0s autopkgtest [04:07:38]: starting date: 2024-03-11 0s autopkgtest [04:07:38]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [04:07:38]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.oou4zy1e/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-3@bos02-arm64-13.secgroup --name adt-noble-arm64-trim-galore-20240311-040737-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 97s autopkgtest [04:09:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 97s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 98s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 98s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 98s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [434 kB] 98s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2623 kB] 100s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [581 kB] 100s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 100s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 100s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 100s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2967 kB] 101s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 101s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 101s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 105s Fetched 6834 kB in 4s (1590 kB/s) 106s Reading package lists... 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s Calculating upgrade... 116s The following packages were automatically installed and are no longer required: 116s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 116s Use 'sudo apt autoremove' to remove them. 116s The following packages will be REMOVED: 116s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 116s The following NEW packages will be installed: 116s libgdbm-compat4t64 libgdbm6t64 116s The following packages have been kept back: 116s libperl5.38 116s The following packages will be upgraded: 116s perl-base perl-modules-5.38 116s 2 upgraded, 2 newly installed, 5 to remove and 1 not upgraded. 116s Need to get 4928 kB of archives. 116s After this operation, 4158 kB disk space will be freed. 116s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB] 117s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB] 117s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B] 117s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 118s Fetched 4928 kB in 1s (5374 kB/s) 118s (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 ... 75856 files and directories currently installed.) 118s Removing dpkg-dev (1.22.4ubuntu5) ... 118s Removing libdpkg-perl (1.22.4ubuntu5) ... 118s Removing perl (5.38.2-3) ... 118s (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 ... 75275 files and directories currently installed.) 118s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ... 118s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 119s Setting up perl-base (5.38.2-3.2) ... 119s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested: 119s python3-gdbm:arm64 depends on libgdbm6 (>= 1.16). 119s man-db depends on libgdbm6 (>= 1.16). 119s libperl5.38:arm64 depends on libgdbm6 (>= 1.21). 119s libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16). 119s 119s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75275 files and directories currently installed.) 119s Removing libgdbm6:arm64 (1.23-5) ... 119s Selecting previously unselected package libgdbm6t64:arm64. 119s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75270 files and directories currently installed.) 119s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ... 119s Unpacking libgdbm6t64:arm64 (1.23-5.1) ... 119s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested: 119s libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3). 119s 119s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75276 files and directories currently installed.) 119s Removing libgdbm-compat4:arm64 (1.23-5) ... 119s Selecting previously unselected package libgdbm-compat4t64:arm64. 120s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75271 files and directories currently installed.) 120s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_arm64.deb ... 120s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 120s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 120s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 121s Setting up libgdbm6t64:arm64 (1.23-5.1) ... 121s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 121s Setting up perl-modules-5.38 (5.38.2-3.2) ... 121s Processing triggers for man-db (2.12.0-3) ... 122s Processing triggers for libc-bin (2.39-0ubuntu2) ... 123s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 123s 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 123s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 123s 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 123s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 123s 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 123s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 123s 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 123s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 123s 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 123s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 123s 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 123s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 123s 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 123s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 123s 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 123s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 123s 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 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s The following packages will be REMOVED: 124s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 125s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. 125s After this operation, 52.0 MB disk space will be freed. 125s (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 ... 75277 files and directories currently installed.) 125s Removing libperl5.38:arm64 (5.38.2-3) ... 125s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ... 125s Removing lto-disabled-list (47) ... 125s Removing make (4.3-4.1build1) ... 125s Removing perl-modules-5.38 (5.38.2-3.2) ... 125s Processing triggers for man-db (2.12.0-3) ... 125s Processing triggers for libc-bin (2.39-0ubuntu2) ... 127s sh: Attempting to set up Debian/Ubuntu apt sources automatically 127s sh: Distribution appears to be Ubuntu 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 135s eatmydata is already the newest version (131-1). 135s dbus is already the newest version (1.14.10-4ubuntu1). 135s dbus set to manually installed. 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s 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 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s 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 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s 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 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s 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 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s 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 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s 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 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s 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 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s 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 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s 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 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 136s rng-tools-debian is already the newest version (2.4). 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s haveged is already the newest version (1.9.14-1ubuntu1). 