0s autopkgtest [14:30:37]: starting date and time: 2025-03-15 14:30:37+0000 0s autopkgtest [14:30:37]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:30:37]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ebnue_uu/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade probcons --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-36.secgroup --name adt-plucky-arm64-probcons-20250315-143037-juju-7f2275-prod-proposed-migration-environment-2-0099f626-f2d0-457e-bf9f-d1797ef44baa --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 151s autopkgtest [14:33:08]: testbed dpkg architecture: arm64 151s autopkgtest [14:33:08]: testbed apt version: 2.9.33 152s autopkgtest [14:33:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 152s autopkgtest [14:33:09]: testbed release detected to be: None 153s autopkgtest [14:33:10]: updating testbed package index (apt update) 153s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 153s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 154s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 154s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 154s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 154s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 154s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 154s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 154s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 154s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 154s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 155s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 155s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 155s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 155s Fetched 1094 kB in 2s (660 kB/s) 156s Reading package lists... 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s Calculating upgrade... 158s Calculating upgrade... 159s The following packages will be upgraded: 159s python3-jinja2 strace 159s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Need to get 608 kB of archives. 159s After this operation, 11.3 kB of additional disk space will be used. 159s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 160s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 160s Fetched 608 kB in 1s (717 kB/s) 161s (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 ... 117701 files and directories currently installed.) 161s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 161s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 161s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 161s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 161s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 161s Setting up strace (6.13+ds-1ubuntu1) ... 161s Processing triggers for man-db (2.13.0-1) ... 162s Reading package lists... 163s Building dependency tree... 163s Reading state information... 164s Solving dependencies... 165s The following packages will be REMOVED: 165s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 165s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 165s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 165s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 166s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 166s After this operation, 267 MB disk space will be freed. 166s (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 ... 117701 files and directories currently installed.) 166s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 166s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 166s Removing libpython3.12t64:arm64 (3.12.9-1) ... 166s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 166s Removing libnsl2:arm64 (1.3.0-3build3) ... 166s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 166s Removing libunwind8:arm64 (1.6.2-3.1) ... 166s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 167s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 169s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 169s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 169s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 169s /etc/kernel/postrm.d/initramfs-tools: 169s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 169s /etc/kernel/postrm.d/zz-flash-kernel: 169s flash-kernel: Kernel 6.11.0-8-generic has been removed. 