc64el (1.23-5) ... 123s 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) ... 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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 128s 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) ... 129s Processing triggers for libc-bin (2.39-0ubuntu2) ... 130s sh: Attempting to set up Debian/Ubuntu apt sources automatically 130s sh: Distribution appears to be Ubuntu 130s 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... 131s rng-tools-debian is already the newest version (2.4). 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 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... 132s The following additional packages will be installed: 132s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 132s make perl perl-modules-5.38 132s Suggested packages: 132s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 132s libterm-readline-gnu-perl | libterm-readline-perl-perl 132s libtap-harness-archive-perl 132s Recommended packages: 132s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 132s libfile-fcntllock-perl 132s The following packages will be REMOVED: 132s libdb5.3 132s The following NEW packages will be installed: 132s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 132s lto-disabled-list make perl perl-modules-5.38 132s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 132s Need to get 7626 kB/10.7 MB of archives. 132s After this operation, 57.2 MB of additional disk space will be used. 132s 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 (8351 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) ... 134s Selecting previously unselected package libgdbm-compat4t64:ppc64el. 134s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_ppc64el.deb ... 134s Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1) ... 134s Selecting previously unselected package libperl5.38t64:ppc64el. 134s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_ppc64el.deb ... 134s 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) ... 139s Reading package lists... 139s Building dependency tree... 139s 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. 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 ... 70114 files and directories currently installed.) 140s Removing cloud-init (24.1.1-0ubuntu1) ... 140s Removing python3-configobj (5.0.8-3) ... 140s Removing python3-debconf (1.5.86) ... 140s Processing triggers for man-db (2.12.0-3) ... 141s (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.) 141s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 141s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 141s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s linux-generic is already the newest version (6.8.0-11.11+1). 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 143s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 143s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 143s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 143s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 147s Reading package lists... 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s 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 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Calculating upgrade... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [12:17:21]: rebooting testbed after setup commands that affected boot 305s autopkgtest [12:19:58]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 306s autopkgtest [12:19:59]: testbed dpkg architecture: ppc64el 307s autopkgtest [12:20:00]: @@@@@@@@@@@@@@@@@@@@ apt-source trim-galore 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 310s Get:1 http://ftpmaster.internal/ubuntu noble/universe trim-galore 0.6.10-1 (dsc) [2077 B] 310s Get:2 http://ftpmaster.internal/ubuntu noble/universe trim-galore 0.6.10-1 (tar) [26.8 MB] 310s Get:3 http://ftpmaster.internal/ubuntu noble/universe trim-galore 0.6.10-1 (diff) [10.8 kB] 310s gpgv: Signature made Sun Feb 5 20:28:48 2023 UTC 310s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 310s gpgv: issuer "tille@debian.org" 310s gpgv: Can't check signature: No public key 310s dpkg-source: warning: cannot verify inline signature for ./trim-galore_0.6.10-1.dsc: no acceptable signature found 311s autopkgtest [12:20:04]: testing package trim-galore version 0.6.10-1 311s autopkgtest [12:20:04]: build not needed 313s autopkgtest [12:20:06]: test run-unit-test: preparing testbed 315s Reading package lists... 315s Building dependency tree... 315s Reading state information... 316s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 316s Starting 2 pkgProblemResolver with broken count: 0 316s Done 316s Done 316s Starting pkgProblemResolver with broken count: 0 316s Starting 2 pkgProblemResolver with broken count: 0 316s Done 316s The following additional packages will be installed: 316s build-essential cpp cpp-13 cpp-13-powerpc64le-linux-gnu 316s cpp-powerpc64le-linux-gnu cutadapt g++ g++-13 g++-13-powerpc64le-linux-gnu 316s g++-powerpc64le-linux-gnu gcc gcc-13 gcc-13-powerpc64le-linux-gnu 316s gcc-powerpc64le-linux-gnu libasan8 libatomic1 libc-dev-bin libc6-dev 316s libcc1-0 libcrypt-dev libgcc-13-dev libgomp1 libisl23 libitm1 liblsan0 316s libmpc3 libnsl-dev libquadmath0 libstdc++-13-dev libtirpc-dev libtsan2 316s libubsan1 linux-libc-dev pigz python3-cutadapt python3-dnaio python3-xopen 316s rpcsvc-proto trim-galore 316s Suggested packages: 316s cpp-doc gcc-13-locales cpp-13-doc gcc-13-doc gcc-multilib manpages-dev 316s autoconf automake libtool flex bison gdb gcc-doc gdb-powerpc64le-linux-gnu 316s glibc-doc libstdc++-13-doc 316s Recommended packages: 316s manpages manpages-dev libc-devtools fastqc 316s The following NEW packages will be installed: 316s build-essential cpp cpp-13 cpp-13-powerpc64le-linux-gnu 316s cpp-powerpc64le-linux-gnu cutadapt g++ g++-13 g++-13-powerpc64le-linux-gnu 316s g++-powerpc64le-linux-gnu gcc gcc-13 gcc-13-powerpc64le-linux-gnu 316s gcc-powerpc64le-linux-gnu libasan8 libatomic1 libc-dev-bin libc6-dev 316s libcc1-0 libcrypt-dev libgcc-13-dev libgomp1 libisl23 libitm1 liblsan0 316s libmpc3 libnsl-dev libquadmath0 libstdc++-13-dev libtirpc-dev libtsan2 316s libubsan1 linux-libc-dev pigz python3-cutadapt python3-dnaio python3-xopen 316s rpcsvc-proto trim-galore 316s 0 upgraded, 39 newly installed, 0 to remove and 0 not upgraded. 316s 1 not fully installed or removed. 316s Need to get 80.3 MB of archives. 