0s autopkgtest [18:48:04]: starting date: 2024-03-09 0s autopkgtest [18:48:04]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [18:48:04]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.87558zsl/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 bali-phy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 db5.3/5.3.28+dfsg2-5 gdbm/1.23-5.1 mmdebstrap/1.4.3-6' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-3.secgroup --name adt-noble-arm64-bali-phy-20240309-184803-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 79s autopkgtest [18:49:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 80s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 80s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [429 kB] 80s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 80s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 80s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2629 kB] 80s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [579 kB] 80s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 80s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 80s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 80s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2931 kB] 81s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 81s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 81s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 82s Fetched 6798 kB in 1s (4553 kB/s) 83s Reading package lists... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Calculating upgrade... 86s The following packages were automatically installed and are no longer required: 86s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 86s ubuntu-advantage-tools 86s Use 'sudo apt autoremove' to remove them. 86s The following packages will be REMOVED: 86s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 86s The following NEW packages will be installed: 86s libgdbm-compat4t64 libgdbm6t64 libnuma1 libsensors-config libsensors5 86s numactl sysstat 86s The following packages have been kept back: 86s libperl5.38 86s The following packages will be upgraded: 86s efibootmgr perl-base perl-modules-5.38 python3-attr ubuntu-minimal 86s ubuntu-standard 87s 6 upgraded, 7 newly installed, 5 to remove and 1 not upgraded. 87s Need to get 5605 kB of archives. 87s After this operation, 1944 kB disk space will be freed. 87s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB] 87s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB] 87s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B] 87s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 87s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.535 [10.5 kB] 87s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1 [23.5 kB] 87s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.535 [10.5 kB] 87s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 efibootmgr arm64 18-1build1 [31.5 kB] 87s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors-config all 1:3.6.0-9 [5458 B] 87s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors5 arm64 1:3.6.0-9 [26.9 kB] 87s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1 [39.5 kB] 87s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 python3-attr all 23.2.0-2 [48.6 kB] 87s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 sysstat arm64 12.6.1-1ubuntu1 [480 kB] 88s Preconfiguring packages ... 88s Fetched 5605 kB in 1s (5960 kB/s) 88s (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 ... 74662 files and directories currently installed.) 88s Removing dpkg-dev (1.22.4ubuntu5) ... 88s Removing libdpkg-perl (1.22.4ubuntu5) ... 88s Removing perl (5.38.2-3) ... 88s (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 ... 74081 files and directories currently installed.) 88s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ... 88s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 88s Setting up perl-base (5.38.2-3.2) ... 88s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested: 88s python3-gdbm:arm64 depends on libgdbm6 (>= 1.16). 88s man-db depends on libgdbm6 (>= 1.16). 88s libperl5.38:arm64 depends on libgdbm6 (>= 1.21). 88s libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16). 88s 88s (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 ... 74081 files and directories currently installed.) 88s Removing libgdbm6:arm64 (1.23-5) ... 88s Selecting previously unselected package libgdbm6t64:arm64. 88s (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 ... 74076 files and directories currently installed.) 88s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ... 88s Unpacking libgdbm6t64:arm64 (1.23-5.1) ... 