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-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sae3s48i/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade probalign --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-15@bos03-arm64-27.secgroup --name adt-plucky-arm64-probalign-20250315-143037-juju-7f2275-prod-proposed-migration-environment-15-74902140-a38f-4451-b9b2-1417ad701275 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 176s autopkgtest [14:33:33]: testbed dpkg architecture: arm64 176s autopkgtest [14:33:33]: testbed apt version: 2.9.33 177s autopkgtest [14:33:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 177s autopkgtest [14:33:34]: testbed release detected to be: None 178s autopkgtest [14:33:35]: updating testbed package index (apt update) 178s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 178s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 178s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 178s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 179s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 179s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 179s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 179s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 179s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 179s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 179s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 179s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 179s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 179s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 180s Fetched 1094 kB in 2s (699 kB/s) 181s Reading package lists... 181s + lsb_release --codename --short 181s + RELEASE=plucky 181s + cat 181s + [ plucky != trusty ] 181s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 182s Calculating upgrade... 182s Calculating upgrade... 183s The following packages will be upgraded: 183s python3-jinja2 strace 183s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 183s Need to get 608 kB of archives. 183s After this operation, 11.3 kB of additional disk space will be used. 183s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 183s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 184s Fetched 608 kB in 1s (690 kB/s) 184s (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.) 184s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 184s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 184s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 185s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 185s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 185s Setting up strace (6.13+ds-1ubuntu1) ... 185s Processing triggers for man-db (2.13.0-1) ... 186s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 186s + /usr/lib/apt/apt-helper analyze-pattern ?true 186s + uname -r 186s + sed s/\./\\./g 186s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 186s + apt list ?obsolete 186s + tail -n+2 186s + cut -d/ -f1+ grep -v ^linux-.*6\.14\.0-10-generic.* 186s 186s + obsolete_pkgs=linux-headers-6.11.0-8-generic 186s linux-headers-6.11.0-8 186s linux-image-6.11.0-8-generic 186s linux-modules-6.11.0-8-generic 186s linux-tools-6.11.0-8-generic 186s linux-tools-6.11.0-8 186s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s Solving dependencies... 188s The following packages will be REMOVED: 188s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 188s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 188s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 188s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 189s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 189s After this operation, 267 MB disk space will be freed. 189s (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.) 189s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 189s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 189s Removing libpython3.12t64:arm64 (3.12.9-1) ... 