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s The following additional packages will be installed: 139s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 139s make perl perl-modules-5.38 139s Suggested packages: 139s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 139s libterm-readline-gnu-perl | libterm-readline-perl-perl 139s libtap-harness-archive-perl 139s Recommended packages: 139s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 139s libfile-fcntllock-perl 139s The following packages will be REMOVED: 139s libdb5.3 139s The following NEW packages will be installed: 139s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 139s lto-disabled-list make perl perl-modules-5.38 139s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 139s Need to get 7257 kB/10.4 MB of archives. 139s After this operation, 56.1 MB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB] 140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB] 141s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB] 141s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB] 141s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB] 141s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] 141s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB] 142s Fetched 7257 kB in 2s (3307 kB/s) 142s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: 142s libsasl2-modules-db:arm64 depends on libdb5.3. 142s libpython3.12-stdlib:arm64 depends on libdb5.3. 142s libpython3.11-stdlib:arm64 depends on libdb5.3. 142s libpam-modules:arm64 depends on libdb5.3. 142s iproute2 depends on libdb5.3. 142s apt-utils depends on libdb5.3. 142s 142s (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 ... 73306 files and directories currently installed.) 142s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ... 142s Selecting previously unselected package libdb5.3t64:arm64. 142s (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 ... 73300 files and directories currently installed.) 142s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ... 142s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 142s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 143s Selecting previously unselected package perl-modules-5.38. 143s (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 ... 73306 files and directories currently installed.) 143s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 143s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 144s Selecting previously unselected package libgdbm-compat4t64:arm64. 144s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ... 144s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 144s Selecting previously unselected package libperl5.38t64:arm64. 144s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ... 144s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ... 144s Selecting previously unselected package perl. 144s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ... 144s Unpacking perl (5.38.2-3.2) ... 144s Selecting previously unselected package libdpkg-perl. 144s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 144s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 144s Selecting previously unselected package make. 145s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ... 145s Unpacking make (4.3-4.1build1) ... 145s Selecting previously unselected package lto-disabled-list. 145s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 145s Unpacking lto-disabled-list (47) ... 145s Selecting previously unselected package dpkg-dev. 145s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 145s Unpacking dpkg-dev (1.22.4ubuntu5) ... 145s Setting up lto-disabled-list (47) ... 145s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 145s Setting up make (4.3-4.1build1) ... 145s Setting up perl-modules-5.38 (5.38.2-3.2) ... 145s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ... 145s Setting up perl (5.38.2-3.2) ... 145s Setting up libdpkg-perl (1.22.4ubuntu5) ... 145s Setting up dpkg-dev (1.22.4ubuntu5) ... 145s Processing triggers for man-db (2.12.0-3) ... 146s Processing triggers for libc-bin (2.39-0ubuntu2) ... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s The following packages will be REMOVED: 148s cloud-init* python3-configobj* python3-debconf* 148s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 148s After this operation, 3248 kB disk space will be freed. 149s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75858 files and directories currently installed.) 149s Removing cloud-init (24.1-0ubuntu1) ... 150s Removing python3-configobj (5.0.8-3) ... 150s Removing python3-debconf (1.5.86) ... 150s Processing triggers for man-db (2.12.0-3) ... 151s (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 ... 75469 files and directories currently installed.) 151s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 152s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 152s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 155s linux-generic is already the newest version (6.8.0-11.11+1). 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 155s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 155s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 155s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 155s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 163s Reading package lists... 163s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 163s 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 163s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 163s 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 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 164s Calculating upgrade... 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s autopkgtest [04:10:24]: rebooting testbed after setup commands that affected boot 318s autopkgtest [04:12:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 319s autopkgtest [04:12:57]: testbed dpkg architecture: arm64 320s autopkgtest [04:12:58]: @@@@@@@@@@@@@@@@@@@@ apt-source trim-galore 321s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 321s 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 321s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 321s 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 321s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 321s 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 321s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 321s 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 321s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 321s 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 321s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 321s 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 321s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 321s 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 321s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 321s 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 321s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 321s 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 325s Get:1 http://ftpmaster.internal/ubuntu noble/universe trim-galore 0.6.10-1 (dsc) [2077 B] 325s Get:2 http://ftpmaster.internal/ubuntu noble/universe trim-galore 0.6.10-1 (tar) [26.8 MB] 325s Get:3 http://ftpmaster.internal/ubuntu noble/universe trim-galore 0.6.10-1 (diff) [10.8 kB] 326s gpgv: Signature made Sun Feb 5 20:28:48 2023 UTC 326s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 326s gpgv: issuer "tille@debian.org" 326s gpgv: Can't check signature: No public key 326s dpkg-source: warning: cannot verify inline signature for ./trim-galore_0.6.10-1.dsc: no acceptable signature found 326s autopkgtest [04:13:04]: testing package trim-galore version 0.6.10-1 326s autopkgtest [04:13:04]: build not needed 328s autopkgtest [04:13:06]: test run-unit-test: preparing testbed 331s Reading package lists... 331s Building dependency tree... 331s Reading state information... 