169s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 169s /etc/kernel/postrm.d/zz-update-grub: 169s Sourcing file `/etc/default/grub' 169s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 169s Generating grub configuration file ... 170s Found linux image: /boot/vmlinuz-6.14.0-10-generic 170s Found initrd image: /boot/initrd.img-6.14.0-10-generic 170s Warning: os-prober will not be executed to detect other bootable partitions. 170s Systems on them will not be added to the GRUB boot configuration. 170s Check GRUB_DISABLE_OS_PROBER documentation entry. 170s Adding boot menu entry for UEFI Firmware Settings ... 170s done 170s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 171s Processing triggers for libc-bin (2.41-1ubuntu1) ... 171s (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 ... 81650 files and directories currently installed.) 171s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 171s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 171s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 171s autopkgtest [14:33:28]: upgrading testbed (apt dist-upgrade and autopurge) 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 174s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 175s Entering ResolveByKeep 176s 176s Calculating upgrade... 177s The following packages will be upgraded: 177s libc-bin libc-dev-bin libc6 libc6-dev locales 177s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Need to get 9530 kB of archives. 177s After this operation, 0 B of additional disk space will be used. 177s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 179s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 179s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 181s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 182s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 186s Preconfiguring packages ... 186s Fetched 9530 kB in 8s (1161 kB/s) 186s (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 ... 81647 files and directories currently installed.) 186s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up libc6:arm64 (2.41-1ubuntu2) ... 187s (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 ... 81647 files and directories currently installed.) 187s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 187s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up libc-bin (2.41-1ubuntu2) ... 187s (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 ... 81647 files and directories currently installed.) 187s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 187s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up locales (2.41-1ubuntu2) ... 188s Generating locales (this might take a while)... 190s en_US.UTF-8... done 190s Generation complete. 190s Setting up libc-dev-bin (2.41-1ubuntu2) ... 190s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 190s Processing triggers for man-db (2.13.0-1) ... 191s Processing triggers for systemd (257.3-1ubuntu3) ... 192s Reading package lists... 192s Building dependency tree... 192s Reading state information... 192s Starting pkgProblemResolver with broken count: 0 192s Starting 2 pkgProblemResolver with broken count: 0 192s Done 193s Solving dependencies... 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 194s autopkgtest [14:33:51]: rebooting testbed after setup commands that affected boot 217s autopkgtest [14:34:14]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 220s autopkgtest [14:34:17]: @@@@@@@@@@@@@@@@@@@@ apt-source probcons 223s Get:1 http://ftpmaster.internal/ubuntu plucky/universe probcons 1.12-14 (dsc) [2049 B] 223s Get:2 http://ftpmaster.internal/ubuntu plucky/universe probcons 1.12-14 (tar) [43.2 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky/universe probcons 1.12-14 (diff) [13.2 kB] 223s gpgv: Signature made Thu Aug 26 08:43:07 2021 UTC 223s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 223s gpgv: issuer "tille@debian.org" 223s gpgv: Can't check signature: No public key 223s dpkg-source: warning: cannot verify inline signature for ./probcons_1.12-14.dsc: no acceptable signature found 223s autopkgtest [14:34:20]: testing package probcons version 1.12-14 224s autopkgtest [14:34:21]: build not needed 225s autopkgtest [14:34:22]: test run-unit-test: preparing testbed 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 226s Starting pkgProblemResolver with broken count: 0 226s Starting 2 pkgProblemResolver with broken count: 0 226s Done 227s The following NEW packages will be installed: 227s probcons probcons-extra 227s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 227s Need to get 165 kB of archives. 