0s autopkgtest [02:24:33]: starting date and time: 2026-02-05 02:24:33+0000 0s autopkgtest [02:24:33]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [02:24:33]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m7q3xfu5/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade bali-phy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-14.secgroup --name adt-resolute-ppc64el-bali-phy-20260205-022433-juju-7f2275-prod-proposed-migration-environment-2-1beb210d-1689-4cd4-aff6-923e8f570337 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 9s Creating nova instance adt-resolute-ppc64el-bali-phy-20260205-022433-juju-7f2275-prod-proposed-migration-environment-2-1beb210d-1689-4cd4-aff6-923e8f570337 from image adt/ubuntu-resolute-ppc64el-server-20260205.img (UUID f866c950-0b62-4023-bac6-0f13279e15ed)... 70s autopkgtest [02:25:43]: testbed dpkg architecture: ppc64el 70s autopkgtest [02:25:43]: testbed apt version: 3.1.14 71s autopkgtest [02:25:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 71s autopkgtest [02:25:44]: testbed release detected to be: None 72s autopkgtest [02:25:45]: updating testbed package index (apt update) 72s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 72s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 72s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 72s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 72s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 73s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 73s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 73s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 73s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [257 kB] 73s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1449 kB] 73s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [21.6 kB] 73s Fetched 3839 kB in 1s (3700 kB/s) 74s Reading package lists... 75s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 75s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 75s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 75s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 76s Reading package lists... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Calculating upgrade... 76s The following packages will be upgraded: 76s libc-bin libc-gconv-modules-extra libc6 locales pollinate 76s python3-referencing sed 76s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Need to get 8612 kB of archives. 76s After this operation, 0 B of additional disk space will be used. 76s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el sed ppc64el 4.9-2build3 [211 kB] 76s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-gconv-modules-extra ppc64el 2.42-2ubuntu5 [1448 kB] 76s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc6 ppc64el 2.42-2ubuntu5 [1913 kB] 76s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-bin ppc64el 2.42-2ubuntu5 [748 kB] 76s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el locales all 2.42-2ubuntu5 [4255 kB] 76s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el pollinate all 4.33-4ubuntu5 [14.0 kB] 76s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 77s dpkg-preconfigure: unable to re-open stdin: No such file or directory 77s Fetched 8612 kB in 0s (26.1 MB/s) 77s (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 ... 82008 files and directories currently installed.) 77s Preparing to unpack .../sed_4.9-2build3_ppc64el.deb ... 77s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 77s Setting up sed (4.9-2build3) ... 78s (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 ... 82008 files and directories currently installed.) 78s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_ppc64el.deb ... 78s Unpacking libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 78s Setting up libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) ... 78s (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 ... 82008 files and directories currently installed.) 78s Preparing to unpack .../libc6_2.42-2ubuntu5_ppc64el.deb ... 79s Unpacking libc6:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 79s Setting up libc6:ppc64el (2.42-2ubuntu5) ... 79s (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 ... 82008 files and directories currently installed.) 79s Preparing to unpack .../libc-bin_2.42-2ubuntu5_ppc64el.deb ... 80s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 80s Setting up libc-bin (2.42-2ubuntu5) ... 80s (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 ... 82008 files and directories currently installed.) 