316s After this operation, 261 MB of additional disk space will be used. 316s Get:1 http://ftpmaster.internal/ubuntu noble/universe ppc64el pigz ppc64el 2.8-1 [76.3 kB] 317s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-xopen all 1.7.0-2 [17.0 kB] 317s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-dnaio ppc64el 1.0.1-1build1 [93.5 kB] 317s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-cutadapt ppc64el 4.4-1build1 [362 kB] 317s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el cutadapt all 4.4-1build1 [6776 B] 317s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el trim-galore all 0.6.10-1 [17.8 MB] 318s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu2 [21.3 kB] 318s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-11.11 [1585 kB] 318s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 318s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1build1 [262 kB] 318s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libnsl-dev ppc64el 1.3.0-3 [79.2 kB] 318s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 318s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu2 [2102 kB] 318s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libisl23 ppc64el 0.26-3 [864 kB] 318s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libmpc3 ppc64el 1.3.1-1 [61.2 kB] 318s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [10.7 MB] 318s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13 ppc64el 13.2.0-17ubuntu2 [1038 B] 318s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] 318s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] 318s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libcc1-0 ppc64el 14-20240303-1ubuntu1 [48.1 kB] 318s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 318s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libitm1 ppc64el 14-20240303-1ubuntu1 [32.4 kB] 318s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libatomic1 ppc64el 14-20240303-1ubuntu1 [10.7 kB] 318s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libasan8 ppc64el 14-20240303-1ubuntu1 [2973 kB] 318s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el liblsan0 ppc64el 14-20240303-1ubuntu1 [1325 kB] 318s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libtsan2 ppc64el 14-20240303-1ubuntu1 [2734 kB] 318s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libubsan1 ppc64el 14-20240303-1ubuntu1 [1194 kB] 318s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libquadmath0 ppc64el 14-20240303-1ubuntu1 [158 kB] 318s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcc-13-dev ppc64el 13.2.0-17ubuntu2 [1581 kB] 318s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [20.6 MB] 319s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13 ppc64el 13.2.0-17ubuntu2 [477 kB] 319s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] 319s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] 319s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libstdc++-13-dev ppc64el 13.2.0-17ubuntu2 [2445 kB] 319s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [12.2 MB] 319s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13 ppc64el 13.2.0-17ubuntu2 [14.5 kB] 319s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] 319s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] 319s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 320s Fetched 80.3 MB in 3s (29.1 MB/s) 320s Selecting previously unselected package pigz. 320s (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.) 320s Preparing to unpack .../00-pigz_2.8-1_ppc64el.deb ... 320s Unpacking pigz (2.8-1) ... 320s Selecting previously unselected package python3-xopen. 320s Preparing to unpack .../01-python3-xopen_1.7.0-2_all.deb ... 320s Unpacking python3-xopen (1.7.0-2) ... 320s Selecting previously unselected package python3-dnaio. 320s Preparing to unpack .../02-python3-dnaio_1.0.1-1build1_ppc64el.deb ... 320s Unpacking python3-dnaio (1.0.1-1build1) ... 320s Selecting previously unselected package python3-cutadapt. 320s Preparing to unpack .../03-python3-cutadapt_4.4-1build1_ppc64el.deb ... 320s Unpacking python3-cutadapt (4.4-1build1) ... 320s Selecting previously unselected package cutadapt. 320s Preparing to unpack .../04-cutadapt_4.4-1build1_all.deb ... 320s Unpacking cutadapt (4.4-1build1) ... 320s Selecting previously unselected package trim-galore. 320s Preparing to unpack .../05-trim-galore_0.6.10-1_all.deb ... 320s Unpacking trim-galore (0.6.10-1) ... 320s Selecting previously unselected package libc-dev-bin. 320s Preparing to unpack .../06-libc-dev-bin_2.39-0ubuntu2_ppc64el.deb ... 320s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 320s Selecting previously unselected package linux-libc-dev:ppc64el. 320s Preparing to unpack .../07-linux-libc-dev_6.8.0-11.11_ppc64el.deb ... 320s Unpacking linux-libc-dev:ppc64el (6.8.0-11.11) ... 320s Selecting previously unselected package libcrypt-dev:ppc64el. 320s Preparing to unpack .../08-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 320s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 320s Selecting previously unselected package libtirpc-dev:ppc64el. 320s Preparing to unpack .../09-libtirpc-dev_1.3.4+ds-1build1_ppc64el.deb ... 320s Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 320s Selecting previously unselected package libnsl-dev:ppc64el. 320s Preparing to unpack .../10-libnsl-dev_1.3.0-3_ppc64el.deb ... 320s Unpacking libnsl-dev:ppc64el (1.3.0-3) ... 320s Selecting previously unselected package rpcsvc-proto. 320s Preparing to unpack .../11-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 320s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 320s Selecting previously unselected package libc6-dev:ppc64el. 320s Preparing to unpack .../12-libc6-dev_2.39-0ubuntu2_ppc64el.deb ... 320s Unpacking libc6-dev:ppc64el (2.39-0ubuntu2) ... 320s Selecting previously unselected package libisl23:ppc64el. 320s Preparing to unpack .../13-libisl23_0.26-3_ppc64el.deb ... 320s Unpacking libisl23:ppc64el (0.26-3) ... 320s Selecting previously unselected package libmpc3:ppc64el. 320s Preparing to unpack .../14-libmpc3_1.3.1-1_ppc64el.deb ... 320s Unpacking libmpc3:ppc64el (1.3.1-1) ... 320s Selecting previously unselected package cpp-13-powerpc64le-linux-gnu. 320s Preparing to unpack .../15-cpp-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 320s Unpacking cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 321s Selecting previously unselected package cpp-13. 321s Preparing to unpack .../16-cpp-13_13.2.0-17ubuntu2_ppc64el.deb ... 321s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 321s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 321s Preparing to unpack .../17-cpp-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 321s Unpacking cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 321s Selecting previously unselected package cpp. 321s Preparing to unpack .../18-cpp_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 321s Unpacking cpp (4:13.2.0-7ubuntu1) ... 