227s After this operation, 418 kB of additional disk space will be used. 227s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 probcons arm64 1.12-14 [129 kB] 227s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 probcons-extra arm64 1.12-14 [36.1 kB] 228s Fetched 165 kB in 1s (311 kB/s) 228s Selecting previously unselected package probcons. 228s (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 ... 81647 files and directories currently installed.) 228s Preparing to unpack .../probcons_1.12-14_arm64.deb ... 228s Unpacking probcons (1.12-14) ... 228s Selecting previously unselected package probcons-extra. 228s Preparing to unpack .../probcons-extra_1.12-14_arm64.deb ... 228s Unpacking probcons-extra (1.12-14) ... 228s Setting up probcons (1.12-14) ... 228s Setting up probcons-extra (1.12-14) ... 228s Processing triggers for man-db (2.13.0-1) ... 230s autopkgtest [14:34:27]: test run-unit-test: [----------------------- 230s 230s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 230s Written by Chuong Do 230s 230s Using parameter set: 230s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 230s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 230s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 230s 230s Loading sequence file: example.fa 230s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 230s 230s 230s 230s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 230s Written by Chuong Do 230s 230s Using parameter set: 230s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 230s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 230s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 230s 230s Loading sequence file: example.fa 231s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 231s 231s 231s 231s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 231s Written by Chuong Do 231s 231s Using parameter set: 231s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 231s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 231s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 231s 231s Loading sequence file: example.fa 231s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 231s 231s 231s 231s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 231s Written by Chuong Do 231s 231s Using parameter set: 231s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 231s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 231s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 231s 231s Loading sequence file: example.fa 232s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 232s 232s 232s 232s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 232s Written by Chuong Do 232s 232s Using parameter set: 232s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 232s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 232s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 232s 232s Loading sequence file: example.fa 232s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 232s 234s 234s 234s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 234s Written by Chuong Do 234s 234s Using parameter set: 234s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 234s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 234s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 234s 234s Loading sequence file: example.fa 234s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 234s 236s 236s 236s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 236s Written by Chuong Do 236s 236s Using parameter set: 236s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 236s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 236s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 236s 236s