80s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 80s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 80s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 80s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 80s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 81s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 81s Setting up locales (2.42-2ubuntu5) ... 81s Generating locales (this might take a while)... 82s en_US.UTF-8... done 82s Generation complete. 83s Setting up pollinate (4.33-4ubuntu5) ... 93s Setting up python3-referencing (0.36.2-1ubuntu2) ... 93s Processing triggers for man-db (2.13.1-1) ... 95s Processing triggers for install-info (7.2-5) ... 95s Processing triggers for systemd (259-1ubuntu3) ... 96s autopkgtest [02:26:09]: upgrading testbed (apt dist-upgrade and autopurge) 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Calculating upgrade... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Solving dependencies... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s autopkgtest [02:26:10]: rebooting testbed after setup commands that affected boot 136s autopkgtest [02:26:49]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026 139s autopkgtest [02:26:52]: @@@@@@@@@@@@@@@@@@@@ apt-source bali-phy 142s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bali-phy 4.0-1build2 (dsc) [2260 B] 142s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bali-phy 4.0-1build2 (tar) [1449 kB] 142s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bali-phy 4.0-1build2 (diff) [5640 B] 143s gpgv: Signature made Wed Aug 6 15:05:04 2025 UTC 143s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 143s gpgv: Can't check signature: No public key 143s dpkg-source: warning: cannot verify inline signature for ./bali-phy_4.0-1build2.dsc: no acceptable signature found 143s autopkgtest [02:26:56]: testing package bali-phy version 4.0-1build2 143s autopkgtest [02:26:56]: build not needed 144s autopkgtest [02:26:57]: test run-unit-test: preparing testbed 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Solving dependencies... 145s The following NEW packages will be installed: 145s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 145s libboost-chrono1.88.0 libboost-json1.88.0 libboost-program-options1.88.0 145s libboost-random1.88.0 libcairo2 libfmt10 libfontconfig1 libpixman-1-0 145s libxcb-render0 libxcb-shm0 libxrender1 145s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 12.9 MB of archives. 145s After this operation, 49.5 MB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libboost-chrono1.88.0 ppc64el 1.88.0-1.4ubuntu3 [248 kB] 145s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libboost-json1.88.0 ppc64el 1.88.0-1.4ubuntu3 [401 kB] 145s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-program-options1.88.0 ppc64el 1.88.0-1.4ubuntu3 [334 kB] 145s Get:4 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libboost-random1.88.0 ppc64el 1.88.0-1.4ubuntu3 [246 kB] 145s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB] 145s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB] 145s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB] 145s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB] 145s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 145s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB] 145s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B] 145s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 145s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB] 145s Get:14 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libfmt10 ppc64el 10.1.1+ds1-4build1 [83.7 kB] 145s Get:15 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bali-phy ppc64el 4.0-1build2 [8888 kB] 146s Fetched 12.9 MB in 1s (13.1 MB/s) 146s Selecting previously unselected package libboost-chrono1.88.0:ppc64el. 146s (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 ... 82008 files and directories currently installed.) 146s Preparing to unpack .../00-libboost-chrono1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 146s Unpacking libboost-chrono1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 146s Selecting previously unselected package libboost-json1.88.0:ppc64el. 146s Preparing to unpack .../01-libboost-json1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 146s Unpacking libboost-json1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 146s Selecting previously unselected package libboost-program-options1.88.0:ppc64el. 146s Preparing to unpack .../02-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 146s Unpacking libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 146s Selecting previously unselected package libboost-random1.88.0:ppc64el. 146s Preparing to unpack .../03-libboost-random1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 146s Unpacking libboost-random1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 146s Selecting previously unselected package fonts-dejavu-mono. 146s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8build1_all.deb ... 