332s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 332s Starting 2 pkgProblemResolver with broken count: 0 332s Done 332s Done 333s Starting pkgProblemResolver with broken count: 0 333s Starting 2 pkgProblemResolver with broken count: 0 333s Done 334s The following additional packages will be installed: 334s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 334s cutadapt g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 334s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libatomic1 334s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev libgomp1 334s libhwasan0 libisl23 libitm1 liblsan0 libmpc3 libnsl-dev libstdc++-13-dev 334s libtirpc-dev libtsan2 libubsan1 linux-libc-dev pigz python3-cutadapt 334s python3-dnaio python3-xopen rpcsvc-proto trim-galore 334s Suggested packages: 334s cpp-doc gcc-13-locales cpp-13-doc gcc-13-doc gcc-multilib manpages-dev 334s autoconf automake libtool flex bison gdb gcc-doc gdb-aarch64-linux-gnu 334s glibc-doc libstdc++-13-doc 334s Recommended packages: 334s manpages manpages-dev libc-devtools fastqc 334s The following NEW packages will be installed: 334s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 334s cutadapt g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 334s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libatomic1 334s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev libgomp1 334s libhwasan0 libisl23 libitm1 liblsan0 libmpc3 libnsl-dev libstdc++-13-dev 334s libtirpc-dev libtsan2 libubsan1 linux-libc-dev pigz python3-cutadapt 334s python3-dnaio python3-xopen rpcsvc-proto trim-galore 334s 0 upgraded, 39 newly installed, 0 to remove and 0 not upgraded. 334s 1 not fully installed or removed. 334s Need to get 80.0 MB of archives. 334s After this operation, 242 MB of additional disk space will be used. 334s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 pigz arm64 2.8-1 [60.7 kB] 334s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-xopen all 1.7.0-2 [17.0 kB] 334s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-dnaio arm64 1.0.1-1build1 [84.9 kB] 334s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cutadapt arm64 4.4-1build1 [324 kB] 335s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 cutadapt all 4.4-1build1 [6776 B] 335s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 trim-galore all 0.6.10-1 [17.8 MB] 336s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 336s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 336s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 336s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] 336s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 336s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 336s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 336s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 336s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 336s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 336s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 336s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 336s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 336s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 336s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 336s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 336s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 336s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 336s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 336s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 336s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 336s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 336s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 337s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 337s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 337s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 337s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 337s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 337s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 337s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 337s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 337s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 337s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 338s Fetched 80.0 MB in 3s (23.4 MB/s) 338s Selecting previously unselected package pigz. 338s (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 ... 75414 files and directories currently installed.) 339s Preparing to unpack .../00-pigz_2.8-1_arm64.deb ... 339s Unpacking pigz (2.8-1) ... 339s Selecting previously unselected package python3-xopen. 339s Preparing to unpack .../01-python3-xopen_1.7.0-2_all.deb ... 339s Unpacking python3-xopen (1.7.0-2) ... 339s Selecting previously unselected package python3-dnaio. 339s Preparing to unpack .../02-python3-dnaio_1.0.1-1build1_arm64.deb ... 339s Unpacking python3-dnaio (1.0.1-1build1) ... 339s Selecting previously unselected package python3-cutadapt. 339s Preparing to unpack .../03-python3-cutadapt_4.4-1build1_arm64.deb ... 339s Unpacking python3-cutadapt (4.4-1build1) ... 339s Selecting previously unselected package cutadapt. 339s Preparing to unpack .../04-cutadapt_4.4-1build1_all.deb ... 339s Unpacking cutadapt (4.4-1build1) ... 339s Selecting previously unselected package trim-galore. 339s Preparing to unpack .../05-trim-galore_0.6.10-1_all.deb ... 339s Unpacking trim-galore (0.6.10-1) ... 339s Selecting previously unselected package libc-dev-bin. 339s Preparing to unpack .../06-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 339s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 339s Selecting previously unselected package linux-libc-dev:arm64. 339s Preparing to unpack .../07-linux-libc-dev_6.8.0-11.11_arm64.deb ... 339s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 340s Selecting previously unselected package libcrypt-dev:arm64. 340s Preparing to unpack .../08-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 340s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 340s Selecting previously unselected package libtirpc-dev:arm64. 340s Preparing to unpack .../09-libtirpc-dev_1.3.4+ds-1build1_arm64.deb ... 340s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 340s Selecting previously unselected package libnsl-dev:arm64. 340s Preparing to unpack .../10-libnsl-dev_1.3.0-3_arm64.deb ... 340s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 340s Selecting previously unselected package rpcsvc-proto. 340s Preparing to unpack .../11-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 340s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 340s Selecting previously unselected package libc6-dev:arm64. 340s Preparing to unpack .../12-libc6-dev_2.39-0ubuntu2_arm64.deb ... 340s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 340s Selecting previously unselected package libisl23:arm64. 340s Preparing to unpack .../13-libisl23_0.26-3_arm64.deb ... 340s Unpacking libisl23:arm64 (0.26-3) ... 340s Selecting previously unselected package libmpc3:arm64. 340s Preparing to unpack .../14-libmpc3_1.3.1-1_arm64.deb ... 340s Unpacking libmpc3:arm64 (1.3.1-1) ... 340s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 340s Preparing to unpack .../15-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 340s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 341s Selecting previously unselected package cpp-13. 341s Preparing to unpack .../16-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 341s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 341s Selecting previously unselected package cpp-aarch64-linux-gnu. 341s Preparing to unpack .../17-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 341s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 341s Selecting previously unselected package cpp. 341s Preparing to unpack .../18-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 341s Unpacking cpp (4:13.2.0-7ubuntu1) ... 341s Selecting previously unselected package libcc1-0:arm64. 