321s Selecting previously unselected package libcc1-0:ppc64el. 321s Preparing to unpack .../19-libcc1-0_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package libgomp1:ppc64el. 321s Preparing to unpack .../20-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package libitm1:ppc64el. 321s Preparing to unpack .../21-libitm1_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking libitm1:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package libatomic1:ppc64el. 321s Preparing to unpack .../22-libatomic1_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking libatomic1:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package libasan8:ppc64el. 321s Preparing to unpack .../23-libasan8_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking libasan8:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package liblsan0:ppc64el. 321s Preparing to unpack .../24-liblsan0_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking liblsan0:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package libtsan2:ppc64el. 321s Preparing to unpack .../25-libtsan2_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking libtsan2:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package libubsan1:ppc64el. 321s Preparing to unpack .../26-libubsan1_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking libubsan1:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package libquadmath0:ppc64el. 321s Preparing to unpack .../27-libquadmath0_14-20240303-1ubuntu1_ppc64el.deb ... 321s Unpacking libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 321s Selecting previously unselected package libgcc-13-dev:ppc64el. 321s Preparing to unpack .../28-libgcc-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 321s Unpacking libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 321s Selecting previously unselected package gcc-13-powerpc64le-linux-gnu. 321s Preparing to unpack .../29-gcc-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 321s Unpacking gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 322s Selecting previously unselected package gcc-13. 322s Preparing to unpack .../30-gcc-13_13.2.0-17ubuntu2_ppc64el.deb ... 322s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 322s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 322s Preparing to unpack .../31-gcc-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 322s Unpacking gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 322s Selecting previously unselected package gcc. 322s Preparing to unpack .../32-gcc_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 322s Unpacking gcc (4:13.2.0-7ubuntu1) ... 322s Selecting previously unselected package libstdc++-13-dev:ppc64el. 322s Preparing to unpack .../33-libstdc++-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 322s Unpacking libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 322s Selecting previously unselected package g++-13-powerpc64le-linux-gnu. 322s Preparing to unpack .../34-g++-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 322s Unpacking g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 322s Selecting previously unselected package g++-13. 322s Preparing to unpack .../35-g++-13_13.2.0-17ubuntu2_ppc64el.deb ... 322s Unpacking g++-13 (13.2.0-17ubuntu2) ... 322s Selecting previously unselected package g++-powerpc64le-linux-gnu. 322s Preparing to unpack .../36-g++-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 322s Unpacking g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 322s Selecting previously unselected package g++. 322s Preparing to unpack .../37-g++_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 322s Unpacking g++ (4:13.2.0-7ubuntu1) ... 322s Selecting previously unselected package build-essential. 322s Preparing to unpack .../38-build-essential_12.10ubuntu1_ppc64el.deb ... 322s Unpacking build-essential (12.10ubuntu1) ... 322s Setting up linux-libc-dev:ppc64el (6.8.0-11.11) ... 322s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 322s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 322s Setting up libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up libmpc3:ppc64el (1.3.1-1) ... 322s Setting up libatomic1:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up libubsan1:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up libnsl-dev:ppc64el (1.3.0-3) ... 322s Setting up pigz (2.8-1) ... 322s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 322s Setting up libasan8:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up libtsan2:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up libisl23:ppc64el (0.26-3) ... 322s Setting up libc-dev-bin (2.39-0ubuntu2) ... 322s Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 322s Setting up libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up liblsan0:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up libitm1:ppc64el (14-20240303-1ubuntu1) ... 322s Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 322s Setting up cpp-13 (13.2.0-17ubuntu2) ... 322s Setting up python3-xopen (1.7.0-2) ... 322s Setting up libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 322s Setting up cpp (4:13.2.0-7ubuntu1) ... 322s Setting up libc6-dev:ppc64el (2.39-0ubuntu2) ... 322s Setting up libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 322s Setting up python3-dnaio (1.0.1-1build1) ... 323s Setting up python3-cutadapt (4.4-1build1) ... 323s Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 323s Setting up gcc-13 (13.2.0-17ubuntu2) ... 323s Setting up cutadapt (4.4-1build1) ... 323s Setting up g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 323s Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 323s Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 323s Setting up g++-13 (13.2.0-17ubuntu2) ... 323s Setting up trim-galore (0.6.10-1) ... 323s Setting up gcc (4:13.2.0-7ubuntu1) ... 323s Setting up g++ (4:13.2.0-7ubuntu1) ... 323s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 323s Setting up build-essential (12.10ubuntu1) ... 323s Setting up autopkgtest-satdep (0) ... 323s Processing triggers for man-db (2.12.0-3) ... 324s Processing triggers for libc-bin (2.39-0ubuntu2) ... 326s (Reading database ... 72653 files and directories currently installed.) 326s Removing autopkgtest-satdep (0) ... 327s autopkgtest [12:20:20]: test run-unit-test: [----------------------- 327s Test 1 327s Multicore support not enabled. Proceeding with single-core trimming. 327s Path to Cutadapt set as: 'cutadapt' (default) 328s Cutadapt seems to be working fine (tested command 'cutadapt --version') 328s Cutadapt version: 4.4 328s single-core operation. 