Loading sequence file: example.fa 237s Recomputed parameter set: 237s initDistrib[] = { 0.6472518444 8.226895261e-06 8.226895261e-06 0.1763658673 0.1763658673 } 237s gapOpen[] = { 0.01773866639 0.01773866639 0.03061322309 0.03061322309 } 237s gapExtend[] = { 0.413000226 0.413000226 0.941649437 0.941649437 } 237s 237s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 237s 237s 237s 237s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 237s Written by Chuong Do 237s 237s Using parameter set: 237s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 237s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 237s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 237s 237s Loading sequence file: example.fa 238s Recomputed parameter set: 238s initDistrib[] = { 0.6472518444 8.226895261e-06 8.226895261e-06 0.1763658673 0.1763658673 } 238s gapOpen[] = { 0.01773866639 0.01773866639 0.03061322309 0.03061322309 } 238s gapExtend[] = { 0.413000226 0.413000226 0.941649437 0.941649437 } 238s 238s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 238s 238s 238s 238s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 238s Written by Chuong Do 238s 238s Using parameter set: 238s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 238s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 238s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 238s 238s Loading sequence file: example.fa 238s 238s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 238s Written by Chuong Do 238s 238s Using parameter set: 238s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 238s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 238s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 238s 238s Loading sequence file: example.fa 238s 238s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 238s Written by Chuong Do 238s 238s Using parameter set: 238s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 238s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 238s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 238s 238s Loading sequence file: example.fa 238s Computing posterior matrix: (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA -- 0.220677346 238s Computing posterior matrix: (1) CALM_HUMAN vs. (3) P53_HUMAN -- 0.3983216584 238s Computing posterior matrix: (1) CALM_HUMAN vs. (4) TUBE_DROME -- 0.2310655862 238s Computing posterior matrix: (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN -- 0.2095304132 239s Computing posterior matrix: (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME -- 0.2289323211 239s Computing posterior matrix: (3) P53_HUMAN vs. (4) TUBE_DROME -- 0.2899678648 239s Relaxing (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA: 2141 --> 1139 -- done. 239s Relaxing (1) CALM_HUMAN vs. (3) P53_HUMAN: 1369 --> 864 -- done. 239s Relaxing (1) CALM_HUMAN vs. (4) TUBE_DROME: 2094 --> 1268 -- done. 239s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN: 5476 --> 3181 -- done. 239s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME: 5680 --> 3332 -- done. 239s Relaxing (3) P53_HUMAN vs. (4) TUBE_DROME: 3329 --> 2222 -- done. 239s Relaxing (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA: 1139 --> 557 -- done. 239s Relaxing (1) CALM_HUMAN vs. (3) P53_HUMAN: 864 --> 525 -- done. 239s Relaxing (1) CALM_HUMAN vs. (4) TUBE_DROME: 1268 --> 732 -- done. 239s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN: 3181 --> 1744 -- done. 239s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME: 3332 --> 1803 -- done. 239s Relaxing (3) P53_HUMAN vs. (4) TUBE_DROME: 2222 --> 1486 -- done. 239s 239s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 239s 239s [0] vs. [2]: 0.1050620601 239s [1] vs. [3]: 0.05934812129 239s [0,2] vs. [1,3]: 0.02306902781 239s [0,2,3] vs. [1]: 0.02062231861 239s [0,1] vs. [2,3]: 0.0215531718 239s [0,1,3] vs. [2]: 0.03732775152 239s [1,2] vs. [0,3]: 0.03665437922 239s [0,2,3] vs. [1]: 0.02072408795 239s [3] vs. [0,1,2]: 0.04131478816 239s [0,1,2] vs. [3]: 0.04131478816 239s [2,3] vs. [0,1]: 0.02140655369 239s [0,2] vs. [1,3]: 0.0238978155 239s [1] vs. [0,2,3]: 0.02052048407 239s [0,2] vs. [1,3]: 0.02381537855 239s [0,3] vs. [1,2]: 0.03669665754 239s [3] vs. [0,1,2]: 0.04147393256 239s [0,1,3] vs. [2]: 0.03778945655 239s [1,3] vs. [0,2]: 0.02382831834 239s [0,1,3] vs. [2]: 0.03782599792 239s [1,3] vs. [0,2]: 0.02382831834 239s [2] vs. [0,1,3]: 0.03782599792 239s [0] vs. [1,2,3]: 0.05896024778 239s [2,3] vs. [0,1]: 0.02192944102 239s [1] vs. [0,2,3]: 0.02071446367 239s [2] vs. [0,1,3]: 0.03613902256 239s [3] vs. [0,1,2]: 0.04358047619 239s [0] vs. [1,2,3]: 0.05896024778 239s [0,1,2] vs. [3]: 0.04358047619 239s [0] vs. [1,2,3]: 0.05896024778 239s [0,3] vs. [1,2]: 0.03590458632 239s [0,1,3] vs. [2]: 0.03613902256 239s [1,2,3] vs. [0]: 0.05896024778 239s [0,1,2] vs. [3]: 0.04358047619 239s [0,1,3] vs. [2]: 0.03613902256 239s [1,2] vs. [0,3]: 0.03590458632 239s [1,3] vs. [0,2]: 0.02533986792 239s [0,1] vs. [2,3]: 0.02192944102 239s [1,3] vs. [0,2]: 0.02533986792 239s [1,3] vs. [0,2]: 0.02533986792 239s [1,2,3] vs. [0]: 0.05896024778 239s [0] vs. [1,2,3]: 0.05896024778 239s [0,2] vs. [1,3]: 0.02533986792 239s [0,2,3] vs. [1]: 0.02071446367 239s [0,1,2] vs. [3]: 0.04358047619 239s [1,2] vs. [0,3]: 0.03590458632 239s [0,1,3] vs. [2]: 0.03613902256 239s [1,2,3] vs. [0]: 0.05896024778 239s [0,1] vs. [2,3]: 0.02192944102 239s [0,1,3] vs. [2]: 0.03613902256 239s [2,3] vs. [0,1]: 0.02192944102 239s [0] vs. [1,2,3]: 0.05896024778 239s [0,1,2] vs. [3]: 0.04358047619 239s [1,3] vs. [0,2]: 0.02533986792 239s [1,3] vs. [0,2]: 0.02533986792 239s [2,3] vs. [0,1]: 0.02192944102 239s [2] vs. [0,1,3]: 0.03613902256 239s [2,3] vs. [0,1]: 0.02192944102 239s [0,3] vs. [1,2]: 0.03590458632 239s [2,3] vs. [0,1]: 0.02192944102 239s [0,2,3] vs. [1]: 0.02071446367 239s [0,3] vs. [1,2]: 0.03590458632 239s [1] vs. [0,2,3]: 0.02071446367 239s [3] vs. [0,1,2]: 0.04358047619 239s [1,2] vs. [0,3]: 0.03590458632 239s [1,2,3] vs. [0]: 0.05896024778 239s [0,2] vs. [1,3]: 0.02533986792 239s [1,2,3] vs. [0]: 0.05896024778 239s [0,2,3] vs. [1]: 0.02071446367 239s [0,3] vs. [1,2]: 0.03590458632 239s [1,2] vs. [0,3]: 0.03590458632 239s [0,2] vs. [1,3]: 0.02533986792 239s [2,3] vs. [0,1]: 0.02192944102 239s [3] vs. [0,1,2]: 0.04358047619 239s [1,2] vs. [0,3]: 0.03590458632 239s [0,2,3] vs. [1]: 0.02071446367 239s [1,2] vs. [0,3]: 0.03590458632 239s [0] vs. [1,2,3]: 0.05896024778 239s [3] vs. [0,1,2]: 0.04358047619 239s [1] vs. [0,2,3]: 0.02071446367 239s [0,1,3] vs. [2]: 0.03613902256 239s [3] vs. [0,1,2]: 0.04358047619 239s [0,1,2] vs. [3]: 0.04358047619 239s [1] vs. [0,2,3]: 0.02071446367 239s [0,1,2] vs. [3]: 0.04358047619 239s [1] vs. [0,2,3]: 0.02071446367 239s [0,2,3] vs. [1]: 0.02071446367 239s [0,1,3] vs. [2]: 0.03613902256 239s [0,3] vs. [1,2]: 0.03590458632 239s [1] vs. [0,2,3]: 0.02071446367 239s 239s 239s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 239s Written by Chuong Do 239s 239s Using parameter set: 239s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 239s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 239s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 239s 239s Loading sequence file: example.fa 239s Computing posterior matrix: (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA -- 0.220677346 239s Computing posterior matrix: (1) CALM_HUMAN vs. (3) P53_HUMAN -- 0.3983216584 239s Computing posterior matrix: (1) CALM_HUMAN vs. (4) TUBE_DROME -- 0.2310655862 239s Computing posterior matrix: (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN -- 0.2095304132 239s Computing posterior matrix: (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME -- 0.2289323211 239s Computing posterior matrix: (3) P53_HUMAN vs. (4) TUBE_DROME -- 0.2899678648 239s Relaxing (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA: 2141 --> 1139 -- done. 239s Relaxing (1) CALM_HUMAN vs. (3) P53_HUMAN: 1369 --> 864 -- done. 239s Relaxing (1) CALM_HUMAN vs. (4) TUBE_DROME: 2094 --> 1268 -- done. 239s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN: 5476 --> 3181 -- done. 239s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME: 5680 --> 3332 -- done. 239s Relaxing (3) P53_HUMAN vs. (4) TUBE_DROME: 3329 --> 2222 -- done. 239s Relaxing (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA: 1139 --> 557 -- done. 239s Relaxing (1) CALM_HUMAN vs. (3) P53_HUMAN: 864 --> 525 -- done. 