89s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested: 89s libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3). 89s 89s (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 ... 74082 files and directories currently installed.) 89s Removing libgdbm-compat4:arm64 (1.23-5) ... 89s Selecting previously unselected package libgdbm-compat4t64:arm64. 89s (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 ... 74077 files and directories currently installed.) 89s Preparing to unpack .../00-libgdbm-compat4t64_1.23-5.1_arm64.deb ... 89s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 89s Preparing to unpack .../01-perl-modules-5.38_5.38.2-3.2_all.deb ... 89s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 89s Preparing to unpack .../02-ubuntu-minimal_1.535_arm64.deb ... 89s Unpacking ubuntu-minimal (1.535) over (1.534) ... 89s Selecting previously unselected package libnuma1:arm64. 89s Preparing to unpack .../03-libnuma1_2.0.18-1_arm64.deb ... 89s Unpacking libnuma1:arm64 (2.0.18-1) ... 89s Preparing to unpack .../04-ubuntu-standard_1.535_arm64.deb ... 89s Unpacking ubuntu-standard (1.535) over (1.534) ... 89s Preparing to unpack .../05-efibootmgr_18-1build1_arm64.deb ... 89s Unpacking efibootmgr (18-1build1) over (18-1) ... 89s Selecting previously unselected package libsensors-config. 89s Preparing to unpack .../06-libsensors-config_1%3a3.6.0-9_all.deb ... 89s Unpacking libsensors-config (1:3.6.0-9) ... 89s Selecting previously unselected package libsensors5:arm64. 89s Preparing to unpack .../07-libsensors5_1%3a3.6.0-9_arm64.deb ... 89s Unpacking libsensors5:arm64 (1:3.6.0-9) ... 89s Selecting previously unselected package numactl. 89s Preparing to unpack .../08-numactl_2.0.18-1_arm64.deb ... 89s Unpacking numactl (2.0.18-1) ... 89s Preparing to unpack .../09-python3-attr_23.2.0-2_all.deb ... 90s Unpacking python3-attr (23.2.0-2) over (23.2.0-1) ... 90s Selecting previously unselected package sysstat. 90s Preparing to unpack .../10-sysstat_12.6.1-1ubuntu1_arm64.deb ... 90s Unpacking sysstat (12.6.1-1ubuntu1) ... 90s Setting up python3-attr (23.2.0-2) ... 90s Setting up efibootmgr (18-1build1) ... 90s Setting up libgdbm6t64:arm64 (1.23-5.1) ... 90s Setting up ubuntu-minimal (1.535) ... 90s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 90s Setting up libsensors-config (1:3.6.0-9) ... 90s Setting up ubuntu-standard (1.535) ... 90s Setting up perl-modules-5.38 (5.38.2-3.2) ... 90s Setting up libsensors5:arm64 (1:3.6.0-9) ... 90s Setting up libnuma1:arm64 (2.0.18-1) ... 90s Setting up sysstat (12.6.1-1ubuntu1) ... 90s 90s Creating config file /etc/default/sysstat with new version 90s update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode 90s Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-collect.timer → /usr/lib/systemd/system/sysstat-collect.timer. 91s Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-summary.timer → /usr/lib/systemd/system/sysstat-summary.timer. 91s Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /usr/lib/systemd/system/sysstat.service. 93s Setting up numactl (2.0.18-1) ... 93s Processing triggers for man-db (2.12.0-3) ... 94s Processing triggers for libc-bin (2.39-0ubuntu2) ... 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s The following packages will be REMOVED: 96s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 96s ubuntu-advantage-tools* 96s 0 upgraded, 0 newly installed, 6 to remove and 0 not upgraded. 96s After this operation, 52.0 MB disk space will be freed. 96s (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 ... 74176 files and directories currently installed.) 96s Removing libperl5.38:arm64 (5.38.2-3) ... 96s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ... 96s Removing lto-disabled-list (47) ... 96s Removing make (4.3-4.1build1) ... 96s Removing perl-modules-5.38 (5.38.2-3.2) ... 96s Removing ubuntu-advantage-tools (31.1) ... 96s Processing triggers for man-db (2.12.0-3) ... 96s Processing triggers for libc-bin (2.39-0ubuntu2) ... 97s (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 ... 72199 files and directories currently installed.) 97s Purging configuration files for ubuntu-advantage-tools (31.1) ... 98s sh: Attempting to set up Debian/Ubuntu apt sources automatically 98s sh: Distribution appears to be Ubuntu 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s eatmydata is already the newest version (131-1). 100s dbus is already the newest version (1.14.10-4ubuntu1). 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s rng-tools-debian is already the newest version (2.4). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s haveged is already the newest version (1.9.14-1ubuntu1). 