328s Proceeding with 'gzip' for decompression 328s To decrease CPU usage of decompression, please install 'igzip' and run again 328s 328s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 328s 328s 328s 328s AUTO-DETECTING ADAPTER TYPE 328s =========================== 328s Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> clock_10K_R1.fastq.gz <<) 328s 328s Found perfect matches for the following adapter sequences: 328s Adapter type Count Sequence Sequences analysed Percentage 328s Illumina 488 AGATCGGAAGAGC 10000 4.88 328s Nextera 0 CTGTCTCTTATA 10000 0.00 328s smallRNA 0 TGGAATTCTCGG 10000 0.00 328s Using Illumina adapter for trimming (count: 488). Second best hit was Nextera (count: 0) 328s 328s Writing report to 'clock_10K_R1.fastq.gz_trimming_report.txt' 328s 328s SUMMARISING RUN PARAMETERS 328s ========================== 328s Input filename: clock_10K_R1.fastq.gz 328s Trimming mode: paired-end 328s Trim Galore version: 0.6.10 328s Cutadapt version: 4.4 328s Number of cores used for trimming: 1 328s Quality Phred score cutoff: 20 328s Quality encoding type selected: ASCII+33 328s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 328s Maximum trimming error rate: 0.1 (default) 328s Minimum required adapter overlap (stringency): 1 bp 328s Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 328s All Read 1 sequences will be trimmed by 15 bp from their 3' end to avoid poor qualities or biases 328s All Read 2 sequences will be trimmed by 15 bp from their 3' end to avoid poor qualities or biases 328s Output file(s) will be GZIP compressed 328s 328s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 328s Writing final adapter and quality trimmed output to clock_10K_R1_trimmed.fq.gz 328s 328s 328s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file clock_10K_R1.fastq.gz <<< 328s This is cutadapt 4.4 with Python 3.12.2 328s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC clock_10K_R1.fastq.gz 328s Processing single-end reads on 1 core ... 328s Finished in 0.170 s (17.048 µs/read; 3.52 M reads/minute). 328s 328s === Summary === 328s 328s Total reads processed: 10,000 328s Reads with adapters: 3,462 (34.6%) 328s Reads written (passing filters): 10,000 (100.0%) 328s 328s Total basepairs processed: 760,000 bp 328s Quality-trimmed: 2,077 bp (0.3%) 328s Total written (filtered): 727,884 bp (95.8%) 328s 328s === Adapter 1 === 328s 328s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3462 times 328s 328s Minimum overlap: 1 328s No. of allowed errors: 328s 1-9 bp: 0; 10-13 bp: 1 328s 328s Bases preceding removed adapters: 328s A: 34.2% 328s C: 4.1% 328s G: 21.6% 328s T: 40.1% 328s none/other: 0.0% 328s 328s Overview of removed sequences 328s length count expect max.err error counts 328s 1 1986 2500.0 0 1986 328s 2 717 625.0 0 717 328s 3 171 156.2 0 171 328s 4 81 39.1 0 81 328s 6 1 2.4 0 1 328s 7 1 0.6 0 1 328s 9 2 0.0 0 2 328s 10 2 0.0 1 2 328s 14 1 0.0 1 1 328s 15 2 0.0 1 2 328s 18 1 0.0 1 1 328s 21 1 0.0 1 1 328s 28 2 0.0 1 2 328s 31 1 0.0 1 1 328s 49 2 0.0 1 2 328s 50 29 0.0 1 29 328s 51 385 0.0 1 376 9 328s 52 12 0.0 1 11 1 328s 53 14 0.0 1 13 1 328s 54 13 0.0 1 13 328s 55 3 0.0 1 3 328s 56 2 0.0 1 2 328s 57 2 0.0 1 2 328s 58 8 0.0 1 7 1 328s 59 1 0.0 1 1 328s 60 4 0.0 1 4 328s 61 1 0.0 1 0 1 328s 62 2 0.0 1 2 328s 64 4 0.0 1 3 1 328s 65 11 0.0 1 11 328s 328s RUN STATISTICS FOR INPUT FILE: clock_10K_R1.fastq.gz 328s ============================================= 328s 10000 sequences processed in total 328s The length threshold of paired-end sequences gets evaluated later on (in the validation step) 328s 328s Writing report to 'clock_10K_R2.fastq.gz_trimming_report.txt' 328s 328s SUMMARISING RUN PARAMETERS 328s ========================== 328s Input filename: clock_10K_R2.fastq.gz 328s Trimming mode: paired-end 328s Trim Galore version: 0.6.10 328s Cutadapt version: 4.4 328s Number of cores used for trimming: 1 328s Quality Phred score cutoff: 20 328s Quality encoding type selected: ASCII+33 328s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 328s Maximum trimming error rate: 0.1 (default) 328s Minimum required adapter overlap (stringency): 1 bp 328s Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 328s All Read 1 sequences will be trimmed by 15 bp from their 3' end to avoid poor qualities or biases 328s All Read 2 sequences will be trimmed by 15 bp from their 3' end to avoid poor qualities or biases 328s Output file(s) will be GZIP compressed 328s 328s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j -j 1 328s Writing final adapter and quality trimmed output to clock_10K_R2_trimmed.fq.gz 328s 328s 328s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file clock_10K_R2.fastq.gz <<< 328s This is cutadapt 4.4 with Python 3.12.2 328s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC clock_10K_R2.fastq.gz 328s Processing single-end reads on 1 core ... 328s Finished in 0.179 s (17.893 µs/read; 3.35 M reads/minute). 328s 328s === Summary === 328s 328s Total reads processed: 10,000 328s Reads with adapters: 4,299 (43.0%) 328s Reads written (passing filters): 10,000 (100.0%) 328s 328s Total basepairs processed: 760,000 bp 328s Quality-trimmed: 2,874 bp (0.4%) 328s Total written (filtered): 728,533 bp (95.9%) 328s 328s === Adapter 1 === 328s 328s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4299 times 328s 328s Minimum overlap: 1 328s No. of allowed errors: 328s 1-9 bp: 0; 10-13 bp: 1 328s 328s Bases preceding removed adapters: 328s A: 51.2% 328s C: 17.5% 328s G: 3.5% 328s T: 27.8% 328s none/other: 0.0% 328s 328s Overview of removed sequences 328s length count expect max.err error counts 328s 1 3805 2500.0 0 3805 328s 2 1 625.0 0 1 328s 3 3 156.2 0 3 328s 4 1 39.1 0 1 328s 6 1 2.4 0 1 328s 7 1 0.6 0 1 328s 9 2 0.0 0 2 328s 10 3 0.0 1 3 328s 14 1 0.0 1 1 328s 16 1 0.0 1 0 1 328s 18 1 0.0 1 1 328s 21 1 0.0 1 1 328s 28 2 0.0 1 2 328s 35 1 0.0 1 1 328s 42 2 0.0 1 2 328s 43 1 0.0 1 1 328s 45 2 0.0 1 2 328s 46 1 0.0 1 1 328s 47 1 0.0 1 1 328s 48 5 0.0 1 5 328s 49 4 0.0 1 3 1 328s 50 21 0.0 1 19 2 328s 51 367 0.0 1 356 11 328s 52 12 0.0 1 11 1 328s 53 12 0.0 1 11 1 328s 54 11 0.0 1 10 1 328s 55 3 0.0 1 3 328s 56 2 0.0 1 2 328s 57 2 0.0 1 2 328s 58 8 0.0 1 8 328s 59 1 0.0 1 1 328s 60 4 0.0 1 4 328s 62 2 0.0 1 2 328s 64 3 0.0 1 3 328s 65 11 0.0 1 11 328s 328s RUN STATISTICS FOR INPUT FILE: clock_10K_R2.fastq.gz 328s ============================================= 328s 10000 sequences processed in total 328s The length threshold of paired-end sequences gets evaluated later on (in the validation step) 328s 328s Validate paired-end files clock_10K_R1_trimmed.fq.gz and clock_10K_R2_trimmed.fq.gz 328s file_1: clock_10K_R1_trimmed.fq.gz, file_2: clock_10K_R2_trimmed.fq.gz 328s 328s 328s >>>>> Now validing the length of the 2 paired-end infiles: clock_10K_R1_trimmed.fq.gz and clock_10K_R2_trimmed.fq.gz <<<<< 328s Writing validated paired-end Read 1 reads to clock_10K_R1_val_1.fq.gz 328s Writing validated paired-end Read 2 reads to clock_10K_R2_val_2.fq.gz 328s 329s Total number of sequences analysed: 10000 329s 329s Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 513 (5.13%) 329s 329s Deleting both intermediate output files clock_10K_R1_trimmed.fq.gz and clock_10K_R2_trimmed.fq.gz 329s 329s ==================================================================================================== 329s 329s Test 2 329s Multicore support not enabled. Proceeding with single-core trimming. 