239s Relaxing (1) CALM_HUMAN vs. (4) TUBE_DROME: 1268 --> 732 -- done. 239s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN: 3181 --> 1744 -- done. 239s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME: 3332 --> 1803 -- done. 239s Relaxing (3) P53_HUMAN vs. (4) TUBE_DROME: 2222 --> 1486 -- done. 239s 239s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 239s 239s [0] vs. [2]: 0.1050620601 239s [1] vs. [3]: 0.05934812129 239s [0,2] vs. [1,3]: 0.02306902781 239s [0,2,3] vs. [1]: 0.02062231861 239s [0,1] vs. [2,3]: 0.0215531718 239s [0,1,3] vs. [2]: 0.03732775152 239s [1,2] vs. [0,3]: 0.03665437922 239s [0,2,3] vs. [1]: 0.02072408795 239s [3] vs. [0,1,2]: 0.04131478816 239s [0,1,2] vs. [3]: 0.04131478816 239s [2,3] vs. [0,1]: 0.02140655369 239s [0,2] vs. [1,3]: 0.0238978155 239s [1] vs. [0,2,3]: 0.02052048407 239s [0,2] vs. [1,3]: 0.02381537855 239s [0,3] vs. [1,2]: 0.03669665754 239s [3] vs. [0,1,2]: 0.04147393256 239s [0,1,3] vs. [2]: 0.03778945655 239s [1,3] vs. [0,2]: 0.02382831834 239s [0,1,3] vs. [2]: 0.03782599792 239s [1,3] vs. [0,2]: 0.02382831834 239s [2] vs. [0,1,3]: 0.03782599792 239s [0] vs. [1,2,3]: 0.05896024778 239s [2,3] vs. [0,1]: 0.02192944102 239s [1] vs. [0,2,3]: 0.02071446367 239s [2] vs. [0,1,3]: 0.03613902256 239s [3] vs. [0,1,2]: 0.04358047619 239s [0] vs. [1,2,3]: 0.05896024778 239s [0,1,2] vs. [3]: 0.04358047619 239s [0] vs. [1,2,3]: 0.05896024778 239s [0,3] vs. [1,2]: 0.03590458632 239s [0,1,3] vs. [2]: 0.03613902256 239s [1,2,3] vs. [0]: 0.05896024778 239s [0,1,2] vs. [3]: 0.04358047619 239s [0,1,3] vs. [2]: 0.03613902256 239s [1,2] vs. [0,3]: 0.03590458632 239s [1,3] vs. [0,2]: 0.02533986792 239s [0,1] vs. [2,3]: 0.02192944102 239s [1,3] vs. [0,2]: 0.02533986792 239s [1,3] vs. [0,2]: 0.02533986792 239s [1,2,3] vs. [0]: 0.05896024778 239s [0] vs. [1,2,3]: 0.05896024778 239s [0,2] vs. [1,3]: 0.02533986792 239s [0,2,3] vs. [1]: 0.02071446367 239s [0,1,2] vs. [3]: 0.04358047619 239s [1,2] vs. [0,3]: 0.03590458632 239s [0,1,3] vs. [2]: 0.03613902256 239s [1,2,3] vs. [0]: 0.05896024778 239s [0,1] vs. [2,3]: 0.02192944102 239s [0,1,3] vs. [2]: 0.03613902256 239s [2,3] vs. [0,1]: 0.02192944102 239s [0] vs. [1,2,3]: 0.05896024778 239s [0,1,2] vs. [3]: 0.04358047619 239s [1,3] vs. [0,2]: 0.02533986792 239s [1,3] vs. [0,2]: 0.02533986792 239s [2,3] vs. [0,1]: 0.02192944102 239s [2] vs. [0,1,3]: 0.03613902256 239s [2,3] vs. [0,1]: 0.02192944102 239s [0,3] vs. [1,2]: 0.03590458632 239s [2,3] vs. [0,1]: 0.02192944102 239s [0,2,3] vs. [1]: 0.02071446367 239s [0,3] vs. [1,2]: 0.03590458632 239s [1] vs. [0,2,3]: 0.02071446367 239s [3] vs. [0,1,2]: 0.04358047619 239s [1,2] vs. [0,3]: 0.03590458632 239s [1,2,3] vs. [0]: 0.05896024778 239s [0,2] vs. [1,3]: 0.02533986792 239s [1,2,3] vs. [0]: 0.05896024778 239s [0,2,3] vs. [1]: 0.02071446367 239s [0,3] vs. [1,2]: 0.03590458632 239s [1,2] vs. [0,3]: 0.03590458632 239s [0,2] vs. [1,3]: 0.02533986792 239s [2,3] vs. [0,1]: 0.02192944102 239s [3] vs. [0,1,2]: 0.04358047619 239s [1,2] vs. [0,3]: 0.03590458632 239s [0,2,3] vs. [1]: 0.02071446367 239s [1,2] vs. [0,3]: 0.03590458632 239s [0] vs. [1,2,3]: 0.05896024778 239s [3] vs. [0,1,2]: 0.04358047619 239s [1] vs. [0,2,3]: 0.02071446367 239s [0,1,3] vs. [2]: 0.03613902256 239s [3] vs. [0,1,2]: 0.04358047619 239s [0,1,2] vs. [3]: 0.04358047619 239s [1] vs. [0,2,3]: 0.02071446367 239s [0,1,2] vs. [3]: 0.04358047619 239s [1] vs. [0,2,3]: 0.02071446367 239s [0,2,3] vs. [1]: 0.02071446367 239s [0,1,3] vs. [2]: 0.03613902256 239s [0,3] vs. [1,2]: 0.03590458632 239s [1] vs. [0,2,3]: 0.02071446367 239s 239s PASS 240s autopkgtest [14:34:37]: test run-unit-test: -----------------------] 240s autopkgtest [14:34:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 240s run-unit-test PASS 240s autopkgtest [14:34:37]: @@@@@@@@@@@@@@@@@@@@ summary 240s run-unit-test PASS 259s nova [W] Using flock in prodstack6-arm64 259s Creating nova instance adt-plucky-arm64-probcons-20250315-143037-juju-7f2275-prod-proposed-migration-environment-2-0099f626-f2d0-457e-bf9f-d1797ef44baa from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 259s nova [W] Timed out waiting for ffb4da3d-91d2-4361-a52e-494b536e73ab to get deleted.