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s The following additional packages will be installed: 103s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 103s make perl perl-modules-5.38 103s Suggested packages: 103s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 103s libterm-readline-gnu-perl | libterm-readline-perl-perl 103s libtap-harness-archive-perl 103s Recommended packages: 103s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 103s libfile-fcntllock-perl 104s The following packages will be REMOVED: 104s libdb5.3 104s The following NEW packages will be installed: 104s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 104s lto-disabled-list make perl perl-modules-5.38 104s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 104s Need to get 7257 kB/10.4 MB of archives. 104s After this operation, 56.1 MB of additional disk space will be used. 104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB] 106s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB] 106s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB] 106s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB] 106s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] 106s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB] 107s Fetched 7257 kB in 2s (2954 kB/s) 107s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: 107s libsasl2-modules-db:arm64 depends on libdb5.3. 107s libpython3.12-stdlib:arm64 depends on libdb5.3. 107s libpam-modules:arm64 depends on libdb5.3. 107s iproute2 depends on libdb5.3. 107s apt-utils depends on libdb5.3. 107s 108s (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 ... 72198 files and directories currently installed.) 108s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ... 108s Selecting previously unselected package libdb5.3t64:arm64. 108s (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 ... 72192 files and directories currently installed.) 108s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ... 108s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 108s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 108s Selecting previously unselected package perl-modules-5.38. 108s (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 ... 72198 files and directories currently installed.) 108s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 108s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 108s Selecting previously unselected package libgdbm-compat4t64:arm64. 108s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ... 108s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 108s Selecting previously unselected package libperl5.38t64:arm64. 108s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ... 108s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ... 108s Selecting previously unselected package perl. 108s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ... 108s Unpacking perl (5.38.2-3.2) ... 108s Selecting previously unselected package libdpkg-perl. 108s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 108s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 109s Selecting previously unselected package make. 109s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ... 109s Unpacking make (4.3-4.1build1) ... 109s Selecting previously unselected package lto-disabled-list. 109s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 109s Unpacking lto-disabled-list (47) ... 109s Selecting previously unselected package dpkg-dev. 109s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 109s Unpacking dpkg-dev (1.22.4ubuntu5) ... 109s Setting up lto-disabled-list (47) ... 109s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 109s Setting up make (4.3-4.1build1) ... 109s Setting up perl-modules-5.38 (5.38.2-3.2) ... 109s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ... 109s Setting up perl (5.38.2-3.2) ... 109s Setting up libdpkg-perl (1.22.4ubuntu5) ... 109s Setting up dpkg-dev (1.22.4ubuntu5) ... 109s Processing triggers for man-db (2.12.0-3) ... 110s Processing triggers for libc-bin (2.39-0ubuntu2) ... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s The following packages will be REMOVED: 111s cloud-init* python3-configobj* python3-debconf* 112s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 112s After this operation, 3248 kB disk space will be freed. 112s (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 ... 74750 files and directories currently installed.) 112s Removing cloud-init (24.1-0ubuntu1) ... 113s Removing python3-configobj (5.0.8-3) ... 113s Removing python3-debconf (1.5.86) ... 113s Processing triggers for man-db (2.12.0-3) ... 