329s Path to Cutadapt set as: 'cutadapt' (default) 329s Cutadapt seems to be working fine (tested command 'cutadapt --version') 329s Cutadapt version: 4.4 329s single-core operation. 329s Proceeding with 'gzip' for decompression 329s To decrease CPU usage of decompression, please install 'igzip' and run again 329s 329s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 329s 329s Writing report to 'illumina_100K.fastq.gz_trimming_report.txt' 329s 329s SUMMARISING RUN PARAMETERS 329s ========================== 329s Input filename: illumina_100K.fastq.gz 329s Trimming mode: single-end 329s Trim Galore version: 0.6.10 329s Cutadapt version: 4.4 329s Number of cores used for trimming: 1 329s Quality Phred score cutoff: 20 329s Quality encoding type selected: ASCII+33 329s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 329s Maximum trimming error rate: 0.1 (default) 329s Minimum required adapter overlap (stringency): 1 bp 329s Minimum required sequence length before a sequence gets removed: 20 bp 329s Output file(s) will be GZIP compressed 329s 329s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 329s Writing final adapter and quality trimmed output to illumina_100K_trimmed.fq.gz 329s 329s 329s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file illumina_100K.fastq.gz <<< 335s This is cutadapt 4.4 with Python 3.12.2 335s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC illumina_100K.fastq.gz 335s Processing single-end reads on 1 core ... 335s Finished in 5.261 s (52.614 µs/read; 1.14 M reads/minute). 335s 335s === Summary === 335s 335s Total reads processed: 100,000 335s Reads with adapters: 64,192 (64.2%) 335s Reads written (passing filters): 100,000 (100.0%) 335s 335s Total basepairs processed: 15,000,000 bp 335s Quality-trimmed: 124,497 bp (0.8%) 335s Total written (filtered): 13,015,369 bp (86.8%) 335s 335s === Adapter 1 === 335s 335s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64192 times 335s 335s Minimum overlap: 1 335s No. of allowed errors: 335s 1-9 bp: 0; 10-13 bp: 1 335s 335s Bases preceding removed adapters: 335s A: 41.1% 335s C: 15.6% 335s G: 11.6% 335s T: 31.8% 335s none/other: 0.0% 335s 335s Overview of removed sequences 335s length count expect max.err error counts 335s 1 25485 25000.0 0 25485 335s 2 2462 6250.0 0 2462 335s 3 897 1562.5 0 897 335s 4 634 390.6 0 634 335s 5 453 97.7 0 453 335s 6 478 24.4 0 478 335s 7 495 6.1 0 495 335s 8 383 1.5 0 383 335s 9 453 0.4 0 442 11 335s 10 476 0.1 1 440 36 335s 11 382 0.0 1 351 31 335s 12 438 0.0 1 407 31 335s 13 367 0.0 1 331 36 335s 14 455 0.0 1 425 30 335s 15 480 0.0 1 443 37 335s 16 371 0.0 1 341 30 335s 17 403 0.0 1 370 33 335s 18 464 0.0 1 430 34 335s 19 459 0.0 1 427 32 335s 20 394 0.0 1 356 38 335s 21 447 0.0 1 413 34 335s 22 385 0.0 1 353 32 335s 23 442 0.0 1 401 41 335s 24 376 0.0 1 347 29 335s 25 400 0.0 1 366 34 335s 26 482 0.0 1 443 39 335s 27 388 0.0 1 354 34 335s 28 368 0.0 1 334 34 335s 29 380 0.0 1 342 38 335s 30 426 0.0 1 389 37 335s 31 413 0.0 1 382 31 335s 32 371 0.0 1 339 32 335s 33 312 0.0 1 287 25 335s 34 399 0.0 1 367 32 335s 35 376 0.0 1 345 31 335s 36 374 0.0 1 346 28 335s 37 403 0.0 1 380 23 335s 38 382 0.0 1 346 36 335s 39 350 0.0 1 323 27 335s 40 366 0.0 1 341 25 335s 41 294 0.0 1 273 21 335s 42 352 0.0 1 316 36 335s 43 344 0.0 1 323 21 335s 44 314 0.0 1 284 30 335s 45 364 0.0 1 334 30 335s 46 286 0.0 1 265 21 335s 47 313 0.0 1 286 27 335s 48 398 0.0 1 356 42 335s 49 307 0.0 1 278 29 335s 50 329 0.0 1 300 29 335s 51 377 0.0 1 353 24 335s 52 307 0.0 1 293 14 335s 53 298 0.0 1 269 29 335s 54 250 0.0 1 238 12 335s 55 304 0.0 1 276 28 335s 56 308 0.0 1 279 29 335s 57 288 0.0 1 262 26 335s 58 286 0.0 1 261 25 335s 59 277 0.0 1 245 32 335s 60 263 0.0 1 248 15 335s 61 284 0.0 1 265 19 335s 62 283 0.0 1 262 21 335s 63 347 0.0 1 323 24 335s 64 178 0.0 1 159 19 335s 65 268 0.0 1 255 13 335s 66 260 0.0 1 239 21 335s 67 234 0.0 1 219 15 335s 68 277 0.0 1 247 30 335s 69 277 0.0 1 259 18 335s 70 204 0.0 1 188 16 335s 71 239 0.0 1 222 17 335s 72 231 0.0 1 216 15 335s 73 264 0.0 1 242 22 335s 74 268 0.0 1 242 26 335s 75 204 0.0 1 186 18 335s 76 217 0.0 1 198 19 335s 77 243 0.0 1 228 15 335s 78 258 0.0 1 235 23 335s 79 278 0.0 1 245 33 335s 80 286 0.0 1 254 32 335s 81 330 0.0 1 315 15 335s 82 453 0.0 1 415 38 335s 83 596 0.0 1 536 60 335s 84 807 0.0 1 741 66 335s 85 745 0.0 1 677 68 335s 86 487 0.0 1 458 29 335s 87 332 0.0 1 314 18 335s 88 285 0.0 1 266 19 335s 89 238 0.0 1 225 13 335s 90 173 0.0 1 153 20 335s 91 158 0.0 1 150 8 335s 92 142 0.0 1 124 18 335s 93 132 0.0 1 116 16 335s 94 118 0.0 1 105 13 335s 95 124 0.0 1 109 15 335s 96 138 0.0 1 123 15 335s 97 116 0.0 1 105 11 335s 98 125 0.0 1 118 7 335s 99 116 0.0 1 103 13 335s 100 107 0.0 1 97 10 335s 101 122 0.0 1 112 10 335s 102 102 0.0 1 91 11 335s 103 107 0.0 1 95 12 335s 104 110 0.0 1 100 10 335s 105 107 0.0 1 97 10 335s 106 119 0.0 1 98 21 335s 107 104 0.0 1 95 9 335s 108 91 0.0 1 76 15 335s 109 102 0.0 1 88 14 335s 110 77 0.0 1 67 10 335s 111 91 0.0 1 80 11 335s 112 90 0.0 1 79 11 335s 113 86 0.0 1 75 11 335s 114 86 0.0 1 73 13 335s 115 98 0.0 1 86 12 335s 116 86 0.0 1 76 10 335s 117 92 0.0 1 81 11 335s 118 93 0.0 1 81 12 335s 119 77 0.0 1 64 13 335s 120 58 0.0 1 52 6 335s 121 74 0.0 1 61 13 335s 122 68 0.0 1 59 9 335s 123 66 0.0 1 59 7 335s 124 58 0.0 1 52 6 335s 125 79 0.0 1 73 6 335s 126 64 0.0 1 54 10 335s 127 59 0.0 1 49 10 335s 128 56 0.0 1 50 6 335s 129 37 0.0 1 33 4 335s 130 57 0.0 1 50 7 335s 131 52 0.0 1 43 9 335s 132 28 0.0 1 23 5 335s 133 29 0.0 1 25 4 335s 134 28 0.0 1 21 7 335s 135 24 0.0 1 22 2 335s 136 27 0.0 1 25 2 335s 137 13 0.0 1 11 2 335s 138 21 0.0 1 17 4 335s 139 18 0.0 1 14 4 335s 140 18 0.0 1 17 1 335s 141 22 0.0 1 15 7 335s 142 20 0.0 1 16 4 335s 143 5 0.0 1 3 2 335s 144 5 0.0 1 2 3 335s 145 6 0.0 1 3 3 335s 146 3 0.0 1 1 2 335s 147 1 0.0 1 0 1 335s 149 5 0.0 1 2 3 335s 150 1 0.0 1 0 1 335s 335s RUN STATISTICS FOR INPUT FILE: illumina_100K.fastq.gz 335s ============================================= 335s 100000 sequences processed in total 335s Sequences removed because they became