341s Preparing to unpack .../19-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 341s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 341s Selecting previously unselected package libgomp1:arm64. 341s Preparing to unpack .../20-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 341s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 341s Selecting previously unselected package libitm1:arm64. 341s Preparing to unpack .../21-libitm1_14-20240303-1ubuntu1_arm64.deb ... 341s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 341s Selecting previously unselected package libatomic1:arm64. 341s Preparing to unpack .../22-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 341s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 341s Selecting previously unselected package libasan8:arm64. 341s Preparing to unpack .../23-libasan8_14-20240303-1ubuntu1_arm64.deb ... 341s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 341s Selecting previously unselected package liblsan0:arm64. 341s Preparing to unpack .../24-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 341s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 342s Selecting previously unselected package libtsan2:arm64. 342s Preparing to unpack .../25-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 342s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 342s Selecting previously unselected package libubsan1:arm64. 342s Preparing to unpack .../26-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 342s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 342s Selecting previously unselected package libhwasan0:arm64. 342s Preparing to unpack .../27-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 342s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 342s Selecting previously unselected package libgcc-13-dev:arm64. 342s Preparing to unpack .../28-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 342s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 342s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 342s Preparing to unpack .../29-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 342s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 343s Selecting previously unselected package gcc-13. 343s Preparing to unpack .../30-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 343s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 343s Selecting previously unselected package gcc-aarch64-linux-gnu. 343s Preparing to unpack .../31-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 343s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 343s Selecting previously unselected package gcc. 343s Preparing to unpack .../32-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 343s Unpacking gcc (4:13.2.0-7ubuntu1) ... 343s Selecting previously unselected package libstdc++-13-dev:arm64. 343s Preparing to unpack .../33-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 343s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 344s Selecting previously unselected package g++-13-aarch64-linux-gnu. 344s Preparing to unpack .../34-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 344s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 345s Selecting previously unselected package g++-13. 345s Preparing to unpack .../35-g++-13_13.2.0-17ubuntu2_arm64.deb ... 345s Unpacking g++-13 (13.2.0-17ubuntu2) ... 345s Selecting previously unselected package g++-aarch64-linux-gnu. 345s Preparing to unpack .../36-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 345s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 345s Selecting previously unselected package g++. 345s Preparing to unpack .../37-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 345s Unpacking g++ (4:13.2.0-7ubuntu1) ... 345s Selecting previously unselected package build-essential. 345s Preparing to unpack .../38-build-essential_12.10ubuntu1_arm64.deb ... 345s Unpacking build-essential (12.10ubuntu1) ... 345s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 345s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 345s Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 345s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 345s Setting up libmpc3:arm64 (1.3.1-1) ... 345s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 345s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 345s Setting up libnsl-dev:arm64 (1.3.0-3) ... 345s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 345s Setting up pigz (2.8-1) ... 345s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 345s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 345s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 345s Setting up libisl23:arm64 (0.26-3) ... 345s Setting up libc-dev-bin (2.39-0ubuntu2) ... 345s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 345s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 345s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 345s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 345s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 345s Setting up python3-xopen (1.7.0-2) ... 345s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 345s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 345s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 345s Setting up python3-dnaio (1.0.1-1build1) ... 345s Setting up cpp-13 (13.2.0-17ubuntu2) ... 345s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 345s Setting up python3-cutadapt (4.4-1build1) ... 346s Setting up gcc-13 (13.2.0-17ubuntu2) ... 346s Setting up cpp (4:13.2.0-7ubuntu1) ... 346s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 346s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 346s Setting up g++-13 (13.2.0-17ubuntu2) ... 346s Setting up cutadapt (4.4-1build1) ... 346s Setting up gcc (4:13.2.0-7ubuntu1) ... 346s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 346s Setting up trim-galore (0.6.10-1) ... 346s Setting up g++ (4:13.2.0-7ubuntu1) ... 346s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 346s Setting up build-essential (12.10ubuntu1) ... 346s Setting up autopkgtest-satdep (0) ... 346s Processing triggers for man-db (2.12.0-3) ... 347s Processing triggers for libc-bin (2.39-0ubuntu2) ... 352s (Reading database ... 78362 files and directories currently installed.) 352s Removing autopkgtest-satdep (0) ... 353s autopkgtest [04:13:31]: test run-unit-test: [----------------------- 354s Test 1 354s Multicore support not enabled. Proceeding with single-core trimming. 354s Path to Cutadapt set as: 'cutadapt' (default) 354s Cutadapt seems to be working fine (tested command 'cutadapt --version') 354s Cutadapt version: 4.4 354s single-core operation. 354s Proceeding with 'gzip' for decompression 354s To decrease CPU usage of decompression, please install 'igzip' and run again 354s 354s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 354s 354s 354s 354s AUTO-DETECTING ADAPTER TYPE 354s =========================== 354s Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> clock_10K_R1.fastq.gz <<) 354s 354s Found perfect matches for the following adapter sequences: 354s Adapter type Count Sequence Sequences analysed Percentage 354s Illumina 488 AGATCGGAAGAGC 10000 4.88 354s smallRNA 0 TGGAATTCTCGG 10000 0.00 354s Nextera 0 CTGTCTCTTATA 10000 0.00 354s Using Illumina adapter for trimming (count: 488). Second best hit was smallRNA (count: 0) 354s 354s Writing report to 'clock_10K_R1.fastq.gz_trimming_report.txt' 354s 354s SUMMARISING RUN PARAMETERS 354s ========================== 354s Input filename: clock_10K_R1.fastq.gz 354s Trimming mode: paired-end 354s Trim Galore version: 0.6.10 354s Cutadapt version: 4.4 354s Number of cores used for trimming: 1 354s Quality Phred score cutoff: 20 354s Quality encoding type selected: ASCII+33 354s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 354s Maximum trimming error rate: 0.1 (default) 354s Minimum required adapter overlap (stringency): 1 bp 354s Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 354s All Read 1 sequences will be trimmed by 15 bp from their 3' end to avoid poor qualities or biases 354s All Read 2 sequences will be trimmed by 15 bp from their 3' end to avoid poor qualities or biases 354s Output file(s) will be GZIP compressed 354s 354s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 354s Writing final adapter and quality trimmed output to clock_10K_R1_trimmed.fq.gz 354s 354s 354s >>> 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 <<< 355s This is cutadapt 4.4 with Python 3.12.2 355s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC clock_10K_R1.fastq.gz 355s Processing single-end reads on 1 core ... 