114s (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 ... 74361 files and directories currently installed.) 114s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 119s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 119s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s linux-generic is already the newest version (6.8.0-11.11+1). 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 122s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 122s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 122s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 123s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s autopkgtest [18:50:10]: rebooting testbed after setup commands that affected boot 378s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 384s autopkgtest [18:54:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 384s autopkgtest [18:54:28]: testbed dpkg architecture: arm64 386s autopkgtest [18:54:30]: @@@@@@@@@@@@@@@@@@@@ apt-source bali-phy 388s Get:1 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (dsc) [2216 B] 388s Get:2 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (tar) [1124 kB] 388s Get:3 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (diff) [5408 B] 389s gpgv: Signature made Tue Dec 19 15:00:40 2023 UTC 389s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 389s gpgv: Can't check signature: No public key 389s dpkg-source: warning: cannot verify inline signature for ./bali-phy_3.6.1+dfsg-2build1.dsc: no acceptable signature found 389s autopkgtest [18:54:33]: testing package bali-phy version 3.6.1+dfsg-2build1 389s autopkgtest [18:54:33]: build not needed 390s autopkgtest [18:54:34]: test run-unit-test: preparing testbed 393s Reading package lists... 393s Building dependency tree... 393s Reading state information... 393s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 393s Starting 2 pkgProblemResolver with broken count: 0 393s Done 394s Done 394s Starting pkgProblemResolver with broken count: 0 394s Starting 2 pkgProblemResolver with broken count: 0 394s Done 395s The following additional packages will be installed: 395s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 395s libboost-chrono1.83.0 libboost-filesystem1.83.0 395s libboost-program-options1.83.0 libboost-random1.83.0 libcairo2 395s libfontconfig1 libpixman-1-0 libxcb-render0 libxcb-shm0 libxrender1 395s Suggested packages: 395s figtree seaview 395s Recommended packages: 395s r-base gnuplot 395s The following NEW packages will be installed: 395s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 395s libboost-chrono1.83.0 libboost-filesystem1.83.0 395s libboost-program-options1.83.0 libboost-random1.83.0 libcairo2 395s libfontconfig1 libpixman-1-0 libxcb-render0 libxcb-shm0 libxrender1 396s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 396s 1 not fully installed or removed. 396s Need to get 11.3 MB of archives. 396s After this operation, 36.9 MB of additional disk space will be used. 396s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-chrono1.83.0 arm64 1.83.0-2ubuntu1 [322 kB] 396s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-2ubuntu1 [366 kB] 396s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2ubuntu1 [410 kB] 396s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-random1.83.0 arm64 1.83.0-2ubuntu1 [320 kB] 396s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 396s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 396s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 396s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 396s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 396s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 396s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 396s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 396s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 397s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 bali-phy arm64 3.6.1+dfsg-2build1 [7575 kB] 398s Fetched 11.3 MB in 2s (5383 kB/s) 398s Selecting previously unselected package libboost-chrono1.83.0:arm64. 398s (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 ... 74306 files and directories currently installed.) 398s Preparing to unpack .../00-libboost-chrono1.83.0_1.83.0-2ubuntu1_arm64.deb ... 398s Unpacking libboost-chrono1.83.0:arm64 (1.83.0-2ubuntu1) ... 399s Selecting previously unselected package libboost-filesystem1.83.0:arm64. 399s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_arm64.deb ... 399s Unpacking libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 399s Selecting previously unselected package libboost-program-options1.83.0:arm64. 399s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_arm64.deb ... 