shorter than the length cutoff of 20 bp: 651 (0.7%) 335s 335s Writing report to 'illumina_10K.fastq.gz_trimming_report.txt' 335s 335s SUMMARISING RUN PARAMETERS 335s ========================== 335s Input filename: illumina_10K.fastq.gz 335s Trimming mode: single-end 335s Trim Galore version: 0.6.10 335s Cutadapt version: 4.4 335s Number of cores used for trimming: 1 335s Quality Phred score cutoff: 20 335s Quality encoding type selected: ASCII+33 335s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 335s Maximum trimming error rate: 0.1 (default) 335s Minimum required adapter overlap (stringency): 1 bp 335s Minimum required sequence length before a sequence gets removed: 20 bp 335s Output file(s) will be GZIP compressed 335s 335s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j -j 1 335s Writing final adapter and quality trimmed output to illumina_10K_trimmed.fq.gz 335s 335s 335s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file illumina_10K.fastq.gz <<< 335s This is cutadapt 4.4 with Python 3.12.2 335s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC illumina_10K.fastq.gz 335s Processing single-end reads on 1 core ... 335s Finished in 0.245 s (24.505 µs/read; 2.45 M reads/minute). 335s 335s === Summary === 335s 335s Total reads processed: 10,000 335s Reads with adapters: 6,382 (63.8%) 335s Reads written (passing filters): 10,000 (100.0%) 335s 335s Total basepairs processed: 1,500,000 bp 335s Quality-trimmed: 13,264 bp (0.9%) 335s Total written (filtered): 1,301,289 bp (86.8%) 335s 335s === Adapter 1 === 335s 335s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6382 times 335s 335s Minimum overlap: 1 335s No. of allowed errors: 335s 1-9 bp: 0; 10-13 bp: 1 335s 335s Bases preceding removed adapters: 335s A: 40.9% 335s C: 16.1% 335s G: 12.0% 335s T: 31.0% 335s none/other: 0.0% 335s 335s Overview of removed sequences 335s length count expect max.err error counts 335s 1 2549 2500.0 0 2549 335s 2 216 625.0 0 216 335s 3 85 156.2 0 85 335s 4 59 39.1 0 59 335s 5 43 9.8 0 43 335s 6 42 2.4 0 42 335s 7 44 0.6 0 44 335s 8 41 0.2 0 41 335s 9 57 0.0 0 54 3 335s 10 53 0.0 1 47 6 335s 11 41 0.0 1 37 4 335s 12 46 0.0 1 44 2 335s 13 26 0.0 1 23 3 335s 14 52 0.0 1 49 3 335s 15 43 0.0 1 39 4 335s 16 41 0.0 1 35 6 335s 17 46 0.0 1 39 7 335s 18 50 0.0 1 48 2 335s 19 54 0.0 1 52 2 335s 20 38 0.0 1 36 2 335s 21 43 0.0 1 35 8 335s 22 35 0.0 1 29 6 335s 23 44 0.0 1 41 3 335s 24 32 0.0 1 27 5 335s 25 28 0.0 1 25 3 335s 26 42 0.0 1 37 5 335s 27 40 0.0 1 36 4 335s 28 41 0.0 1 35 6 335s 29 29 0.0 1 29 335s 30 51 0.0 1 46 5 335s 31 39 0.0 1 37 2 335s 32 31 0.0 1 28 3 335s 33 32 0.0 1 30 2 335s 34 43 0.0 1 36 7 335s 35 40 0.0 1 33 7 335s 36 41 0.0 1 40 1 335s 37 43 0.0 1 41 2 335s 38 39 0.0 1 34 5 335s 39 39 0.0 1 36 3 335s 40 33 0.0 1 31 2 335s 41 29 0.0 1 27 2 335s 42 38 0.0 1 32 6 335s 43 40 0.0 1 39 1 335s 44 32 0.0 1 25 7 335s 45 42 0.0 1 40 2 335s 46 33 0.0 1 32 1 335s 47 18 0.0 1 15 3 335s 48 38 0.0 1 36 2 335s 49 30 0.0 1 29 1 335s 50 24 0.0 1 21 3 335s 51 40 0.0 1 39 1 335s 52 33 0.0 1 32 1 335s 53 34 0.0 1 29 5 335s 54 24 0.0 1 23 1 335s 55 36 0.0 1 32 4 335s 56 33 0.0 1 26 7 335s 57 31 0.0 1 30 1 335s 58 34 0.0 1 30 4 335s 59 31 0.0 1 29 2 335s 60 24 0.0 1 22 2 335s 61 28 0.0 1 27 1 335s 62 31 0.0 1 29 2 335s 63 28 0.0 1 26 2 335s 64 13 0.0 1 12 1 335s 65 19 0.0 1 18 1 335s 66 25 0.0 1 25 335s 67 28 0.0 1 25 3 335s 68 28 0.0 1 23 5 335s 69 31 0.0 1 31 335s 70 16 0.0 1 15 1 335s 71 29 0.0 1 28 1 335s 72 30 0.0 1 28 2 335s 73 30 0.0 1 28 2 335s 74 24 0.0 1 23 1 335s 75 24 0.0 1 22 2 335s 76 28 0.0 1 26 2 335s 77 19 0.0 1 16 3 335s 78 33 0.0 1 31 2 335s 79 29 0.0 1 24 5 335s 80 30 0.0 1 30 335s 81 33 0.0 1 32 1 335s 82 41 0.0 1 36 5 335s 83 69 0.0 1 64 5 335s 84 64 0.0 1 58 6 335s 85 68 0.0 1 60 8 335s 86 53 0.0 1 53 335s 87 24 0.0 1 23 1 335s 88 34 0.0 1 32 2 335s 89 16 0.0 1 16 335s 90 14 0.0 1 14 335s 91 13 0.0 1 13 335s 92 10 0.0 1 8 2 335s 93 19 0.0 1 17 2 335s 94 9 0.0 1 9 335s 95 9 0.0 1 8 1 335s 96 13 0.0 1 13 335s 97 12 0.0 1 11 1 335s 98 10 0.0 1 9 1 335s 99 13 0.0 1 13 335s 100 12 0.0 1 11 1 335s 101 12 0.0 1 11 1 335s 102 9 0.0 1 8 1 335s 103 12 0.0 1 11 1 335s 104 13 0.0 1 12 1 335s 105 8 0.0 1 6 2 335s 106 11 0.0 1 9 2 335s 107 12 0.0 1 11 1 335s 108 11 0.0 1 11 335s 109 7 0.0 1 5 2 335s 110 5 0.0 1 5 335s 111 10 0.0 1 9 1 335s 112 17 0.0 1 16 1 335s 113 4 0.0 1 3 1 335s 114 7 0.0 1 5 2 335s 115 9 0.0 1 8 1 335s 116 6 0.0 1 6 335s 117 6 0.0 1 3 3 335s 118 11 0.0 1 9 2 335s 119 9 0.0 1 8 1 335s 120 4 0.0 1 4 335s 121 6 0.0 1 5 1 335s 122 6 0.0 1 5 1 335s 123 5 0.0 1 5 335s 124 10 0.0 1 8 2 335s 125 9 0.0 1 8 1 335s 126 6 0.0 1 5 1 335s 127 6 0.0 1 4 2 335s 128 10 0.0 1 9 1 335s 129 6 0.0 1 6 335s 130 4 0.0 1 4 335s 131 7 0.0 1 6 1 335s 132 6 0.0 1 5 1 335s 133 2 0.0 1 2 335s 134 5 0.0 1 5 335s 135 2 0.0 1 2 335s 136 2 0.0 1 2 335s 137 1 0.0 1 1 335s 138 2 0.0 1 1 1 335s 139 2 0.0 1 1 1 335s 140 3 0.0 1 2 1 335s 141 1 0.0 1 1 335s 142 2 0.0 1 2 335s 149 2 0.0 1 0 2 335s 335s RUN STATISTICS FOR INPUT FILE: illumina_10K.fastq.gz 335s ============================================= 335s 10000 sequences processed in total 335s Sequences removed because they became shorter than the length cutoff of 20 bp: 77 (0.8%) 335s 335s Writing report to 'illumina_10K_trimmed.fq.gz_trimming_report.txt' 335s 335s SUMMARISING RUN PARAMETERS 335s ========================== 335s Input filename: illumina_10K_trimmed.fq.gz 335s Trimming mode: single-end 335s Trim Galore version: 0.6.10 335s Cutadapt version: 4.4 335s Number of cores used for trimming: 1 335s Quality Phred score cutoff: 20 335s Quality encoding type selected: ASCII+33 335s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 335s Maximum trimming error rate: 0.1 (default) 335s Minimum required adapter overlap (stringency): 1 bp 335s Minimum required sequence length before a sequence gets removed: 20 bp 335s Output file(s) will be GZIP compressed 335s 335s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j -j 1 335s Writing final adapter and quality trimmed output to illumina_10K_trimmed_trimmed.fq.gz 335s 335s 335s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file illumina_10K_trimmed.fq.gz <<< 336s This is cutadapt 4.4 with Python 3.12.2 336s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC illumina_10K_trimmed.fq.gz 336s Processing single-end reads on 1 core ... 336s Finished in 0.219 s (22.039 µs/read; 2.72 M reads/minute). 