189s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 189s Removing libnsl2:arm64 (1.3.0-3build3) ... 189s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 189s Removing libunwind8:arm64 (1.6.2-3.1) ... 189s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 190s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 191s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 191s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 191s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 191s /etc/kernel/postrm.d/initramfs-tools: 191s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 192s /etc/kernel/postrm.d/zz-flash-kernel: 192s flash-kernel: Kernel 6.11.0-8-generic has been removed. 192s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 192s /etc/kernel/postrm.d/zz-update-grub: 192s Sourcing file `/etc/default/grub' 192s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 192s Generating grub configuration file ... 192s Found linux image: /boot/vmlinuz-6.14.0-10-generic 192s Found initrd image: /boot/initrd.img-6.14.0-10-generic 193s Warning: os-prober will not be executed to detect other bootable partitions. 193s Systems on them will not be added to the GRUB boot configuration. 193s Check GRUB_DISABLE_OS_PROBER documentation entry. 193s Adding boot menu entry for UEFI Firmware Settings ... 193s done 193s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 193s Processing triggers for libc-bin (2.41-1ubuntu1) ... 193s (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.) 193s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 193s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 193s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 193s + grep -q trusty /etc/lsb-release 193s + [ ! -d /usr/share/doc/unattended-upgrades ] 193s + [ ! -d /usr/share/doc/lxd ] 193s + [ ! -d /usr/share/doc/lxd-client ] 193s + [ ! -d /usr/share/doc/snapd ] 193s + type iptables 193s + cat 193s + chmod 755 /etc/rc.local 193s + . /etc/rc.local 193s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 193s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 193s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 193s + uname -m 193s + [ aarch64 = ppc64le ] 193s + [ -d /run/systemd/system ] 193s + systemd-detect-virt --quiet --vm 193s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 193s + cat 193s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 193s + echo COMPRESS=lz4 193s autopkgtest [14:33:50]: upgrading testbed (apt dist-upgrade and autopurge) 193s Reading package lists... 194s Building dependency tree... 194s Reading state information... 195s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 195s Starting 2 pkgProblemResolver with broken count: 0 195s Done 196s Entering ResolveByKeep 197s 197s Calculating upgrade... 198s The following packages will be upgraded: 198s libc-bin libc-dev-bin libc6 libc6-dev locales 198s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Need to get 9530 kB of archives. 198s After this operation, 0 B of additional disk space will be used. 198s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 200s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 200s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 202s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 203s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 208s Preconfiguring packages ... 208s Fetched 9530 kB in 9s (1004 kB/s) 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 ... 81647 files and directories currently installed.) 208s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 208s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 208s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 208s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 208s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 208s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 209s Setting up libc6:arm64 (2.41-1ubuntu2) ... 209s (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.) 