399s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 399s Selecting previously unselected package libboost-random1.83.0:arm64. 399s Preparing to unpack .../03-libboost-random1.83.0_1.83.0-2ubuntu1_arm64.deb ... 399s Unpacking libboost-random1.83.0:arm64 (1.83.0-2ubuntu1) ... 399s Selecting previously unselected package fonts-dejavu-mono. 399s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8_all.deb ... 399s Unpacking fonts-dejavu-mono (2.37-8) ... 399s Selecting previously unselected package fonts-dejavu-core. 399s Preparing to unpack .../05-fonts-dejavu-core_2.37-8_all.deb ... 399s Unpacking fonts-dejavu-core (2.37-8) ... 399s Selecting previously unselected package fontconfig-config. 399s Preparing to unpack .../06-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 399s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 399s Selecting previously unselected package libfontconfig1:arm64. 399s Preparing to unpack .../07-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 399s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 399s Selecting previously unselected package libpixman-1-0:arm64. 399s Preparing to unpack .../08-libpixman-1-0_0.42.2-1_arm64.deb ... 399s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 400s Selecting previously unselected package libxcb-render0:arm64. 400s Preparing to unpack .../09-libxcb-render0_1.15-1_arm64.deb ... 400s Unpacking libxcb-render0:arm64 (1.15-1) ... 400s Selecting previously unselected package libxcb-shm0:arm64. 400s Preparing to unpack .../10-libxcb-shm0_1.15-1_arm64.deb ... 400s Unpacking libxcb-shm0:arm64 (1.15-1) ... 400s Selecting previously unselected package libxrender1:arm64. 400s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 400s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 400s Selecting previously unselected package libcairo2:arm64. 400s Preparing to unpack .../12-libcairo2_1.18.0-1_arm64.deb ... 400s Unpacking libcairo2:arm64 (1.18.0-1) ... 400s Selecting previously unselected package bali-phy. 400s Preparing to unpack .../13-bali-phy_3.6.1+dfsg-2build1_arm64.deb ... 400s Unpacking bali-phy (3.6.1+dfsg-2build1) ... 400s Setting up libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 400s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 400s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 400s Setting up libxcb-render0:arm64 (1.15-1) ... 400s Setting up libboost-random1.83.0:arm64 (1.83.0-2ubuntu1) ... 400s Setting up libxcb-shm0:arm64 (1.15-1) ... 400s Setting up libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 400s Setting up fonts-dejavu-mono (2.37-8) ... 400s Setting up fonts-dejavu-core (2.37-8) ... 400s Setting up libboost-chrono1.83.0:arm64 (1.83.0-2ubuntu1) ... 400s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 400s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 400s Setting up libcairo2:arm64 (1.18.0-1) ... 400s Setting up bali-phy (3.6.1+dfsg-2build1) ... 400s Setting up autopkgtest-satdep (0) ... 400s Processing triggers for man-db (2.12.0-3) ... 401s Processing triggers for libc-bin (2.39-0ubuntu2) ... 408s (Reading database ... 75031 files and directories currently installed.) 408s Removing autopkgtest-satdep (0) ... 409s autopkgtest [18:54:53]: test run-unit-test: [----------------------- 409s VERSION: 3.6.1 [3.6.1] 409s BUILD: Dec 19 2023 14:51:09 409s ARCH: linux aarch64 409s COMPILER: gcc 13.2.0 aarch64 409s Bayesian Inference of Alignment and Phylogeny 409s Usage: bali-phy [ ...] [OPTIONS] 409s Basic options: 409s 409s General options: 409s -h [ --help ] [=arg(=basic)] Print usage information. 409s -v [ --version ] Print version information. 409s -t [ --test ] Analyze the initial values and exit. 409s -c [ --config ] arg Command file to read. 409s 409s MCMC options: 409s -i [ --iterations ] arg The number of iterations to run. 409s -n [ --name ] arg Name for the output directory to create. 409s 409s Parameter options: 409s --align arg Sequence file & initial alignment. 409s -T [ --tree ] arg File with initial tree 409s 409s Model options: 409s -A [ --alphabet ] arg The alphabet. 409s -S [ --smodel ] arg Substitution model. 409s -I [ --imodel ] arg Insertion-deletion model. 409s -R [ --scale ] arg Prior on the scale. 409s -L [ --link ] arg Link partitions. 409s 409s Showing basic command line options. Not all options are shown! 409s * See `bali-phy help advanced` to see more options. 409s 409s See `bali-phy help option` for help on option. For example, 409s * `bali-phy help alphabet` shows help on the --alphabet command. 409s * `bali-phy help normal` shows help on the normal distribution. 