355s Finished in 0.314 s (31.382 µs/read; 1.91 M reads/minute). 355s 355s === Summary === 355s 355s Total reads processed: 10,000 355s Reads with adapters: 3,462 (34.6%) 355s Reads written (passing filters): 10,000 (100.0%) 355s 355s Total basepairs processed: 760,000 bp 355s Quality-trimmed: 2,077 bp (0.3%) 355s Total written (filtered): 727,884 bp (95.8%) 355s 355s === Adapter 1 === 355s 355s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3462 times 355s 355s Minimum overlap: 1 355s No. of allowed errors: 355s 1-9 bp: 0; 10-13 bp: 1 355s 355s Bases preceding removed adapters: 355s A: 34.2% 355s C: 4.1% 355s G: 21.6% 355s T: 40.1% 355s none/other: 0.0% 355s 355s Overview of removed sequences 355s length count expect max.err error counts 355s 1 1986 2500.0 0 1986 355s 2 717 625.0 0 717 355s 3 171 156.2 0 171 355s 4 81 39.1 0 81 355s 6 1 2.4 0 1 355s 7 1 0.6 0 1 355s 9 2 0.0 0 2 355s 10 2 0.0 1 2 355s 14 1 0.0 1 1 355s 15 2 0.0 1 2 355s 18 1 0.0 1 1 355s 21 1 0.0 1 1 355s 28 2 0.0 1 2 355s 31 1 0.0 1 1 355s 49 2 0.0 1 2 355s 50 29 0.0 1 29 355s 51 385 0.0 1 376 9 355s 52 12 0.0 1 11 1 355s 53 14 0.0 1 13 1 355s 54 13 0.0 1 13 355s 55 3 0.0 1 3 355s 56 2 0.0 1 2 355s 57 2 0.0 1 2 355s 58 8 0.0 1 7 1 355s 59 1 0.0 1 1 355s 60 4 0.0 1 4 355s 61 1 0.0 1 0 1 355s 62 2 0.0 1 2 355s 64 4 0.0 1 3 1 355s 65 11 0.0 1 11 355s 355s RUN STATISTICS FOR INPUT FILE: clock_10K_R1.fastq.gz 355s ============================================= 355s 10000 sequences processed in total 355s The length threshold of paired-end sequences gets evaluated later on (in the validation step) 355s 355s Writing report to 'clock_10K_R2.fastq.gz_trimming_report.txt' 355s 355s SUMMARISING RUN PARAMETERS 355s ========================== 355s Input filename: clock_10K_R2.fastq.gz 355s Trimming mode: paired-end 355s Trim Galore version: 0.6.10 355s Cutadapt version: 4.4 355s Number of cores used for trimming: 1 355s Quality Phred score cutoff: 20 355s Quality encoding type selected: ASCII+33 355s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 355s Maximum trimming error rate: 0.1 (default) 355s Minimum required adapter overlap (stringency): 1 bp 355s Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 355s All Read 1 sequences will be trimmed by 15 bp from their 3' end to avoid poor qualities or biases 355s All Read 2 sequences will be trimmed by 15 bp from their 3' end to avoid poor qualities or biases 355s Output file(s) will be GZIP compressed 355s 355s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j -j 1 355s Writing final adapter and quality trimmed output to clock_10K_R2_trimmed.fq.gz 355s 355s 355s >>> 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 <<< 355s This is cutadapt 4.4 with Python 3.12.2 355s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC clock_10K_R2.fastq.gz 355s Processing single-end reads on 1 core ... 355s Finished in 0.322 s (32.206 µs/read; 1.86 M reads/minute). 355s 355s === Summary === 355s 355s Total reads processed: 10,000 355s Reads with adapters: 4,299 (43.0%) 355s Reads written (passing filters): 10,000 (100.0%) 355s 355s Total basepairs processed: 760,000 bp 355s Quality-trimmed: 2,874 bp (0.4%) 355s Total written (filtered): 728,533 bp (95.9%) 355s 355s === Adapter 1 === 355s 355s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4299 times 355s 355s Minimum overlap: 1 355s No. of allowed errors: 355s 1-9 bp: 0; 10-13 bp: 1 355s 355s Bases preceding removed adapters: 355s A: 51.2% 355s C: 17.5% 355s G: 3.5% 355s T: 27.8% 355s none/other: 0.0% 355s 355s Overview of removed sequences 355s length count expect max.err error counts 355s 1 3805 2500.0 0 3805 355s 2 1 625.0 0 1 355s 3 3 156.2 0 3 355s 4 1 39.1 0 1 355s 6 1 2.4 0 1 355s 7 1 0.6 0 1 355s 9 2 0.0 0 2 355s 10 3 0.0 1 3 355s 14 1 0.0 1 1 355s 16 1 0.0 1 0 1 355s 18 1 0.0 1 1 355s 21 1 0.0 1 1 355s 28 2 0.0 1 2 355s 35 1 0.0 1 1 355s 42 2 0.0 1 2 355s 43 1 0.0 1 1 355s 45 2 0.0 1 2 355s 46 1 0.0 1 1 355s 47 1 0.0 1 1 355s 48 5 0.0 1 5 355s 49 4 0.0 1 3 1 355s 50 21 0.0 1 19 2 355s 51 367 0.0 1 356 11 355s 52 12 0.0 1 11 1 355s 53 12 0.0 1 11 1 355s 54 11 0.0 1 10 1 355s 55 3 0.0 1 3 355s 56 2 0.0 1 2 355s 57 2 0.0 1 2 355s 58 8 0.0 1 8 355s 59 1 0.0 1 1 355s 60 4 0.0 1 4 355s 62 2 0.0 1 2 355s 64 3 0.0 1 3 355s 65 11 0.0 1 11 355s 355s RUN STATISTICS FOR INPUT FILE: clock_10K_R2.fastq.gz 355s ============================================= 355s 10000 sequences processed in total 355s The length threshold of paired-end sequences gets evaluated later on (in the validation step) 355s 355s Validate paired-end files clock_10K_R1_trimmed.fq.gz and clock_10K_R2_trimmed.fq.gz 355s file_1: clock_10K_R1_trimmed.fq.gz, file_2: clock_10K_R2_trimmed.fq.gz 355s 355s 355s >>>>> Now validing the length of the 2 paired-end infiles: clock_10K_R1_trimmed.fq.gz and clock_10K_R2_trimmed.fq.gz <<<<< 355s Writing validated paired-end Read 1 reads to clock_10K_R1_val_1.fq.gz 355s Writing validated paired-end Read 2 reads to clock_10K_R2_val_2.fq.gz 355s 356s Total number of sequences analysed: 10000 356s 356s Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 513 (5.13%) 356s 356s Deleting both intermediate output files clock_10K_R1_trimmed.fq.gz and clock_10K_R2_trimmed.fq.gz 356s 356s ==================================================================================================== 356s 356s Test 2 356s Multicore support not enabled. Proceeding with single-core trimming. 356s Path to Cutadapt set as: 'cutadapt' (default) 356s Cutadapt seems to be working fine (tested command 'cutadapt --version') 356s Cutadapt version: 4.4 356s single-core operation. 356s Proceeding with 'gzip' for decompression 356s To decrease CPU usage of decompression, please install 'igzip' and run again 356s 356s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 356s 356s Writing report to 'illumina_100K.fastq.gz_trimming_report.txt' 356s 356s SUMMARISING RUN PARAMETERS 356s ========================== 356s Input filename: illumina_100K.fastq.gz 356s Trimming mode: single-end 356s Trim Galore version: 0.6.10 356s Cutadapt version: 4.4 356s Number of cores used for trimming: 1 356s Quality Phred score cutoff: 20 356s Quality encoding type selected: ASCII+33 356s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 356s Maximum trimming error rate: 0.1 (default) 356s Minimum required adapter overlap (stringency): 1 bp 356s Minimum required sequence length before a sequence gets removed: 20 bp 356s Output file(s) will be GZIP compressed 356s 356s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 356s Writing final adapter and quality trimmed output to illumina_100K_trimmed.fq.gz 356s 356s 356s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file illumina_100K.fastq.gz <<< 363s This is cutadapt 4.4 with Python 3.12.2 363s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC illumina_100K.fastq.gz 363s Processing single-end reads on 1 core ... 363s Finished in 6.291 s (62.910 µs/read; 0.95 M reads/minute). 