209s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 209s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 209s Setting up libc-bin (2.41-1ubuntu2) ... 209s (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.) 209s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 209s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 209s Setting up locales (2.41-1ubuntu2) ... 210s Generating locales (this might take a while)... 212s en_US.UTF-8... done 212s Generation complete. 212s Setting up libc-dev-bin (2.41-1ubuntu2) ... 212s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 212s Processing triggers for man-db (2.13.0-1) ... 213s Processing triggers for systemd (257.3-1ubuntu3) ... 216s Reading package lists...autopkgtest [14:34:13]: rebooting testbed after setup commands that affected boot 216s 216s Building dependency tree... 216s Reading state information... 216s Starting pkgProblemResolver with broken count: 0 216s Starting 2 pkgProblemResolver with broken count: 0 216s Done 216s Solving dependencies... 216s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 239s autopkgtest [14:34:36]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 242s autopkgtest [14:34:39]: @@@@@@@@@@@@@@@@@@@@ apt-source probalign 244s Get:1 http://ftpmaster.internal/ubuntu plucky/universe probalign 1.4-10 (dsc) [1971 B] 244s Get:2 http://ftpmaster.internal/ubuntu plucky/universe probalign 1.4-10 (tar) [30.1 kB] 244s Get:3 http://ftpmaster.internal/ubuntu plucky/universe probalign 1.4-10 (diff) [4916 B] 244s gpgv: Signature made Thu Jan 19 13:18:09 2023 UTC 244s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 244s gpgv: issuer "tille@debian.org" 244s gpgv: Can't check signature: No public key 244s dpkg-source: warning: cannot verify inline signature for ./probalign_1.4-10.dsc: no acceptable signature found 244s autopkgtest [14:34:41]: testing package probalign version 1.4-10 245s autopkgtest [14:34:42]: build not needed 245s autopkgtest [14:34:42]: test run-unit-test: preparing testbed 245s Reading package lists... 246s Building dependency tree... 246s Reading state information... 246s Starting pkgProblemResolver with broken count: 0 246s Starting 2 pkgProblemResolver with broken count: 0 246s Done 247s The following NEW packages will be installed: 247s probalign 247s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 247s Need to get 67.3 kB of archives. 247s After this operation, 154 kB of additional disk space will be used. 247s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 probalign arm64 1.4-10 [67.3 kB] 248s Fetched 67.3 kB in 0s (204 kB/s) 248s Selecting previously unselected package probalign. 248s (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.) 248s Preparing to unpack .../probalign_1.4-10_arm64.deb ... 248s Unpacking probalign (1.4-10) ... 248s Setting up probalign (1.4-10) ... 248s Processing triggers for man-db (2.13.0-1) ... 250s autopkgtest [14:34:47]: test run-unit-test: [----------------------- 250s 250s PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the 250s standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS 250s version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). 250s 250s Loading sequence file: test_data_p.fas 250s Alignment tree: ((s1 s0) (s3 s2)) 250s 250s >s1 250s LLSPNGAGWVVAPITMHDSAQINMPWQRRKDFLVQACVPVLKNLYKRKYEKVIKSIVYER 250s LYIFRGLWSGGCA--RYFDPPRCYKRSPEFYLGQFHGPLVHIGTMGHTECLHYGYDIQVN 250s CNKHDNKVTPK 250s >s0 250s -----------------------------KTLCVTDEVAKPRILNRKEYERVVIYGGYQW 250s TILFTKVWNGGSG--FKCDPNRCLKQAKLYYLPLFHAPIVEAAHQAGGKSLKFELDIRQV 250s SAMNASHKSGN 250s >s3 250s -----------------------------KVYYVEEAGSPTKGTFEEDYDGLELGAGFGW 250s RTQLVRLWAKDCFNDTSKEPNTCFRKPSKLYNGEVREIVLEAAGYTKAGDMRYAAVQSVA 250s AAHTRNKTTDS 250s >s2 250s -----------------------------KTFYINVDTNPMKALYKHEYNRELSGIPLDW 250s SSLVGRLWAKDCFTTKLNDPSERFRPPTKGFNKEDCLIVLAVNVQTHGGTLRFGIPERVK 250s CDRSRSKSTGK 250s 250s 250s PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the 250s standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS 250s version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). 