409s * `bali-phy help tn93` shows help on the TN93 model. 409s * `bali-phy help log` shows help on the log function. 409s 409s To see help on one of the following topics, run `bali-phy help topic` 409s 409s alphabets/ commands/ distributions/ functions/ models/ 409s parameters/ 409s 411s T:topology ~ uniform on tree topologies 411s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 411s 411s Partition P1: 411s file = sequences/5S-rRNA/5d.fasta 411s alphabet = DNA 411s subst = tn93 (S1) 411s indel = rs07 (I1) 411s scale ~ gamma[0.5,2] (Scale1) 411s 411s Substitution model S1 priors: 411s tn93:kappaPur ~ log_normal[log[2],0.25] 411s tn93:kappaPyr ~ log_normal[log[2],0.25] 411s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 411s 411s Insertion/deletion model I1 priors: 411s rs07:log_rate ~ laplace[-4,0.707] 411s rs07:mean_length ~ shifted_exponential[10,1] 411s 411s iter = 0 prior = -33.790694740510119 likelihood = -1483.234816657316969 posterior = -1517.025511397827131 prior_A = -37.769371881270153 |A| = 126 #indels = 4 |indels| = 12 #substs = 260 P1/likelihood = -1483.234816657316969 P1/prior_A = -37.769371881270153 P1/|A| = 126 P1/#indels = 4 P1/|indels| = 12 P1/#substs = 260 Scale[1]*|T| = 0.312887353008491 |T| = 0.480024947609822 rs07:log_rate = -4.360922545264546 rs07:mean_length = 4.97131803540848 tn93:kappaPur = 2.674531993935546 tn93:kappaPyr = 1.9206197631901862 tn93:pi[A] = 0.3300618075544738 tn93:pi[C] = 0.1097957500009612 tn93:pi[G] = 0.32253993433256817 tn93:pi[T] = 0.23760250811199682 scale[1] = 0.6518147745579553 scale1 = 0.6518147745579553 411s 411s start time: Sat Mar 9 18:54:53 2024 411s 411s end time: Sat Mar 9 18:54:55 2024 411s 411s total (elapsed) time: 2 seconds 411s total (CPU) time: 1 second 412s Created directory '5d-1/' for output files. 414s T:topology ~ uniform on tree topologies 414s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 414s 414s Partition P1: 414s file = sequences/5S-rRNA/5d.fasta 414s alphabet = DNA 414s subst = tn93 (S1) 414s indel = rs07 (I1) 414s scale ~ gamma[0.5,2] (Scale1) 414s 414s Substitution model S1 priors: 414s tn93:kappaPur ~ log_normal[log[2],0.25] 414s tn93:kappaPyr ~ log_normal[log[2],0.25] 414s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 414s 414s Insertion/deletion model I1 priors: 414s rs07:log_rate ~ laplace[-4,0.707] 414s rs07:mean_length ~ shifted_exponential[10,1] 414s 414s Beginning pre-burnin: 3 iterations. 414s Start #1 prior = -33.7907 likelihood = -1483.23 |T| = 0.480025 Scale1*|T| = 0.312887 414s 414s Tree (S)ize #1 prior = -15.3853 likelihood = -918.651 |T| = 0.351153 Scale1*|T| = 13.4823 414s Tree (S)ize #2 prior = -8.67375 likelihood = -921.505 |T| = 0.557146 Scale1*|T| = 11.6476 414s Tree (S)ize #3 prior = -10.9776 likelihood = -916.148 |T| = 1.76036 Scale1*|T| = 17.2445 414s 414s (S)+Branch (L)engths #1 prior = -16.2584 likelihood = -913.26 |T| = 2.47609 Scale1*|T| = 13.0113 414s (S)+Branch (L)engths #2 prior = -16.8078 likelihood = -894.729 |T| = 3.04489 Scale1*|T| = 6.59351 414s (S)+Branch (L)engths #3 prior = -13.1975 likelihood = -886.107 |T| = 2.05444 Scale1*|T| = 5.6581 414s 414s (S)+(L)+(P)arameters #1 prior = -18.8487 likelihood = -843.212 |T| = 1.94953 Scale1*|T| = 5.31078 414s (S)+(L)+(P)arameters #2 prior = -13.6692 likelihood = -799.58 |T| = 1.45035 Scale1*|T| = 5.99899 414s (S)+(L)+(P)arameters #3 prior = -16.2199 likelihood = -794.492 |T| = 1.25891 Scale1*|T| = 6.13717 414s 414s (S)+(L)+(P)+NNI #1 prior = -14.3438 likelihood = -794.463 |T| = 0.950972 Scale1*|T| = 8.25425 414s (S)+(L)+(P)+NNI #2 prior = -13.0194 likelihood = -796.879 |T| = 0.922848 Scale1*|T| = 5.82845 414s (S)+(L)+(P)+NNI #3 prior = -20.7114 likelihood = -793.84 |T| = 2.12375 Scale1*|T| = 5.74906 414s (S)+(L)+(P)+NNI #4 prior = -17.9262 likelihood = -792.257 |T| = 1.86364 Scale1*|T| = 6.4008 414s 414s SPR #1 prior = -17.1706 likelihood = -791.452 |T| = 2.03026 Scale1*|T| = 7.65838 414s 414s (S)+(L)+(P)+NNI #1 prior = -19.9971 likelihood = -792.17 |T| = 2.12702 Scale1*|T| = 8.17853 414s (S)+(L)+(P)+NNI #2 prior = -12.6645 likelihood = -794.309 |T| = 1.28717 Scale1*|T| = 7.80855 414s (S)+(L)+(P)+NNI #3 prior = -14.7901 likelihood = -792.908 |T| = 1.42784 Scale1*|T| = 10.0019 414s 414s Finished pre-burnin in 0.06 seconds. 414s 414s 414s BAli-Phy does NOT detect how many iterations is sufficient: 414s You need to monitor convergence and kill it when done. 414s Maximum number of iterations set to 50. 414s 414s Beginning MCMC computations. 