146s Unpacking fonts-dejavu-mono (2.37-8build1) ... 146s Selecting previously unselected package fonts-dejavu-core. 146s Preparing to unpack .../05-fonts-dejavu-core_2.37-8build1_all.deb ... 146s Unpacking fonts-dejavu-core (2.37-8build1) ... 146s Selecting previously unselected package fontconfig-config. 146s Preparing to unpack .../06-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ... 146s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 147s Selecting previously unselected package libfontconfig1:ppc64el. 147s Preparing to unpack .../07-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ... 147s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 147s Selecting previously unselected package libpixman-1-0:ppc64el. 147s Preparing to unpack .../08-libpixman-1-0_0.46.4-1_ppc64el.deb ... 147s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 147s Selecting previously unselected package libxcb-render0:ppc64el. 147s Preparing to unpack .../09-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ... 147s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 147s Selecting previously unselected package libxcb-shm0:ppc64el. 147s Preparing to unpack .../10-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ... 147s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 147s Selecting previously unselected package libxrender1:ppc64el. 147s Preparing to unpack .../11-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 147s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 147s Selecting previously unselected package libcairo2:ppc64el. 147s Preparing to unpack .../12-libcairo2_1.18.4-3_ppc64el.deb ... 147s Unpacking libcairo2:ppc64el (1.18.4-3) ... 147s Selecting previously unselected package libfmt10:ppc64el. 147s Preparing to unpack .../13-libfmt10_10.1.1+ds1-4build1_ppc64el.deb ... 147s Unpacking libfmt10:ppc64el (10.1.1+ds1-4build1) ... 147s Selecting previously unselected package bali-phy. 147s Preparing to unpack .../14-bali-phy_4.0-1build2_ppc64el.deb ... 147s Unpacking bali-phy (4.0-1build2) ... 147s Setting up libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 147s Setting up libpixman-1-0:ppc64el (0.46.4-1) ... 147s Setting up libxrender1:ppc64el (1:0.9.12-1) ... 147s Setting up libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 147s Setting up libboost-random1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 147s Setting up libboost-json1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 147s Setting up libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 147s Setting up fonts-dejavu-mono (2.37-8build1) ... 147s Setting up fonts-dejavu-core (2.37-8build1) ... 147s Setting up libboost-chrono1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 147s Setting up libfmt10:ppc64el (10.1.1+ds1-4build1) ... 147s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 147s Setting up libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 147s Setting up libcairo2:ppc64el (1.18.4-3) ... 147s Setting up bali-phy (4.0-1build2) ... 147s Processing triggers for man-db (2.13.1-1) ... 148s Processing triggers for libc-bin (2.42-2ubuntu5) ... 149s autopkgtest [02:27:02]: test run-unit-test: [----------------------- 149s + pkg=bali-phy 149s + [ /tmp/autopkgtest.87hY3O/autopkgtest_tmp = ] 149s + cp -a /usr/share/doc/bali-phy/examples/5S-rRNA /usr/share/doc/bali-phy/examples/Duplications /usr/share/doc/bali-phy/examples/EF-Tu /usr/share/doc/bali-phy/examples/Enolase /usr/share/doc/bali-phy/examples/Feng-Doolittle-1987 /usr/share/doc/bali-phy/examples/Globins /usr/share/doc/bali-phy/examples/HIV /usr/share/doc/bali-phy/examples/ITS /usr/share/doc/bali-phy/examples/Miklos-2008 /usr/share/doc/bali-phy/examples/ferns /usr/share/doc/bali-phy/examples/lrRNA /usr/share/doc/bali-phy/examples/microbotryum /tmp/autopkgtest.87hY3O/autopkgtest_tmp 149s + cd /tmp/autopkgtest.87hY3O/autopkgtest_tmp 149s + export HOME=/tmp/autopkgtest.87hY3O/autopkgtest_tmp 149s + bali-phy --version 149s VERSION: 4.0 [4.0] 149s BUILD: Aug 6 2025 15:05:03 149s ARCH: linux ppc64 149s COMPILER: gcc 15.1.0 ppc64 149s + bali-phy --help 149s Bayesian Inference of Alignment and Phylogeny 149s Usage: bali-phy [ ...] [OPTIONS] 149s Basic options: 149s 149s General options: 149s -h [ --help ] [=arg(=basic)] Print usage information. 