250s 250s Loading sequence file: test_data_n.fas 250s Alignment tree: ((s1 s2) (s0 s3)) 250s 250s >s1 250s ACGTTT-----TCGAACCCCCCGAAATTTTGGGCGCGCG-------------CACACACT 250s CATCACTCTCGACGCAAAAC------GGCT---GCACACACTCATCACTC----TCGACG 250s C-AAA--ACGGCTGCAAAACG-GCTGCACACACTCATCAC-- 250s >s0 250s A--TTTCTCTCTCAAACCCCCCGAAATTTTGGGCGCGCG-------------CACACACT 250s CATCACTCTCGACGCAAAACATTTTGGGCGCGCGCACACACTCATCACTCATTTT-G--- 250s ---------GGC-GC-------GC-GCACACACTCATCACTC 250s >s3 250s A--TTTCTCTCTCAAACCCCCCGAAATTTTGGGCGCGCG-------------CACACACT 250s CATCACTCTCGACGCAAAACATTTTGGGCGCGCGCACACACTCG----------TCG-CG 250s CGAAACTA---C-GC---ACGTGC-GCACACACTCATCACTC 250s >s2 250s ACGTTT-----TCGAACCCCCCGAAATTTT---C-CCCCCCCCCCCCCCCCCCCC-CACT 250s CATCACTCTCGACGCAAAAC------GGCT---GCACACACTCATCACTC----TCGACG 250s C-AAA--ACGGCTGCAAAACG-GCTGCACACACTCATCAC-- 250s 250s 250s PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the 250s standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS 250s version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). 250s 250s Loading sequence file: test_data_p.fas 250s Computing posterior matrix: (1) s1 vs. (2) s0 -- 250s 0 129 250s 1 100 250s ------------- 250s 0.5564424396 250s Computing posterior matrix: (1) s1 vs. (3) s3 -- 250s 0 129 250s 2 102 250s ------------- 250s 0.2607336938 250s Computing posterior matrix: (1) s1 vs. (4) s2 -- 250s 0 129 250s 3 102 250s ------------- 250s 0.4842562675 250s Computing posterior matrix: (2) s0 vs. (3) s3 -- 250s 1 100 250s 2 102 250s ------------- 250s 0.3741489649 250s Computing posterior matrix: (2) s0 vs. (4) s2 -- 250s 1 100 250s 3 102 250s ------------- 250s 0.3683230281 250s Computing posterior matrix: (3) s3 vs. (4) s2 -- 250s 2 102 250s 3 102 250s ------------- 250s 0.8540496826 250s Relaxing (1) s1 vs. (2) s0: 654 --> 516 -- done. 250s Relaxing (1) s1 vs. (3) s3: 864 --> 608 -- done. 250s Relaxing (1) s1 vs. (4) s2: 628 --> 499 -- done. 250s Relaxing (2) s0 vs. (3) s3: 694 --> 531 -- done. 250s Relaxing (2) s0 vs. (4) s2: 766 --> 588 -- done. 250s Relaxing (3) s3 vs. (4) s2: 249 --> 227 -- done. 250s Relaxing (1) s1 vs. (2) s0: 516 --> 397 -- done. 250s Relaxing (1) s1 vs. (3) s3: 608 --> 430 -- done. 250s Relaxing (1) s1 vs. (4) s2: 499 --> 405 -- done. 250s Relaxing (2) s0 vs. (3) s3: 531 --> 402 -- done. 250s Relaxing (2) s0 vs. (4) s2: 588 --> 425 -- done. 250s Relaxing (3) s3 vs. (4) s2: 227 --> 203 -- done. 250s 250s Alignment tree: ((s1 s0) (s3 s2)) 250s 250s [0] vs. [1]: 0.2394420803 250s [2] vs. [3]: 0.3004739285 250s [0,1] vs. [2,3]: 0.2197821587 250s [0,2,3] vs. [1]: 0.2272425592 250s [0,1] vs. [2,3]: 0.2197821587 250s [0,1,3] vs. [2]: 0.2441207469 250s [1,2] vs. [0,3]: 0.2414343655 250s [0,2,3] vs. [1]: 0.2272425592 250s [3] vs. [0,1,2]: 0.2492380887 250s [0,1,2] vs. [3]: 0.2492380887 250s [2,3] vs. [0,1]: 0.2197821587 250s [0,2] vs. [1,3]: 0.2459582537 250s [1] vs. [0,2,3]: 0.2272425592 250s [0,2] vs. [1,3]: 0.2459582537 250s [0,3] vs. [1,2]: 0.2414343655 250s [3] vs. [0,1,2]: 0.2492380887 250s [0,1,3] vs. [2]: 0.2441207469 250s [1,3] vs. [0,2]: 0.2459582537 250s [0,1,3] vs. [2]: 0.2441207469 250s [1,3] vs. [0,2]: 0.2459582537 250s [2] vs. [0,1,3]: 0.2441207469 250s [0] vs. [1,2,3]: 0.2267541587 250s [2,3] vs. [0,1]: 0.2197821587 250s [1] vs. [0,2,3]: 0.2272425592 250s [2] vs. [0,1,3]: 0.2441207469 250s [3] vs. [0,1,2]: 0.2492380887 250s [0] vs. [1,2,3]: 0.2267541587 250s [0,1,2] vs. [3]: 0.2492380887 250s [0] vs. [1,2,3]: 0.2267541587 250s [0,3] vs. [1,2]: 0.2414343655 250s [0,1,3] vs. [2]: 0.2441207469 250s [1,2,3] vs. [0]: 0.2267541587 250s [0,1,2] vs. [3]: 0.2492380887 250s [0,1,3] vs. [2]: 0.2441207469 250s [1,2] vs. [0,3]: 0.2414343655 250s [1,3] vs. [0,2]: 0.2459582537 250s [0,1] vs. [2,3]: 0.2197821587 250s [1,3] vs. [0,2]: 0.2459582537 250s [1,3] vs. [0,2]: 0.2459582537 250s [1,2,3] vs. [0]: 0.2267541587 250s [0] vs. [1,2,3]: 