0s autopkgtest [23:16:46]: starting date: 2024-03-11 0s autopkgtest [23:16:46]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [23:16:46]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9c0gsspa/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:glib2.0,src:elfutils --apt-upgrade exonerate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glib2.0/2.79.3-3ubuntu5 elfutils/0.190-1.1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-19.secgroup --name adt-noble-arm64-exonerate-20240311-231646-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/ 93s autopkgtest [23:18:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 94s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.2 kB] 95s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 95s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [452 kB] 95s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2641 kB] 95s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [593 kB] 95s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 95s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 95s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 95s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2984 kB] 95s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 95s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.1 kB] 95s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 97s Fetched 6899 kB in 2s (3146 kB/s) 97s Reading package lists... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s Calculating upgrade... 102s The following packages will be REMOVED: 102s libglib2.0-0 102s The following NEW packages will be installed: 102s libglib2.0-0t64 xdg-user-dirs 102s The following packages will be upgraded: 102s gir1.2-glib-2.0 klibc-utils libglib2.0-data libklibc 102s 4 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 102s Need to get 1940 kB of archives. 102s After this operation, 138 kB of additional disk space will be used. 102s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 103s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 103s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 103s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 103s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 klibc-utils arm64 2.0.13-4 [114 kB] 103s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libklibc arm64 2.0.13-4 [51.4 kB] 104s Fetched 1940 kB in 1s (2574 kB/s) 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74748 files and directories currently installed.) 104s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 104s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 105s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 105s udisks2 depends on libglib2.0-0 (>= 2.77.0). 105s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 105s python3-gi depends on libglib2.0-0 (>= 2.77.0). 105s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 105s netplan.io depends on libglib2.0-0 (>= 2.70.0). 105s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 105s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 105s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 105s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 105s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 105s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 105s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 105s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 105s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 105s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 105s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 105s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 105s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 105s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 105s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 105s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 105s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 105s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 105s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 105s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 105s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 105s fwupd depends on libglib2.0-0 (>= 2.79.0). 105s bolt depends on libglib2.0-0 (>= 2.56.0). 105s 105s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74748 files and directories currently installed.) 105s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 105s Selecting previously unselected package libglib2.0-0t64:arm64. 105s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74723 files and directories currently installed.) 105s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 105s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 105s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 105s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 105s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 105s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 105s Selecting previously unselected package xdg-user-dirs. 105s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 105s Unpacking xdg-user-dirs (0.18-1) ... 105s Preparing to unpack .../klibc-utils_2.0.13-4_arm64.deb ... 105s Unpacking klibc-utils (2.0.13-4) over (2.0.13-2ubuntu1) ... 105s Preparing to unpack .../libklibc_2.0.13-4_arm64.deb ... 105s Unpacking libklibc:arm64 (2.0.13-4) over (2.0.13-2ubuntu1) ... 105s Setting up xdg-user-dirs (0.18-1) ... 105s Setting up libklibc:arm64 (2.0.13-4) ... 105s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 105s No schema files found: doing nothing. 