363s 363s === Summary === 363s 363s Total reads processed: 100,000 363s Reads with adapters: 64,192 (64.2%) 363s Reads written (passing filters): 100,000 (100.0%) 363s 363s Total basepairs processed: 15,000,000 bp 363s Quality-trimmed: 124,497 bp (0.8%) 363s Total written (filtered): 13,015,369 bp (86.8%) 363s 363s === Adapter 1 === 363s 363s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64192 times 363s 363s Minimum overlap: 1 363s No. of allowed errors: 363s 1-9 bp: 0; 10-13 bp: 1 363s 363s Bases preceding removed adapters: 363s A: 41.1% 363s C: 15.6% 363s G: 11.6% 363s T: 31.8% 363s none/other: 0.0% 363s 363s Overview of removed sequences 363s length count expect max.err error counts 363s 1 25485 25000.0 0 25485 363s 2 2462 6250.0 0 2462 363s 3 897 1562.5 0 897 363s 4 634 390.6 0 634 363s 5 453 97.7 0 453 363s 6 478 24.4 0 478 363s 7 495 6.1 0 495 363s 8 383 1.5 0 383 363s 9 453 0.4 0 442 11 363s 10 476 0.1 1 440 36 363s 11 382 0.0 1 351 31 363s 12 438 0.0 1 407 31 363s 13 367 0.0 1 331 36 363s 14 455 0.0 1 425 30 363s 15 480 0.0 1 443 37 363s 16 371 0.0 1 341 30 363s 17 403 0.0 1 370 33 363s 18 464 0.0 1 430 34 363s 19 459 0.0 1 427 32 363s 20 394 0.0 1 356 38 363s 21 447 0.0 1 413 34 363s 22 385 0.0 1 353 32 363s 23 442 0.0 1 401 41 363s 24 376 0.0 1 347 29 363s 25 400 0.0 1 366 34 363s 26 482 0.0 1 443 39 363s 27 388 0.0 1 354 34 363s 28 368 0.0 1 334 34 363s 29 380 0.0 1 342 38 363s 30 426 0.0 1 389 37 363s 31 413 0.0 1 382 31 363s 32 371 0.0 1 339 32 363s 33 312 0.0 1 287 25 363s 34 399 0.0 1 367 32 363s 35 376 0.0 1 345 31 363s 36 374 0.0 1 346 28 363s 37 403 0.0 1 380 23 363s 38 382 0.0 1 346 36 363s 39 350 0.0 1 323 27 363s 40 366 0.0 1 341 25 363s 41 294 0.0 1 273 21 363s 42 352 0.0 1 316 36 363s 43 344 0.0 1 323 21 363s 44 314 0.0 1 284 30 363s 45 364 0.0 1 334 30 363s 46 286 0.0 1 265 21 363s 47 313 0.0 1 286 27 363s 48 398 0.0 1 356 42 363s 49 307 0.0 1 278 29 363s 50 329 0.0 1 300 29 363s 51 377 0.0 1 353 24 363s 52 307 0.0 1 293 14 363s 53 298 0.0 1 269 29 363s 54 250 0.0 1 238 12 363s 55 304 0.0 1 276 28 363s 56 308 0.0 1 279 29 363s 57 288 0.0 1 262 26 363s 58 286 0.0 1 261 25 363s 59 277 0.0 1 245 32 363s 60 263 0.0 1 248 15 363s 61 284 0.0 1 265 19 363s 62 283 0.0 1 262 21 363s 63 347 0.0 1 323 24 363s 64 178 0.0 1 159 19 363s 65 268 0.0 1 255 13 363s 66 260 0.0 1 239 21 363s 67 234 0.0 1 219 15 363s 68 277 0.0 1 247 30 363s 69 277 0.0 1 259 18 363s 70 204 0.0 1 188 16 363s 71 239 0.0 1 222 17 363s 72 231 0.0 1 216 15 363s 73 264 0.0 1 242 22 363s 74 268 0.0 1 242 26 363s 75 204 0.0 1 186 18 363s 76 217 0.0 1 198 19 363s 77 243 0.0 1 228 15 363s 78 258 0.0 1 235 23 363s 79 278 0.0 1 245 33 363s 80 286 0.0 1 254 32 363s 81 330 0.0 1 315 15 363s 82 453 0.0 1 415 38 363s 83 596 0.0 1 536 60 363s 84 807 0.0 1 741 66 363s 85 745 0.0 1 677 68 363s 86 487 0.0 1 458 29 363s 87 332 0.0 1 314 18 363s 88 285 0.0 1 266 19 363s 89 238 0.0 1 225 13 363s 90 173 0.0 1 153 20 363s 91 158 0.0 1 150 8 363s 92 142 0.0 1 124 18 363s 93 132 0.0 1 116 16 363s 94 118 0.0 1 105 13 363s 95 124 0.0 1 109 15 363s 96 138 0.0 1 123 15 363s 97 116 0.0 1 105 11 363s 98 125 0.0 1 118 7 363s 99 116 0.0 1 103 13 363s 100 107 0.0 1 97 10 363s 101 122 0.0 1 112 10 363s 102 102 0.0 1 91 11 363s 103 107 0.0 1 95 12 363s 104 110 0.0 1 100 10 363s 105 107 0.0 1 97 10 363s 106 119 0.0 1 98 21 363s 107 104 0.0 1 95 9 363s 108 91 0.0 1 76 15 363s 109 102 0.0 1 88 14 363s 110 77 0.0 1 67 10 363s 111 91 0.0 1 80 11 363s 112 90 0.0 1 79 11 363s 113 86 0.0 1 75 11 363s 114 86 0.0 1 73 13 363s 115 98 0.0 1 86 12 363s 116 86 0.0 1 76 10 363s 117 92 0.0 1 81 11 363s 118 93 0.0 1 81 12 363s 119 77 0.0 1 64 13 363s 120 58 0.0 1 52 6 363s 121 74 0.0 1 61 13 363s 122 68 0.0 1 59 9 363s 123 66 0.0 1 59 7 363s 124 58 0.0 1 52 6 363s 125 79 0.0 1 73 6 363s 126 64 0.0 1 54 10 363s 127 59 0.0 1 49 10 363s 128 56 0.0 1 50 6 363s 129 37 0.0 1 33 4 363s 130 57 0.0 1 50 7 363s 131 52 0.0 1 43 9 363s 132 28 0.0 1 23 5 363s 133 29 0.0 1 25 4 363s 134 28 0.0 1 21 7 363s 135 24 0.0 1 22 2 363s 136 27 0.0 1 25 2 363s 137 13 0.0 1 11 2 363s 138 21 0.0 1 17 4 363s 139 18 0.0 1 14 4 363s 140 18 0.0 1 17 1 363s 141 22 0.0 1 15 7 363s 142 20 0.0 1 16 4 363s 143 5 0.0 1 3 2 363s 144 5 0.0 1 2 3 363s 145 6 0.0 1 3 3 363s 146 3 0.0 1 1 2 363s 147 1 0.0 1 0 1 363s 149 5 0.0 1 2 3 363s 150 1 0.0 1 0 1 363s 363s RUN STATISTICS FOR INPUT FILE: illumina_100K.fastq.gz 363s ============================================= 363s 100000 sequences processed in total 363s Sequences removed because they became shorter than the length cutoff of 20 bp: 651 (0.7%) 363s 363s Writing report to 'illumina_10K.fastq.gz_trimming_report.txt' 363s 363s SUMMARISING RUN PARAMETERS 363s ========================== 363s Input filename: illumina_10K.fastq.gz 363s Trimming mode: single-end 363s Trim Galore version: 0.6.10 363s Cutadapt version: 4.4 363s Number of cores used for trimming: 1 363s Quality Phred score cutoff: 20 363s Quality encoding type selected: ASCII+33 363s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 363s Maximum trimming error rate: 0.1 (default) 363s Minimum required adapter overlap (stringency): 1 bp 363s Minimum required sequence length before a sequence gets removed: 20 bp 363s Output file(s) will be GZIP compressed 363s 363s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j -j 1 363s Writing final adapter and quality trimmed output to illumina_10K_trimmed.fq.gz 363s 363s 363s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file illumina_10K.fastq.gz <<< 364s This is cutadapt 4.4 with Python 3.12.2 364s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC illumina_10K.fastq.gz 364s Processing single-end reads on 1 core ... 364s Finished in 0.626 s (62.648 µs/read; 0.96 M reads/minute). 364s 364s === Summary === 364s 364s Total reads processed: 10,000 364s Reads with adapters: 6,382 (63.8%) 364s Reads written (passing filters): 10,000 (100.0%) 364s 364s Total basepairs processed: 1,500,000 bp 364s Quality-trimmed: 13,264 bp (0.9%) 364s Total written (filtered): 1,301,289 bp (86.8%) 364s 364s === Adapter 1 === 364s 364s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6382 times 364s 364s Minimum overlap: 1 364s No. of allowed errors: 364s 1-9 bp: 0; 10-13 bp: 1 364s 364s Bases preceding removed adapters: 364s A: 40.9% 364s C: 16.1% 364s G: 12.0% 364s T: 31.0% 364s none/other: 0.0% 364s 364s Overview of removed sequences 364s length count expect max.err error counts 364s 1 2549 2500.0 0 2549 364s 2 216 625.0 0 216 364s 3 85 156.2 0 85 364s 4 59 39.1 0 59 364s 5 43 9.8 0 43 364s 6 42 2.4 0 42 364s 7 44 0.6 0 44 364s 8 41 0.2 0 41 364s 9 57 0.0 0 54 3 364s 10 53 0.0 1 47 6 364s 11 41 0.0 1 37 4 364s 12 46 0.0 1 44 2 364s 13 26 0.0 1 23 3 364s 14 52 0.0 1 49 3 364s 15 43 0.0 1 39 4 364s 16 41 0.0 1 35 6 364s 17 46 0.0 1 39 7 364s 18 50 0.0 1 48 2 364s 19 54 0.0 1 52 2 364s 20 38 0.0 1 36 2 364s 21 43 0.0 1 35 8 364s 22 35 0.0 1 29 6 364s 23 44 0.0 1 41 3 364s 24 32 0.0 1 27 5 364s 25 28 0.0 1 25 3 364s 26 42 0.0 1 37 5 364s 27 40 0.0 1 36 4 364s 28 41 0.0 1 35 6 364s 29 29 0.0 1 29 364s 30 51 0.0 1 46 5 364s 31 39 0.0 1 37 2 364s 32 31 0.0 1 28 3 364s 33 32 0.0 1 30 2 364s 34 43 0.0 1 36 7 364s 35 40 0.0 1 33 7 364s 36 41 0.0 1 40 1 364s 37 43 0.0 1 41 2 364s 38 39 0.0 1 34 5 364s 39 39 0.0 1 36 3 364s 40 33 0.0 1 31 2 364s 41 29 0.0 1 27 2 364s 42 38 0.0 1 32 6 364s 43 40 0.0 1 39 1 364s 44 32 0.0 1 25 7 364s 45 42 0.0 1 40 2 364s 46 33 0.0 1 32 1 364s 47 18 0.0 1 15 3 364s 48 38 0.0 1 36 2 364s 49 30 0.0 1 29 1 364s 50 24 0.0 1 21 3 364s 51 40 0.0 1 39 1 364s 52 33 0.0 1 32 1 364s 53 34 0.0 1 29 5 364s 54 24 0.0 1 23 1 364s 55 36 0.0 1 32 4 364s 56 33 0.0 1 26 7 364s 57 31 0.0 1 30 1 364s 58 34 0.0 1 30 4 364s 59 31 0.0 1 29 2 364s 60 24 0.0 1 22 2 364s 61 28 0.0 1 27 1 364s 62 31 0.0 1 29 2 364s 63 28 0.0 1 26 2 364s 64 13 0.0 1 12 1 364s 65 19 0.0 1 18 1 364s 66 25 0.0 1 25 364s 67 28 0.0 1 25 3 364s 68 28 0.0 1 23 5 364s 69 31 0.0 1 31 364s 70 16 0.0 1 15 1 364s 71 29 0.0 1 28 1 364s 72 30 0.0 1 28 2 364s 73 30 0.0 1 28 2 364s 74 24 0.0 1 23 1 364s 75 24 0.0 1 22 2 364s 76 28 0.0 1 26 2 364s 77 19 0.0 1 16 3 364s 78 33 0.0 1 31 2 364s 79 29 0.0 1 24 5 364s 80 30 0.0 1 30 364s 81 33 0.0 1 32 1 364s 82 41 0.0 1 36 5 364s 83 69 0.0 1 64 5 364s 84 64 0.0 1 58 6 364s 85 68 0.0 1 60 8 364s 86 53 0.0 1 53 364s 87 24 0.0 1 23 1 364s 88 34 0.0 1 32 2 364s 89 16 0.0 1 16 364s 90 14 0.0 1 14 364s 91 13 0.0 1 13 364s 92 10 0.0 1 8 2 364s 