336s 336s === Summary === 336s 336s Total reads processed: 9,923 336s Reads with adapters: 2,772 (27.9%) 336s Reads written (passing filters): 9,923 (100.0%) 336s 336s Total basepairs processed: 1,300,218 bp 336s Quality-trimmed: 636 bp (0.0%) 336s Total written (filtered): 1,296,486 bp (99.7%) 336s 336s === Adapter 1 === 336s 336s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2772 times 336s 336s Minimum overlap: 1 336s No. of allowed errors: 336s 1-9 bp: 0; 10-13 bp: 1 336s 336s Bases preceding removed adapters: 336s A: 46.9% 336s C: 17.9% 336s G: 7.2% 336s T: 28.1% 336s none/other: 0.0% 336s 336s Overview of removed sequences 336s length count expect max.err error counts 336s 1 2540 2480.8 0 2540 336s 2 160 620.2 0 160 336s 3 57 155.0 0 57 336s 4 13 38.8 0 13 336s 6 1 2.4 0 1 336s 7 1 0.6 0 1 336s 336s RUN STATISTICS FOR INPUT FILE: illumina_10K_trimmed.fq.gz 336s ============================================= 336s 9923 sequences processed in total 336s Sequences removed because they became shorter than the length cutoff of 20 bp: 3 (0.0%) 336s 336s Test 3 336s Multicore support not enabled. Proceeding with single-core trimming. 336s Path to Cutadapt set as: 'cutadapt' (default) 336s Cutadapt seems to be working fine (tested command 'cutadapt --version') 336s Cutadapt version: 4.4 336s single-core operation. 336s Proceeding with 'gzip' for decompression 336s To decrease CPU usage of decompression, please install 'igzip' and run again 336s 336s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 336s 336s 336s 336s AUTO-DETECTING ADAPTER TYPE 336s =========================== 336s Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> 4_seqs_with_Ns.fastq.gz <<) 336s 336s Found perfect matches for the following adapter sequences: 336s Adapter type Count Sequence Sequences analysed Percentage 336s Illumina 1 AGATCGGAAGAGC 4 25.00 336s smallRNA 0 TGGAATTCTCGG 4 0.00 336s Nextera 0 CTGTCTCTTATA 4 0.00 336s Using Illumina adapter for trimming (count: 1). Second best hit was smallRNA (count: 0) 336s 336s Writing report to '4_seqs_with_Ns.fastq.gz_trimming_report.txt' 336s 336s SUMMARISING RUN PARAMETERS 336s ========================== 336s Input filename: 4_seqs_with_Ns.fastq.gz 336s Trimming mode: single-end 336s Trim Galore version: 0.6.10 336s Cutadapt version: 4.4 336s Number of cores used for trimming: 1 336s Quality Phred score cutoff: 20 336s Quality encoding type selected: ASCII+33 336s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 336s Maximum trimming error rate: 0.1 (default) 336s Minimum required adapter overlap (stringency): 1 bp 336s Minimum required sequence length before a sequence gets removed: 20 bp 336s Removing Ns from the start and end of reads 336s Running FastQC on the data once trimming has completed 336s Running FastQC with the following extra arguments: '--nogroup' 336s Output file(s) will be GZIP compressed 336s 336s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 336s Writing final adapter and quality trimmed output to 4_seqs_with_Ns_trimmed.fq.gz 336s 336s 336s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 4_seqs_with_Ns.fastq.gz <<< 336s This is cutadapt 4.4 with Python 3.12.2 336s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 --trim-n -a AGATCGGAAGAGC 4_seqs_with_Ns.fastq.gz 336s Processing single-end reads on 1 core ... 336s Finished in 0.005 s (1305.223 µs/read; 0.05 M reads/minute). 336s 336s === Summary === 336s 336s Total reads processed: 4 336s Reads with adapters: 4 (100.0%) 336s Reads written (passing filters): 4 (100.0%) 336s 336s Total basepairs processed: 604 bp 336s Quality-trimmed: 0 bp (0.0%) 336s Total written (filtered): 548 bp (90.7%) 336s 336s === Adapter 1 === 336s 336s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times 336s 336s Minimum overlap: 1 336s No. of allowed errors: 336s 1-9 bp: 0; 10-13 bp: 1 336s 336s Bases preceding removed adapters: 336s A: 0.0% 336s C: 75.0% 336s G: 25.0% 336s T: 0.0% 336s none/other: 0.0% 336s 336s Overview of removed sequences 336s length count expect max.err error counts 336s 1 3 1.0 0 3 336s 49 1 0.0 1 1 336s 336s RUN STATISTICS FOR INPUT FILE: 4_seqs_with_Ns.fastq.gz 336s ============================================= 336s 4 sequences processed in total 336s Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%) 336s 336s 336s >>> Now running FastQC on the data <<< 336s 336s Can't exec "fastqc": No such file or directory at /usr/bin/trim_galore line 1503. 336s Test 4 336s Multicore support not enabled. Proceeding with single-core trimming. 336s Path to Cutadapt set as: 'cutadapt' (default) 336s Cutadapt seems to be working fine (tested command 'cutadapt --version') 336s Cutadapt version: 4.4 336s single-core operation. 336s Proceeding with 'gzip' for decompression 336s To decrease CPU usage of decompression, please install 'igzip' and run again 336s 336s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 336s 336s Reducing length cutoff to 18bp for small RNA-Seq reads because a cutoff of 20bp may remove some short species of small RNAs if they had been trimmed by 1,2 or 3bp 336s Writing report to 'smallRNA_100K.fastq.gz_trimming_report.txt' 336s 336s SUMMARISING RUN PARAMETERS 336s ========================== 336s Input filename: smallRNA_100K.fastq.gz 336s Trimming mode: single-end 336s Trim Galore version: 0.6.10 336s Cutadapt version: 4.4 336s Number of cores used for trimming: 1 336s Quality Phred score cutoff: 20 336s Quality encoding type selected: ASCII+33 336s Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; user defined) 336s Maximum trimming error rate: 0.1 (default) 336s Minimum required adapter overlap (stringency): 1 bp 336s Minimum required sequence length before a sequence gets removed: 18 bp 336s Removing Ns from the start and end of reads 336s Output file(s) will be GZIP compressed 336s 336s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 336s Writing final adapter and quality trimmed output to smallRNA_100K_trimmed.fq.gz 336s 336s 336s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file smallRNA_100K.fastq.gz <<< 338s This is cutadapt 4.4 with Python 3.12.2 338s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 --trim-n -a TGGAATTCTCGG smallRNA_100K.fastq.gz 338s Processing single-end reads on 1 core ... 338s Finished in 1.781 s (17.811 µs/read; 3.37 M reads/minute). 