0.2267541587 250s [0,2] vs. [1,3]: 0.2459582537 250s [0,2,3] vs. [1]: 0.2272425592 250s [0,1,2] vs. [3]: 0.2492380887 250s [1,2] vs. [0,3]: 0.2414343655 250s [0,1,3] vs. [2]: 0.2441207469 250s [1,2,3] vs. [0]: 0.2267541587 250s [0,1] vs. [2,3]: 0.2197821587 250s [0,1,3] vs. [2]: 0.2441207469 250s [2,3] vs. [0,1]: 0.2197821587 250s [0] vs. [1,2,3]: 0.2267541587 250s [0,1,2] vs. [3]: 0.2492380887 250s [1,3] vs. [0,2]: 0.2459582537 250s [1,3] vs. [0,2]: 0.2459582537 250s [2,3] vs. [0,1]: 0.2197821587 250s [2] vs. [0,1,3]: 0.2441207469 250s [2,3] vs. [0,1]: 0.2197821587 250s [0,3] vs. [1,2]: 0.2414343655 250s [2,3] vs. [0,1]: 0.2197821587 250s [0,2,3] vs. [1]: 0.2272425592 250s [0,3] vs. [1,2]: 0.2414343655 250s [1] vs. [0,2,3]: 0.2272425592 250s [3] vs. [0,1,2]: 0.2492380887 250s [1,2] vs. [0,3]: 0.2414343655 250s [1,2,3] vs. [0]: 0.2267541587 250s [0,2] vs. [1,3]: 0.2459582537 250s [1,2,3] vs. [0]: 0.2267541587 250s [0,2,3] vs. [1]: 0.2272425592 250s [0,3] vs. [1,2]: 0.2414343655 250s [1,2] vs. [0,3]: 0.2414343655 250s [0,2] vs. [1,3]: 0.2459582537 250s [2,3] vs. [0,1]: 0.2197821587 250s [3] vs. [0,1,2]: 0.2492380887 250s [1,2] vs. [0,3]: 0.2414343655 250s [0,2,3] vs. [1]: 0.2272425592 250s [1,2] vs. [0,3]: 0.2414343655 250s [0] vs. [1,2,3]: 0.2267541587 250s [3] vs. [0,1,2]: 0.2492380887 250s [1] vs. [0,2,3]: 0.2272425592 250s [0,1,3] vs. [2]: 0.2441207469 250s [3] vs. [0,1,2]: >s1 250s LLSPNGAGWVVAPITMHDSAQINMPWQRRKDFLVQACVPVLKNLYKRKYEKVIKSIVYER 250s LYIFRGLWSGGCA--RYFDPPRCYKRSPEFYLGQFHGPLVHIGTMGHTECLHYGYDIQVN 250s CNKHDNKVTPK 250s >s0 250s -----------------------------KTLCVTDEVAKPRILNRKEYERVVIYGGYQW 250s TILFTKVWNGGSG--FKCDPNRCLKQAKLYYLPLFHAPIVEAAHQAGGKSLKFELDIRQV 250s SAMNASHKSGN 250s >s3 250s -----------------------------KVYYVEEAGSPTKGTFEEDYDGLELGAGFGW 250s RTQLVRLWAKDCFNDTSKEPNTCFRKPSKLYNGEVREIVLEAAGYTKAGDMRYAAVQSVA 250s AAHTRNKTTDS 250s >s2 250s -----------------------------KTFYINVDTNPMKALYKHEYNRELSGIPLDW 250s SSLVGRLWAKDCFTTKLNDPSERFRPPTKGFNKEDCLIVLAVNVQTHGGTLRFGIPERVK 250s CDRSRSKSTGK 250s 0.2492380887 250s [0,1,2] vs. [3]: 0.2492380887 250s [1] vs. [0,2,3]: 0.2272425592 250s [0,1,2] vs. [3]: 0.2492380887 250s [1] vs. [0,2,3]: 0.2272425592 250s [0,2,3] vs. [1]: 0.2272425592 250s [0,1,3] vs. [2]: 0.2441207469 250s [0,3] vs. [1,2]: 0.2414343655 250s [1] vs. [0,2,3]: 0.2272425592 250s 250s 250s PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the 250s standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS 250s version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). 250s 250s Loading sequence file: test_data_n.fas 250s Alignment tree: ((s1 s2) (s0 s3)) 250s 250s >s1 250s ACGTTT-----TCGAACCCCCCGAAATTTTGGGCGCGCG-----------CACACACTCA 250s TCACTCTCGACGCAAAAC------GGCTG----CACACACTCATCACTC---TCGACGC- 250s AAA--ACGGCTGCAAAACG-GCTGCACACACTCATCAC-- 250s >s2 250s ACGTTT-----TCGAACCCCCCGAAATTTT---CCCCCCCCCCCCCCCCCCCCCCACTCA 250s TCACTCTCGACGCAAAAC------GGCTG----CACACACTCATCACTC---TCGACGC- 250s AAA--ACGGCTGCAAAACG-GCTGCACACACTCATCAC-- 250s >s0 250s A--TTTCTCTCTCAAACCCCCCGAAATTTTGGGCGCGCG-----------CACACACTCA 250s TCACTCTCGACGCAAAACATTTTGGGC-GCGCGCACACACTCATCACTCATTTTG----- 250s -------GGC-GC-------GC-GCACACACTCATCACTC 250s >s3 250s A--TTTCTCTCTCAAACCCCCCGAAATTTTGGGCGCGCG-----------CACACACTCA 250s TCACTCTCGACGCAAAACATTTTGGGC-G----CGCGCA--CA-CACTC--GTCG-CGCG 250s AAACTA---C-GC---ACGTGC-GCACACACTCATCACTC 250s 250s autopkgtest [14:34:47]: test run-unit-test: -----------------------] 251s autopkgtest [14:34:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 251s run-unit-test PASS 251s autopkgtest [14:34:48]: @@@@@@@@@@@@@@@@@@@@ summary 251s run-unit-test PASS 269s nova [W] Using flock in prodstack6-arm64 269s Creating nova instance adt-plucky-arm64-probalign-20250315-143037-juju-7f2275-prod-proposed-migration-environment-15-74902140-a38f-4451-b9b2-1417ad701275 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 269s nova [W] Timed out waiting for 341ae8e3-5c3a-4819-8148-acb86cc03ce3 to get deleted.