414s - Future screen output sent to '5d-1/C1.out' 414s - Future debugging output sent to '5d-1/C1.err' 414s - Sampled trees logged to '5d-1/C1.trees' 414s - Sampled alignments logged to '5d-1/C1.P.fastas' 414s - Run info written to '5d-1/C1.run.json' 414s - Sampled numerical parameters logged to '5d-1/C1.log' as TSV 414s 414s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 414s See the manual at http://www.bali-phy.org/README.xhtml for further information. 418s Created directory '5d-2/' for output files. 419s Partition #1: 126 columns -> 110 unique patterns. 419s T:topology ~ uniform on tree topologies 419s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 419s 419s Partition P1: 419s file = sequences/5S-rRNA/5d.fasta 419s alphabet = DNA 419s subst = tn93 (S1) 419s indel = none 419s scale ~ gamma[0.5,2] (Scale1) 419s 420s Substitution model S1 priors: 420s tn93:kappaPur ~ log_normal[log[2],0.25] 420s tn93:kappaPyr ~ log_normal[log[2],0.25] 420s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 420s 420s Beginning pre-burnin: 3 iterations. 420s Start #1 prior = 3.66627 likelihood = -1521.58 |T| = 0.596738 Scale1*|T| = 0.388962 420s 420s Tree (S)ize #1 prior = -20.0519 likelihood = -925.895 |T| = 0.882719 Scale1*|T| = 34.6447 420s Tree (S)ize #2 prior = -24.3393 likelihood = -921.384 |T| = 0.882719 Scale1*|T| = 42.0429 420s Tree (S)ize #3 prior = -24.233 likelihood = -921.47 |T| = 0.882719 Scale1*|T| = 41.8591 420s 420s (S)+Branch (L)engths #1 prior = -21.242 likelihood = -918.932 |T| = 2.6265 Scale1*|T| = 54.994 420s (S)+Branch (L)engths #2 prior = -20.0058 likelihood = -915.641 |T| = 2.85599 Scale1*|T| = 52.1019 420s (S)+Branch (L)engths #3 prior = -18.7336 likelihood = -915.654 |T| = 3.4078 Scale1*|T| = 36.1988 420s 420s (S)+(L)+(P)arameters #1 prior = -14.0743 likelihood = -838.854 |T| = 2.16918 Scale1*|T| = 17.0259 420s (S)+(L)+(P)arameters #2 prior = -8.3735 likelihood = -827.845 |T| = 1.26424 Scale1*|T| = 9.98903 420s (S)+(L)+(P)arameters #3 prior = -9.91045 likelihood = -825.447 |T| = 1.00143 Scale1*|T| = 10.5296 420s 420s (S)+(L)+(P)+NNI #1 prior = -15.3467 likelihood = -816.19 |T| = 2.26734 Scale1*|T| = 8.40198 420s (S)+(L)+(P)+NNI #2 prior = -8.19633 likelihood = -792.187 |T| = 1.91628 Scale1*|T| = 6.5609 420s (S)+(L)+(P)+NNI #3 prior = -10.4653 likelihood = -794.019 |T| = 2.00651 Scale1*|T| = 7.691 420s (S)+(L)+(P)+NNI #4 prior = -10.5093 likelihood = -794.981 |T| = 1.83101 Scale1*|T| = 8.14948 420s 420s SPR #1 prior = -9.71503 likelihood = -794.17 |T| = 2.01453 Scale1*|T| = 9.01076 420s 420s (S)+(L)+(P)+NNI #1 prior = -7.67389 likelihood = -790.993 |T| = 0.925182 Scale1*|T| = 6.89699 420s (S)+(L)+(P)+NNI #2 prior = -7.38032 likelihood = -793.615 |T| = 1.83607 Scale1*|T| = 6.24615 420s (S)+(L)+(P)+NNI #3 prior = -6.06074 likelihood = -791.981 |T| = 1.24881 Scale1*|T| = 7.05904 420s 420s Finished pre-burnin in 0.06 seconds. 420s 420s 420s BAli-Phy does NOT detect how many iterations is sufficient: 420s You need to monitor convergence and kill it when done. 420s Maximum number of iterations set to 200. 420s 420s Beginning MCMC computations. 420s - Future screen output sent to '5d-2/C1.out' 420s - Future debugging output sent to '5d-2/C1.err' 420s - Sampled trees logged to '5d-2/C1.trees' 420s - Sampled alignments logged to '5d-2/C1.P.fastas' 420s - Run info written to '5d-2/C1.run.json' 420s - Sampled numerical parameters logged to '5d-2/C1.log' as TSV 420s 420s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 420s See the manual at http://www.bali-phy.org/README.xhtml for further information. 421s Created directory '5d-3/' for output files. 423s T:topology ~ uniform on tree topologies 423s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 423s 423s Partition P1: 423s file = sequences/5S-rRNA/5d.fasta 423s alphabet = DNA 423s subst = tn93 (S1) 423s indel = rs07 (I1) 423s scale ~ gamma[0.5,2] (Scale1) 423s 423s Substitution model S1 priors: 423s tn93:kappaPur ~ log_normal[log[2],0.25] 423s tn93:kappaPyr ~ log_normal[log[2],0.25] 423s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 423s 423s Insertion/deletion model I1 priors: 423s rs07:log_rate ~ laplace[-4,0.707] 423s rs07:mean_length ~ shifted_exponential[10,1] 423s 423s Beginning pre-burnin: 3 iterations. 