105s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 105s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 105s Setting up klibc-utils (2.0.13-4) ... 105s Processing triggers for libc-bin (2.39-0ubuntu2) ... 106s Processing triggers for man-db (2.12.0-3) ... 107s Processing triggers for initramfs-tools (0.142ubuntu20) ... 107s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 107s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 125s System running in EFI mode, skipping. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s sh: Attempting to set up Debian/Ubuntu apt sources automatically 127s sh: Distribution appears to be Ubuntu 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s eatmydata is already the newest version (131-1). 129s dbus is already the newest version (1.14.10-4ubuntu1). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s rng-tools-debian is already the newest version (2.4). 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 131s haveged is already the newest version (1.9.14-1ubuntu1). 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s The following packages will be REMOVED: 132s cloud-init* python3-configobj* python3-debconf* 133s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 133s After this operation, 3248 kB disk space will be freed. 133s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74762 files and directories currently installed.) 133s Removing cloud-init (24.1-0ubuntu1) ... 133s Removing python3-configobj (5.0.8-3) ... 133s Removing python3-debconf (1.5.86) ... 134s Processing triggers for man-db (2.12.0-3) ... 134s (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 ... 74373 files and directories currently installed.) 134s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 135s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 135s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 136s linux-generic is already the newest version (6.8.0-11.11+1). 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 137s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 137s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 137s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 138s Reading package lists... 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Calculating upgrade... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s autopkgtest [23:19:07]: rebooting testbed after setup commands that affected boot 180s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 195s autopkgtest [23:20:01]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 195s autopkgtest [23:20:01]: testbed dpkg architecture: arm64 196s autopkgtest [23:20:02]: @@@@@@@@@@@@@@@@@@@@ apt-source exonerate 199s Get:1 http://ftpmaster.internal/ubuntu noble/universe exonerate 2.4.0-5 (dsc) [2109 B] 199s Get:2 http://ftpmaster.internal/ubuntu noble/universe exonerate 2.4.0-5 (tar) [521 kB] 199s Get:3 http://ftpmaster.internal/ubuntu noble/universe exonerate 2.4.0-5 (diff) [9192 B] 199s gpgv: Signature made Thu Dec 3 21:18:18 2020 UTC 199s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 199s gpgv: issuer "tille@debian.org" 199s gpgv: Can't check signature: No public key 199s dpkg-source: warning: cannot verify inline signature for ./exonerate_2.4.0-5.dsc: no acceptable signature found 200s autopkgtest [23:20:05]: testing package exonerate version 2.4.0-5 200s autopkgtest [23:20:06]: build not needed 200s autopkgtest [23:20:06]: test run-unit-test: preparing testbed 203s Reading package lists... 204s Building dependency tree... 204s Reading state information... 204s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 204s Starting 2 pkgProblemResolver with broken count: 0 204s Done 204s Done 205s Starting pkgProblemResolver with broken count: 0 205s Starting 2 pkgProblemResolver with broken count: 0 205s Done 205s The following additional packages will be installed: 205s exonerate 205s Suggested packages: 205s wise 206s The following NEW packages will be installed: 206s exonerate 206s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 206s 1 not fully installed or removed. 206s Need to get 1424 kB of archives. 206s After this operation, 8155 kB of additional disk space will be used. 206s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 exonerate arm64 2.4.0-5 [1424 kB] 208s Fetched 1424 kB in 1s (1940 kB/s) 208s Selecting previously unselected package exonerate. 208s (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 ... 74318 files and directories currently installed.) 208s Preparing to unpack .../exonerate_2.4.0-5_arm64.deb ... 208s Unpacking exonerate (2.4.0-5) ... 208s Setting up exonerate (2.4.0-5) ... 208s Setting up autopkgtest-satdep (0) ... 208s Processing triggers for man-db (2.12.0-3) ... 212s (Reading database ... 74416 files and directories currently installed.) 212s Removing autopkgtest-satdep (0) ... 