93 19 0.0 1 17 2 364s 94 9 0.0 1 9 364s 95 9 0.0 1 8 1 364s 96 13 0.0 1 13 364s 97 12 0.0 1 11 1 364s 98 10 0.0 1 9 1 364s 99 13 0.0 1 13 364s 100 12 0.0 1 11 1 364s 101 12 0.0 1 11 1 364s 102 9 0.0 1 8 1 364s 103 12 0.0 1 11 1 364s 104 13 0.0 1 12 1 364s 105 8 0.0 1 6 2 364s 106 11 0.0 1 9 2 364s 107 12 0.0 1 11 1 364s 108 11 0.0 1 11 364s 109 7 0.0 1 5 2 364s 110 5 0.0 1 5 364s 111 10 0.0 1 9 1 364s 112 17 0.0 1 16 1 364s 113 4 0.0 1 3 1 364s 114 7 0.0 1 5 2 364s 115 9 0.0 1 8 1 364s 116 6 0.0 1 6 364s 117 6 0.0 1 3 3 364s 118 11 0.0 1 9 2 364s 119 9 0.0 1 8 1 364s 120 4 0.0 1 4 364s 121 6 0.0 1 5 1 364s 122 6 0.0 1 5 1 364s 123 5 0.0 1 5 364s 124 10 0.0 1 8 2 364s 125 9 0.0 1 8 1 364s 126 6 0.0 1 5 1 364s 127 6 0.0 1 4 2 364s 128 10 0.0 1 9 1 364s 129 6 0.0 1 6 364s 130 4 0.0 1 4 364s 131 7 0.0 1 6 1 364s 132 6 0.0 1 5 1 364s 133 2 0.0 1 2 364s 134 5 0.0 1 5 364s 135 2 0.0 1 2 364s 136 2 0.0 1 2 364s 137 1 0.0 1 1 364s 138 2 0.0 1 1 1 364s 139 2 0.0 1 1 1 364s 140 3 0.0 1 2 1 364s 141 1 0.0 1 1 364s 142 2 0.0 1 2 364s 149 2 0.0 1 0 2 364s 364s RUN STATISTICS FOR INPUT FILE: illumina_10K.fastq.gz 364s ============================================= 364s 10000 sequences processed in total 364s Sequences removed because they became shorter than the length cutoff of 20 bp: 77 (0.8%) 364s 364s Writing report to 'illumina_10K_trimmed.fq.gz_trimming_report.txt' 364s 364s SUMMARISING RUN PARAMETERS 364s ========================== 364s Input filename: illumina_10K_trimmed.fq.gz 364s Trimming mode: single-end 364s Trim Galore version: 0.6.10 364s Cutadapt version: 4.4 364s Number of cores used for trimming: 1 364s Quality Phred score cutoff: 20 364s Quality encoding type selected: ASCII+33 364s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 364s Maximum trimming error rate: 0.1 (default) 364s Minimum required adapter overlap (stringency): 1 bp 364s Minimum required sequence length before a sequence gets removed: 20 bp 364s Output file(s) will be GZIP compressed 364s 364s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j -j 1 364s Writing final adapter and quality trimmed output to illumina_10K_trimmed_trimmed.fq.gz 364s 364s 364s >>> 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 <<< 364s This is cutadapt 4.4 with Python 3.12.2 364s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC illumina_10K_trimmed.fq.gz 364s Processing single-end reads on 1 core ... 364s Finished in 0.575 s (57.964 µs/read; 1.04 M reads/minute). 364s 364s === Summary === 364s 364s Total reads processed: 9,923 364s Reads with adapters: 2,772 (27.9%) 364s Reads written (passing filters): 9,923 (100.0%) 364s 364s Total basepairs processed: 1,300,218 bp 364s Quality-trimmed: 636 bp (0.0%) 364s Total written (filtered): 1,296,486 bp (99.7%) 364s 364s === Adapter 1 === 364s 364s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2772 times 364s 364s Minimum overlap: 1 364s No. of allowed errors: 364s 1-9 bp: 0; 10-13 bp: 1 364s 364s Bases preceding removed adapters: 364s A: 46.9% 364s C: 17.9% 364s G: 7.2% 364s T: 28.1% 364s none/other: 0.0% 364s 364s Overview of removed sequences 364s length count expect max.err error counts 364s 1 2540 2480.8 0 2540 364s 2 160 620.2 0 160 364s 3 57 155.0 0 57 364s 4 13 38.8 0 13 364s 6 1 2.4 0 1 364s 7 1 0.6 0 1 364s 364s RUN STATISTICS FOR INPUT FILE: illumina_10K_trimmed.fq.gz 364s ============================================= 364s 9923 sequences processed in total 364s Sequences removed because they became shorter than the length cutoff of 20 bp: 3 (0.0%) 364s 365s Test 3 365s Multicore support not enabled. Proceeding with single-core trimming. 365s Path to Cutadapt set as: 'cutadapt' (default) 365s Cutadapt seems to be working fine (tested command 'cutadapt --version') 365s Cutadapt version: 4.4 365s single-core operation. 365s Proceeding with 'gzip' for decompression 365s To decrease CPU usage of decompression, please install 'igzip' and run again 365s 365s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 365s 365s 365s 365s AUTO-DETECTING ADAPTER TYPE 365s =========================== 365s Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> 4_seqs_with_Ns.fastq.gz <<) 365s 365s Found perfect matches for the following adapter sequences: 365s Adapter type Count Sequence Sequences analysed Percentage 365s Illumina 1 AGATCGGAAGAGC 4 25.00 365s smallRNA 0 TGGAATTCTCGG 4 0.00 365s Nextera 0 CTGTCTCTTATA 4 0.00 365s Using Illumina adapter for trimming (count: 1). Second best hit was smallRNA (count: 0) 365s 365s Writing report to '4_seqs_with_Ns.fastq.gz_trimming_report.txt' 365s 365s SUMMARISING RUN PARAMETERS 365s ========================== 365s Input filename: 4_seqs_with_Ns.fastq.gz 365s Trimming mode: single-end 365s Trim Galore version: 0.6.10 365s Cutadapt version: 4.4 365s Number of cores used for trimming: 1 365s Quality Phred score cutoff: 20 365s Quality encoding type selected: ASCII+33 365s Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 365s Maximum trimming error rate: 0.1 (default) 365s Minimum required adapter overlap (stringency): 1 bp 365s Minimum required sequence length before a sequence gets removed: 20 bp 365s Removing Ns from the start and end of reads 365s Running FastQC on the data once trimming has completed 365s Running FastQC with the following extra arguments: '--nogroup' 365s Output file(s) will be GZIP compressed 365s 365s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 365s Writing final adapter and quality trimmed output to 4_seqs_with_Ns_trimmed.fq.gz 365s 365s 365s >>> 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 <<< 365s This is cutadapt 4.4 with Python 3.12.2 365s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 --trim-n -a AGATCGGAAGAGC 4_seqs_with_Ns.fastq.gz 365s Processing single-end reads on 1 core ... 365s Finished in 0.010 s (2481.282 µs/read; 0.02 M reads/minute). 365s 365s === Summary === 365s 365s Total reads processed: 4 365s Reads with adapters: 4 (100.0%) 365s Reads written (passing filters): 4 (100.0%) 365s 365s Total basepairs processed: 604 bp 365s Quality-trimmed: 0 bp (0.0%) 365s Total written (filtered): 548 bp (90.7%) 365s 365s === Adapter 1 === 365s 365s Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times 365s 365s Minimum overlap: 1 365s No. of allowed errors: 365s 1-9 bp: 0; 10-13 bp: 1 365s 365s Bases preceding removed adapters: 365s A: 0.0% 365s C: 75.0% 365s G: 25.0% 365s T: 0.0% 365s none/other: 0.0% 365s 365s Overview of removed sequences 365s length count expect max.err error counts 365s 1 3 1.0 0 3 365s 49 1 0.0 1 1 365s 365s RUN STATISTICS FOR INPUT FILE: 4_seqs_with_Ns.fastq.gz 365s ============================================= 365s 4 sequences processed in total 365s Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%) 365s 365s 365s >>> Now running FastQC on the data <<< 365s 365s Can't exec "fastqc": No such file or directory at /usr/bin/trim_galore line 1503. 365s Test 4 365s Multicore support not enabled. Proceeding with single-core trimming. 365s Path to Cutadapt set as: 'cutadapt' (default) 366s Cutadapt seems to be working fine (tested command 'cutadapt --version') 366s Cutadapt version: 4.4 366s single-core operation. 366s Proceeding with 'gzip' for decompression 366s To decrease CPU usage of decompression, please install 'igzip' and run again 366s 366s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 366s 366s 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 366s Writing report to 'smallRNA_100K.fastq.gz_trimming_report.txt' 366s 366s SUMMARISING RUN PARAMETERS 366s ========================== 366s Input filename: smallRNA_100K.fastq.gz 366s Trimming mode: single-end 366s Trim Galore version: 0.6.10 366s Cutadapt version: 4.4 366s Number of cores used for trimming: 1 366s Quality Phred score cutoff: 20 366s Quality encoding type selected: ASCII+33 366s Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; user defined) 366s Maximum trimming error rate: 0.1 (default) 366s Minimum required adapter overlap (stringency): 1 bp 366s Minimum required sequence length before a sequence gets removed: 18 bp 366s Removing Ns from the start and end of reads 366s Output file(s) will be GZIP compressed 366s 366s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 366s Writing final adapter and quality trimmed output to smallRNA_100K_trimmed.fq.gz 366s 366s 366s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file smallRNA_100K.fastq.gz <<< 369s This is cutadapt 4.4 with Python 3.12.2 369s Command line parameters: -j 1 -e 0.1 -q 20 -O 1 --trim-n -a TGGAATTCTCGG smallRNA_100K.fastq.gz 369s Processing single-end reads on 1 core ... 