423s Start #1 prior = -47.9409 likelihood = -1440.04 |T| = 1.6202 Scale1*|T| = 0.774233 423s 423s Tree (S)ize #1 prior = -23.936 likelihood = -1090.06 |T| = 1.55109 Scale1*|T| = 38.3738 423s Tree (S)ize #2 prior = -16.9491 likelihood = -1061.21 |T| = 1.98453 Scale1*|T| = 14.3606 423s Tree (S)ize #3 prior = -17.0466 likelihood = -1061.12 |T| = 1.98453 Scale1*|T| = 14.7012 423s 423s (S)+Branch (L)engths #1 prior = -10.9357 likelihood = -1012.14 |T| = 1.02422 Scale1*|T| = 6.38795 423s (S)+Branch (L)engths #2 prior = -10.5604 likelihood = -1005.09 |T| = 1.00336 Scale1*|T| = 6.42769 424s (S)+Branch (L)engths #3 prior = -13.9769 likelihood = -1008.5 |T| = 1.64121 Scale1*|T| = 6.77867 424s 424s (S)+(L)+(P)arameters #1 prior = -19.603 likelihood = -890.296 |T| = 1.77355 Scale1*|T| = 9.38177 424s (S)+(L)+(P)arameters #2 prior = -26.1965 likelihood = -805.829 |T| = 1.56125 Scale1*|T| = 9.75419 424s (S)+(L)+(P)arameters #3 prior = -19.3711 likelihood = -795.866 |T| = 1.19902 Scale1*|T| = 6.66913 424s 424s (S)+(L)+(P)+NNI #1 prior = -18.9506 likelihood = -798.228 |T| = 1.90563 Scale1*|T| = 6.32012 424s (S)+(L)+(P)+NNI #2 prior = -19.2306 likelihood = -795.256 |T| = 1.56343 Scale1*|T| = 6.15883 424s (S)+(L)+(P)+NNI #3 prior = -18.0138 likelihood = -800.008 |T| = 1.04069 Scale1*|T| = 5.78605 424s (S)+(L)+(P)+NNI #4 prior = -22.1681 likelihood = -793.584 |T| = 1.19718 Scale1*|T| = 7.41751 424s 424s SPR #1 prior = -19.4803 likelihood = -791.401 |T| = 0.833946 Scale1*|T| = 7.17006 424s 424s (S)+(L)+(P)+NNI #1 prior = -20.3729 likelihood = -791.776 |T| = 1.41557 Scale1*|T| = 6.71665 424s (S)+(L)+(P)+NNI #2 prior = -21.2962 likelihood = -791.517 |T| = 1.34375 Scale1*|T| = 6.42068 424s (S)+(L)+(P)+NNI #3 prior = -18.2609 likelihood = -794.356 |T| = 1.66645 Scale1*|T| = 5.84807 424s 424s Finished pre-burnin in 0.1 seconds. 424s 424s 424s BAli-Phy does NOT detect how many iterations is sufficient: 424s You need to monitor convergence and kill it when done. 424s Maximum number of iterations set to 100. 424s 424s Beginning MCMC computations. 424s - Future screen output sent to '5d-3/C1.out' 424s - Future debugging output sent to '5d-3/C1.err' 424s - Sampled trees logged to '5d-3/C1.trees' 424s - Sampled alignments logged to '5d-3/C1.P.fastas' 424s - Run info written to '5d-3/C1.run.json' 424s - Sampled numerical parameters logged to '5d-3/C1.log' as TSV 424s 424s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 424s See the manual at http://www.bali-phy.org/README.xhtml for further information. 430s /usr/bin/bp-analyze:452: SyntaxWarning: invalid escape sequence '\s' 430s self.version = self.find_header_attribute("VERSION").split('\s+')[0] 430s /usr/bin/bp-analyze:1118: SyntaxWarning: invalid escape sequence '\s' 430s m = re.search('([^\s]+) ~ ([^\s]+)\s+\((.+),(.+)\)',line) 430s /usr/bin/bp-analyze:1126: SyntaxWarning: invalid escape sequence '\s' 430s m = re.search('t @ (.+)\s+Ne = ([^ ]+)\s+burnin = (Not Converged!|[^ ]+)', lines[i]) 430s /usr/bin/bp-analyze:1135: SyntaxWarning: invalid escape sequence '\s' 430s m = re.search('PSRF-80%CI = ([^ ]+)\s+PSRF-RCF = ([^ ]+)',lines[i]) 430s /usr/bin/bp-analyze:1142: SyntaxWarning: invalid escape sequence '\s' 430s m = re.search('\s+(.+) = (.+)', line) 430s /usr/bin/bp-analyze:1227: SyntaxWarning: invalid escape sequence '\(' 430s m = re.search(' const.: ([^ ]+) \(([^ ]+)\%\)', line) 430s /usr/bin/bp-analyze:1232: SyntaxWarning: invalid escape sequence '\(' 430s m = re.search('inform.: ([^ ]+) \(([^ ]+)\%\)', line) 430s /usr/bin/bp-analyze:2092: SyntaxWarning: invalid escape sequence '\[' 430s asdsf = self.get_value_from_file('Results/partitions.bs','ASDSF\[min=0.100\] =') 430s Program 'gnuplot' not found: Some graphs will not be generated. 430s 430s Program 'R' not found: Some mixing graphs will not be generated. 430s 430s Creating new directory Results/ for summary files. 430s Summarizing distribution of numerical parameters: done. 430s Analyzing scalar variables: done. 430s 430s Summarizing topology distribution: done. 431s Drawing trees: c50 c66 c80 c90 c95 c99 c100 greedy MAP . done. 431s 431s Generate mixing diagnostics for topologies ... done. 431s Generate SRQ plot for partitions: done. 431s Generate SRQ plot for c50 tree: done. 431s Computing initial alignments: done. 431s 431s Computing WPD alignments: done. 431s Computing ancestral state alignment: done. 431s Drawing alignments: **** done. 431s Generating AU values for 'P1.initial'... done. 431s Generating AU values for 'P1.max'... done. 431s 431s NOTE: burnin (scalar) <= Not Converged! 431s NOTE: min_ESS (scalar) = 8.008 431s NOTE: min_ESS (partition) = 0.000 431s NOTE: ASDSF = NA 431s NOTE: MSDSF = NA 431s NOTE: PSRF-80%CI = NA 431s NOTE: PSRF-RCF = NA 431s 431s Report written to 'Results/index.html 432s autopkgtest [18:55:16]: test run-unit-test: -----------------------] 432s run-unit-test PASS 432s autopkgtest [18:55:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 432s autopkgtest [18:55:16]: @@@@@@@@@@@@@@@@@@@@ summary 432s run-unit-test PASS 437s Creating nova instance adt-noble-arm64-bali-phy-20240309-184803-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240308.img (UUID ddbc0ee7-bb97-4aa3-b5e1-9386758c2ba2)...