213s autopkgtest [23:20:19]: test run-unit-test: [----------------------- 214s 214s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/ipcress/ipcress.simple.test.sh 214s Ipcress run successfully 214s ** Message: 23:20:21.048: Loaded [1] experiments 214s Found 1 product, as expected 214s 214s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/exonerate/exonerate.simple.test.sh 214s Exonerate simple test OK 214s Score as expected: 10875 214s 214s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastaindex.fastafetch.test.sh 214s Made index fastafetch.test.idx 214s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx CALM_HUMAN 214s expect 0 214s >CALM_HUMAN 214s MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL 214s TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 214s EFVQMMTAK 214s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx P53_HUMAN 214s expect 0 214s >P53_HUMAN 214s MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA 214s PPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT 214s CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN 214s TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGR 214s DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL 214s KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD 214s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx A_MISSING_FROM_START 214s expect 1 214s ** FATAL ERROR **: Could not find identifier [A_MISSING_FROM_START] (missing -F ?) 214s exiting ... 214s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx M_MISSING_FROM_MIDDLE 214s expect 1 214s ** FATAL ERROR **: Could not find identifier [M_MISSING_FROM_MIDDLE] (missing -F ?) 214s exiting ... 214s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx z_MISSING_FROM_END 214s expect 1 214s ** FATAL ERROR **: Could not find identifier [z_MISSING_FROM_END] (missing -F ?) 214s exiting ... 214s fastaindex fastafetch test OK 214s 214s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastarevcomp.test.sh 214s Reverse complement created : ./data/cdna/calm.human.dna.fasta 214s Reverse complement created : fastarevcomp.rc.test.fasta 214s RC length is the same 214s RC length is the same 214s 2nd reverse complement same as original 214s 214s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastatranslate.test.sh 214s Extraced CDS for translation 214s Tranlated sequence 214s Tranlsated sequence correct 214s 214s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastasoftmask.fastahardmask.test.sh 214s Softmasked OK 214s >test 214s ACGNAACCGGNNAAACCCGGGNNNAAAACCCCGGGGNNNN 214s Hardmasked OK 214s Hardmasked file is same as original masked file 214s 214s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastasplit.test.sh 214s Split fastasplit.test.fasta OK 214s Split into two files as expected 215s Input len 2136 215s Output len 2136 215s Input and output lengths match 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastarefomat.test.sh 215s Reformatted OK 215s >test 215s ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT 215s Reformatted length consistent 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastasubseq.test.sh 215s Generated correct subseq 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastalength.test.sh 215s 149 CALM_HUMAN 215s Calmodulin length OK 215s Calmodulin identifier OK 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastadiff.test.sh 215s fastadiff: id mismatch: CALM_HUMAN P53_HUMAN 215s Different seqs recognised as different 215s Identity test OK 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastaclip.test.sh 215s Clipped OK 215s >test:subseq(0,4) 215s ACGT 215s Clipped input correctly 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastaclean.test.sh 215s >CALM_HUMAN:filter(clean) 215s MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL 215s TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 215s EFVQMMTAK 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastaremove.test.sh 215s Have calmodulin in input 215s ** FATAL ERROR **: Could not open list for removal [CALM_HUMAN] 215s exiting ... 215s Calmodulin successfully removed 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastasort.test.sh 215s Sorted CALM_HUMAN 149 215s Sorted P53_HUMAN 393 215s Sorted TUBE_DROME 462 215s Sorted AF01595 1132 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastanrdb.test.sh 215s Made input file for fastanrdb 215s Successfully ran fastanrdb on: fastanrdb.input.test.fasta 215s Expected number of seqs in output: 4 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastavalidcds.test.sh 215s 215s ** (process:1274): WARNING **: 23:20:21.501: odd_length length (7) not divisible by 3 215s 215s ** (process:1274): WARNING **: 23:20:21.501: too_short length (4) not divisible by 3 215s 215s ** (process:1274): WARNING **: 23:20:21.501: no_start missing start codon (has:AAA) 215s 215s ** (process:1274): WARNING **: 23:20:21.501: no_end missing stop codon (has:TTT) 215s 215s ** (process:1274): WARNING **: 23:20:21.501: in_frame_stop contains in-frame stop codon (pos:9, codon:TAG) 215s 215s ** (process:1274): WARNING **: 23:20:21.501: non_acgt_base contains non-ACGT base: [pos: 5 base: N] 215s Validiated CDS sequences OK 215s >valid_seq 215s ATGAAACCCGGGTTTTAA 215s Validated correctly a single seq from input 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastacomposition.test.sh 215s Calmodulin cDNA composition correct 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastaoverlap.test.sh 215s /usr/bin/fastaoverlap working OK 215s Generated 15 215s 215s /tmp/autopkgtest.Iw8PG5/autopkgtest_tmp/util/fastaexpode.test.sh 215s Made input file for fastaexplode 215s Make output directory for fastaexplode 215s Successfully ran fastaexplode on: fastaexplode.test.fasta 215s Expected number of seqs in output: 4 215s PASS 215s autopkgtest [23:20:21]: test run-unit-test: -----------------------] 215s run-unit-test PASS 215s autopkgtest [23:20:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 216s autopkgtest [23:20:22]: @@@@@@@@@@@@@@@@@@@@ summary 216s run-unit-test PASS 241s Creating nova instance adt-noble-arm64-exonerate-20240311-231646-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240311.img (UUID 900cfff9-7f1a-42c7-81a7-22635cd2a5f9)...