338s 338s === Summary === 338s 338s Total reads processed: 100,000 338s Reads with adapters: 95,333 (95.3%) 338s Reads written (passing filters): 100,000 (100.0%) 338s 338s Total basepairs processed: 5,100,000 bp 338s Quality-trimmed: 9,993 bp (0.2%) 338s Total written (filtered): 2,413,662 bp (47.3%) 338s 338s === Adapter 1 === 338s 338s Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 95333 times 338s 338s Minimum overlap: 1 338s No. of allowed errors: 338s 1-9 bp: 0; 10-12 bp: 1 338s 338s Bases preceding removed adapters: 338s A: 17.3% 338s C: 21.7% 338s G: 13.9% 338s T: 45.7% 338s none/other: 1.3% 338s 338s Overview of removed sequences 338s length count expect max.err error counts 338s 1 1602 25000.0 0 1602 338s 2 1038 6250.0 0 1038 338s 3 1333 1562.5 0 1333 338s 4 357 390.6 0 357 338s 5 617 97.7 0 617 338s 6 651 24.4 0 651 338s 7 212 6.1 0 212 338s 8 295 1.5 0 295 338s 9 616 0.4 0 615 1 338s 10 275 0.1 1 268 7 338s 11 197 0.0 1 195 2 338s 12 255 0.0 1 254 1 338s 13 215 0.0 1 193 22 338s 14 255 0.0 1 246 9 338s 15 326 0.0 1 300 26 338s 16 326 0.0 1 311 15 338s 17 1736 0.0 1 1714 22 338s 18 804 0.0 1 792 12 338s 19 557 0.0 1 545 12 338s 20 302 0.0 1 294 8 338s 21 314 0.0 1 306 8 338s 22 313 0.0 1 293 20 338s 23 524 0.0 1 481 43 338s 24 469 0.0 1 429 40 338s 25 1736 0.0 1 1702 34 338s 26 3778 0.0 1 3695 83 338s 27 9628 0.0 1 9468 160 338s 28 16293 0.0 1 16101 192 338s 29 23970 0.0 1 23710 260 338s 30 5878 0.0 1 5793 85 338s 31 1846 0.0 1 1819 27 338s 32 849 0.0 1 831 18 338s 33 617 0.0 1 611 6 338s 34 1905 0.0 1 1878 27 338s 35 934 0.0 1 923 11 338s 36 2745 0.0 1 2721 24 338s 37 1253 0.0 1 1237 16 338s 38 853 0.0 1 843 10 338s 39 780 0.0 1 769 11 338s 40 1165 0.0 1 1152 13 338s 41 673 0.0 1 667 6 338s 42 737 0.0 1 729 8 338s 43 743 0.0 1 733 10 338s 44 1018 0.0 1 1009 9 338s 45 1144 0.0 1 1133 11 338s 46 894 0.0 1 889 5 338s 47 622 0.0 1 615 7 338s 48 141 0.0 1 141 338s 49 235 0.0 1 232 3 338s 50 65 0.0 1 63 2 338s 51 1242 0.0 1 1164 78 338s 338s RUN STATISTICS FOR INPUT FILE: smallRNA_100K.fastq.gz 338s ============================================= 338s 100000 sequences processed in total 338s Sequences removed because they became shorter than the length cutoff of 18 bp: 17177 (17.2%) 338s Test 5 338s 338s Multicore support not enabled. Proceeding with single-core trimming. 338s Path to Cutadapt set as: 'cutadapt' (default) 338s Cutadapt seems to be working fine (tested command 'cutadapt --version') 339s Cutadapt version: 4.4 339s single-core operation. 339s Proceeding with 'gzip' for decompression 339s To decrease CPU usage of decompression, please install 'igzip' and run again 339s 339s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 339s 339s 339s 339s AUTO-DETECTING ADAPTER TYPE 339s =========================== 339s Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> smallRNA_100K.fastq.gz <<) 339s 339s Found perfect matches for the following adapter sequences: 339s Adapter type Count Sequence Sequences analysed Percentage 339s smallRNA 86814 TGGAATTCTCGG 100000 86.81 339s Nextera 0 CTGTCTCTTATA 100000 0.00 339s Illumina 0 AGATCGGAAGAGC 100000 0.00 339s Using smallRNA adapter for trimming (count: 86814). Second best hit was Nextera (count: 0) 339s 339s Reducing length cutoff to 18bp for small RNA-Seq reads because a cutoff of 20bp may remove some short species of small RNAs if they had been trimmed by 1,2 or 3bp 339s Writing report to 'smallRNA_100K.fastq.gz_trimming_report.txt' 339s 339s SUMMARISING RUN PARAMETERS 339s ========================== 339s Input filename: smallRNA_100K.fastq.gz 339s Trimming mode: single-end 339s Trim Galore version: 0.6.10 339s Cutadapt version: 4.4 339s Number of cores used for trimming: 1 339s Quality Phred score cutoff: 20 339s Quality encoding type selected: ASCII+33 339s Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) 339s Maximum trimming error rate: 0.15 339s Maximum number of tolerated Ns: 10 339s Minimum required adapter overlap (stringency): 1 bp 339s Minimum required sequence length before a sequence gets removed: 18 bp 339s Output file(s) will be GZIP compressed 339s 339s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 339s Writing final adapter and quality trimmed output to smallRNA_100K_trimmed.fq.gz 339s 339s 339s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file smallRNA_100K.fastq.gz <<< 341s This is cutadapt 4.4 with Python 3.12.2 341s Command line parameters: -j 1 -e 0.15 -q 20 -O 1 -a TGGAATTCTCGG smallRNA_100K.fastq.gz 341s Processing single-end reads on 1 core ... 341s Finished in 1.678 s (16.782 µs/read; 3.58 M reads/minute). 341s 341s === Summary === 341s 341s Total reads processed: 100,000 341s Reads with adapters: 95,338 (95.3%) 341s Reads written (passing filters): 100,000 (100.0%) 341s 341s Total basepairs processed: 5,100,000 bp 341s Quality-trimmed: 9,993 bp (0.2%) 341s Total written (filtered): 2,414,353 bp (47.3%) 341s 341s === Adapter 1 === 341s 341s Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 95338 times 341s 341s Minimum overlap: 1 341s No. of allowed errors: 341s 1-5 bp: 0; 6-12 bp: 1 341s 341s Bases preceding removed adapters: 341s A: 17.3% 341s C: 21.7% 341s G: 13.9% 341s T: 45.7% 341s none/other: 1.3% 341s 341s Overview of removed sequences 341s length count expect max.err error counts 341s 1 1571 25000.0 0 1571 341s 2 1038 6250.0 0 1038 341s 3 1333 1562.5 0 1333 341s 4 357 390.6 0 357 341s 5 617 97.7 0 617 341s 6 658 24.4 0 651 7 341s 7 227 6.1 1 212 15 341s 8 299 1.5 1 295 4 341s 9 626 0.4 1 615 11 341s 10 275 0.1 1 268 7 341s 11 197 0.0 1 195 2 341s 12 255 0.0 1 254 1 341s 13 215 0.0 1 193 22 341s 14 255 0.0 1 246 9 341s 15 326 0.0 1 300 26 341s 16 326 0.0 1 311 15 341s 17 1736 0.0 1 1714 22 341s 18 804 0.0 1 792 12 341s 19 557 0.0 1 545 12 341s 20 302 0.0 1 294 8 341s 21 314 0.0 1 306 8 341s 22 313 0.0 1 293 20 341s 23 524 0.0 1 481 43 341s 24 469 0.0 1 429 40 341s 25 1736 0.0 1 1702 34 341s 26 3778 0.0 1 3695 83 341s 27 9628 0.0 1 9468 160 341s 28 16293 0.0 1 16101 192 341s 29 23970 0.0 1 23710 260 341s 30 5878 0.0 1 5793 85 341s 31 1846 0.0 1 1819 27 341s 32 849 0.0 1 831 18 341s 33 617 0.0 1 611 6 341s 34 1905 0.0 1 1878 27 341s 35 934 0.0 1 923 11 341s 36 2745 0.0 1 2721 24 341s 37 1253 0.0 1 1237 16 341s 38 853 0.0 1 843 10 341s 39 780 0.0 1 769 11 341s 40 1165 0.0 1 1152 13 341s 41 673 0.0 1 667 6 341s 42 737 0.0 1 729 8 341s 43 743 0.0 1 733 10 341s 44 1018 0.0 1 1009 9 341s 45 1144 0.0 1 1133 11 341s 46 894 0.0 1 889 5 341s 47 622 0.0 1 615 7 341s 48 141 0.0 1 141 341s 49 235 0.0 1 232 3 341s 50 65 0.0 1 63 2 341s 51 1242 0.0 1 1164 78 341s 341s RUN STATISTICS FOR INPUT FILE: smallRNA_100K.fastq.gz 341s ============================================= 341s 100000 sequences processed in total 341s Sequences removed because they became shorter than the length cutoff of 18 bp: 17170 (17.2%) 341s Sequences removed because they contained more Ns than the cutoff of 10: 0 (0.0%) 341s 341s autopkgtest [12:20:34]: test run-unit-test: -----------------------] 341s autopkgtest [12:20:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 341s run-unit-test PASS 342s autopkgtest [12:20:35]: @@@@@@@@@@@@@@@@@@@@ summary 342s run-unit-test PASS 356s Creating nova instance adt-noble-ppc64el-trim-galore-20240313-121453-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240312.img (UUID 2068c266-b1f4-4468-a3e5-e52b1c42dc85)...