369s Finished in 2.546 s (25.457 µs/read; 2.36 M reads/minute). 369s 369s === Summary === 369s 369s Total reads processed: 100,000 369s Reads with adapters: 95,333 (95.3%) 369s Reads written (passing filters): 100,000 (100.0%) 369s 369s Total basepairs processed: 5,100,000 bp 369s Quality-trimmed: 9,993 bp (0.2%) 369s Total written (filtered): 2,413,662 bp (47.3%) 369s 369s === Adapter 1 === 369s 369s Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 95333 times 369s 369s Minimum overlap: 1 369s No. of allowed errors: 369s 1-9 bp: 0; 10-12 bp: 1 369s 369s Bases preceding removed adapters: 369s A: 17.3% 369s C: 21.7% 369s G: 13.9% 369s T: 45.7% 369s none/other: 1.3% 369s 369s Overview of removed sequences 369s length count expect max.err error counts 369s 1 1602 25000.0 0 1602 369s 2 1038 6250.0 0 1038 369s 3 1333 1562.5 0 1333 369s 4 357 390.6 0 357 369s 5 617 97.7 0 617 369s 6 651 24.4 0 651 369s 7 212 6.1 0 212 369s 8 295 1.5 0 295 369s 9 616 0.4 0 615 1 369s 10 275 0.1 1 268 7 369s 11 197 0.0 1 195 2 369s 12 255 0.0 1 254 1 369s 13 215 0.0 1 193 22 369s 14 255 0.0 1 246 9 369s 15 326 0.0 1 300 26 369s 16 326 0.0 1 311 15 369s 17 1736 0.0 1 1714 22 369s 18 804 0.0 1 792 12 369s 19 557 0.0 1 545 12 369s 20 302 0.0 1 294 8 369s 21 314 0.0 1 306 8 369s 22 313 0.0 1 293 20 369s 23 524 0.0 1 481 43 369s 24 469 0.0 1 429 40 369s 25 1736 0.0 1 1702 34 369s 26 3778 0.0 1 3695 83 369s 27 9628 0.0 1 9468 160 369s 28 16293 0.0 1 16101 192 369s 29 23970 0.0 1 23710 260 369s 30 5878 0.0 1 5793 85 369s 31 1846 0.0 1 1819 27 369s 32 849 0.0 1 831 18 369s 33 617 0.0 1 611 6 369s 34 1905 0.0 1 1878 27 369s 35 934 0.0 1 923 11 369s 36 2745 0.0 1 2721 24 369s 37 1253 0.0 1 1237 16 369s 38 853 0.0 1 843 10 369s 39 780 0.0 1 769 11 369s 40 1165 0.0 1 1152 13 369s 41 673 0.0 1 667 6 369s 42 737 0.0 1 729 8 369s 43 743 0.0 1 733 10 369s 44 1018 0.0 1 1009 9 369s 45 1144 0.0 1 1133 11 369s 46 894 0.0 1 889 5 369s 47 622 0.0 1 615 7 369s 48 141 0.0 1 141 369s 49 235 0.0 1 232 3 369s 50 65 0.0 1 63 2 369s 51 1242 0.0 1 1164 78 369s 369s RUN STATISTICS FOR INPUT FILE: smallRNA_100K.fastq.gz 369s ============================================= 369s 100000 sequences processed in total 369s Sequences removed because they became shorter than the length cutoff of 18 bp: 17177 (17.2%) 369s 369s Test 5 369s Multicore support not enabled. Proceeding with single-core trimming. 369s Path to Cutadapt set as: 'cutadapt' (default) 369s Cutadapt seems to be working fine (tested command 'cutadapt --version') 369s Cutadapt version: 4.4 369s single-core operation. 369s Proceeding with 'gzip' for decompression 369s To decrease CPU usage of decompression, please install 'igzip' and run again 369s 369s No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) 369s 369s 369s 369s AUTO-DETECTING ADAPTER TYPE 369s =========================== 369s Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> smallRNA_100K.fastq.gz <<) 369s 369s Found perfect matches for the following adapter sequences: 369s Adapter type Count Sequence Sequences analysed Percentage 369s smallRNA 86814 TGGAATTCTCGG 100000 86.81 369s Illumina 0 AGATCGGAAGAGC 100000 0.00 369s Nextera 0 CTGTCTCTTATA 100000 0.00 369s Using smallRNA adapter for trimming (count: 86814). Second best hit was Illumina (count: 0) 369s 369s 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 369s Writing report to 'smallRNA_100K.fastq.gz_trimming_report.txt' 369s 369s SUMMARISING RUN PARAMETERS 369s ========================== 369s Input filename: smallRNA_100K.fastq.gz 369s Trimming mode: single-end 369s Trim Galore version: 0.6.10 369s Cutadapt version: 4.4 369s Number of cores used for trimming: 1 369s Quality Phred score cutoff: 20 369s Quality encoding type selected: ASCII+33 369s Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) 369s Maximum trimming error rate: 0.15 369s Maximum number of tolerated Ns: 10 369s Minimum required adapter overlap (stringency): 1 bp 369s Minimum required sequence length before a sequence gets removed: 18 bp 369s Output file(s) will be GZIP compressed 369s 369s Cutadapt seems to be fairly up-to-date (version 4.4). Setting -j 1 369s Writing final adapter and quality trimmed output to smallRNA_100K_trimmed.fq.gz 369s 369s 369s >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file smallRNA_100K.fastq.gz <<< 372s This is cutadapt 4.4 with Python 3.12.2 372s Command line parameters: -j 1 -e 0.15 -q 20 -O 1 -a TGGAATTCTCGG smallRNA_100K.fastq.gz 372s Processing single-end reads on 1 core ... 372s Finished in 2.276 s (22.764 µs/read; 2.64 M reads/minute). 372s 372s === Summary === 372s 372s Total reads processed: 100,000 372s Reads with adapters: 95,338 (95.3%) 372s Reads written (passing filters): 100,000 (100.0%) 372s 372s Total basepairs processed: 5,100,000 bp 372s Quality-trimmed: 9,993 bp (0.2%) 372s Total written (filtered): 2,414,353 bp (47.3%) 372s 372s === Adapter 1 === 372s 372s Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 95338 times 372s 372s Minimum overlap: 1 372s No. of allowed errors: 372s 1-5 bp: 0; 6-12 bp: 1 372s 372s Bases preceding removed adapters: 372s A: 17.3% 372s C: 21.7% 372s G: 13.9% 372s T: 45.7% 372s none/other: 1.3% 372s 372s Overview of removed sequences 372s length count expect max.err error counts 372s 1 1571 25000.0 0 1571 372s 2 1038 6250.0 0 1038 372s 3 1333 1562.5 0 1333 372s 4 357 390.6 0 357 372s 5 617 97.7 0 617 372s 6 658 24.4 0 651 7 372s 7 227 6.1 1 212 15 372s 8 299 1.5 1 295 4 372s 9 626 0.4 1 615 11 372s 10 275 0.1 1 268 7 372s 11 197 0.0 1 195 2 372s 12 255 0.0 1 254 1 372s 13 215 0.0 1 193 22 372s 14 255 0.0 1 246 9 372s 15 326 0.0 1 300 26 372s 16 326 0.0 1 311 15 372s 17 1736 0.0 1 1714 22 372s 18 804 0.0 1 792 12 372s 19 557 0.0 1 545 12 372s 20 302 0.0 1 294 8 372s 21 314 0.0 1 306 8 372s 22 313 0.0 1 293 20 372s 23 524 0.0 1 481 43 372s 24 469 0.0 1 429 40 372s 25 1736 0.0 1 1702 34 372s 26 3778 0.0 1 3695 83 372s 27 9628 0.0 1 9468 160 372s 28 16293 0.0 1 16101 192 372s 29 23970 0.0 1 23710 260 372s 30 5878 0.0 1 5793 85 372s 31 1846 0.0 1 1819 27 372s 32 849 0.0 1 831 18 372s 33 617 0.0 1 611 6 372s 34 1905 0.0 1 1878 27 372s 35 934 0.0 1 923 11 372s 36 2745 0.0 1 2721 24 372s 37 1253 0.0 1 1237 16 372s 38 853 0.0 1 843 10 372s 39 780 0.0 1 769 11 372s 40 1165 0.0 1 1152 13 372s 41 673 0.0 1 667 6 372s 42 737 0.0 1 729 8 372s 43 743 0.0 1 733 10 372s 44 1018 0.0 1 1009 9 372s 45 1144 0.0 1 1133 11 372s 46 894 0.0 1 889 5 372s 47 622 0.0 1 615 7 372s 48 141 0.0 1 141 372s 49 235 0.0 1 232 3 372s 50 65 0.0 1 63 2 372s 51 1242 0.0 1 1164 78 372s 372s RUN STATISTICS FOR INPUT FILE: smallRNA_100K.fastq.gz 372s ============================================= 372s 100000 sequences processed in total 372s Sequences removed because they became shorter than the length cutoff of 18 bp: 17170 (17.2%) 372s Sequences removed because they contained more Ns than the cutoff of 10: 0 (0.0%) 372s 372s autopkgtest [04:13:50]: test run-unit-test: -----------------------] 373s autopkgtest [04:13:51]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 373s run-unit-test PASS 373s autopkgtest [04:13:51]: @@@@@@@@@@@@@@@@@@@@ summary 373s run-unit-test PASS 384s Creating nova instance adt-noble-arm64-trim-galore-20240311-040737-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240310.img (UUID c166432c-3f89-460f-aeaa-f7e9d80d14b5)...