149s -v [ --version ] Print version information. 149s -t [ --test ] Analyze the initial values and exit. 149s -c [ --config ] arg Command file to read. 149s 149s MCMC options: 149s -i [ --iterations ] arg The number of iterations to run. 149s -n [ --name ] arg Name for the output directory to create. 149s 149s Parameter options: 149s --align arg Sequence file & initial alignment. 149s -T [ --tree ] arg Tree prior: ~uniform_tree(taxa), 149s ~uniform_rooted_tree(taxa), ~yule(taxa), etc. 149s 149s Model options: 149s -A [ --alphabet ] arg The alphabet. 149s -S [ --smodel ] arg Substitution model. 149s -I [ --imodel ] arg Insertion-deletion model. 149s -R [ --scale ] arg Prior on the scale. 149s -F [ --fix ] arg Fix topology,tree,alignment 149s --variables arg Variable definitions 149s -L [ --link ] arg Link partitions. 149s --subst-rates arg (=constant) Subst rates: *constant, relaxed, or an 149s expression. 149s --indel-rates arg (=relaxed) Indel rates: constant, *relaxed, or an 149s expression. 149s 149s Showing basic command line options. Not all options are shown! 149s * See `bali-phy help advanced` to see more options. 149s 149s See `bali-phy help option` for help on option. For example, 149s * `bali-phy help alphabet` shows help on the --alphabet command. 149s * `bali-phy help normal` shows help on the normal distribution. 149s * `bali-phy help tn93` shows help on the TN93 model. 149s * `bali-phy help log` shows help on the log function. 149s 149s To see help on one of the following topics, run `bali-phy help topic` 149s 149s alphabets/ commands/ distributions/ functions/ models/ 149s parameters/ 149s 149s + bali-phy 5S-rRNA/5d.fasta --test --seed=0 149s tree ~ uniform_tree(taxa, gamma(0.5, 1/length(@taxa))) 149s subst rates = constant 149s indel rates = map(|x:pow(x, sigma)|, ~iidMap(branches(tree), logNormal(0, 1))) where {sigma ~ logLaplace(-3, 1)} 149s 149s Partition P1: 149s file = 5S-rRNA/5d.fasta 149s alphabet = DNA 149s subst = tn93 (S1) 149s indel = rs07 (I1) 149s scale ~ gamma(0.5, 2) (Scale1) 149s 149s Substitution model S1 priors: 149s tn93:kappaPur ~ logNormal(log(2), 0.25) 149s tn93:kappaPyr ~ logNormal(log(2), 0.25) 149s tn93:pi ~ symmetric_dirichlet_on(letters(@a), 1) 149s 149s Insertion/deletion model I1 priors: 149s rs07:rate ~ logLaplace(-4, 0.707) 149s rs07:mean_length ~ shifted_exponential(10, 1) 149s 168s iter = 0 prior = -5.823164954659224E1 likelihood = -3.072890587203336E3 posterior = -3.131122236749928E3 prior_A = -4.404203470092577E1 |T| = 1.1616694710568025E0 scale1 = 8.365772878720175E-3 scale1*|T| = 9.71826295500421E-3 #substs = 251 |indels| = 9 P1/|A| = 129 P1/#indels = 3 P1/|indels| = 9 P1/prior_A = -4.404203470092577E1 P1/likelihood = -3.072890587203336E3 P1/#substs = 251 scale = 8.365772878720175E-3 scale*|T| = 9.71826295500421E-3 |A| = 129 #indels = 3 sigma = 4.183142526100789E-2 tn93:kappaPur = 1.5206189450352174E0 tn93:kappaPyr = 3.1719431583067887E0 tn93:pi[A] = 8.35543398998562E-2 tn93:pi[C] = 4.282236507613509E-1 tn93:pi[G] = 2.544742596340091E-3 tn93:pi[T] = 4.856772667424529E-1 rs07:rate = 1.632531326779878E-2 rs07:mean_length = 3.73890484197585E1 168s + bali-phy 5S-rRNA/5d.fasta --iter=50 --seed=0 168s Created directory "5d-1" for output files. 168s 168s tree ~ uniform_tree(taxa, gamma(0.5, 1/length(@taxa))) 168s subst rates = constant 168s indel rates = map(|x:pow(x, sigma)|, ~iidMap(branches(tree), logNormal(0, 1))) where {sigma ~ logLaplace(-3, 1)} 168s 168s Partition P1: 168s file = 5S-rRNA/5d.fasta 168s alphabet = DNA 168s subst = tn93 (S1) 168s indel = rs07 (I1) 168s scale ~ gamma(0.5, 2) (Scale1) 168s 168s Substitution model S1 priors: 168s tn93:kappaPur ~ logNormal(log(2), 0.25) 168s tn93:kappaPyr ~ logNormal(log(2), 0.25) 168s tn93:pi ~ symmetric_dirichlet_on(letters(@a), 1) 168s 168s Insertion/deletion model I1 priors: 168s rs07:rate ~ logLaplace(-4, 0.707) 168s rs07:mean_length ~ shifted_exponential(10, 1) 168s 171s Run info written to "5d-1/C1.run.json" 171s 171s Beginning MCMC computations. 171s - Sampled numerical parameters logged to "5d-1/C1.log" as TSV 171s - Sampled trees logged to "5d-1/C1.trees" 171s - Sampled alignments logged to "5d-1/C1.P.fastas" 171s 171s BAli-Phy does NOT detect how many iterations is sufficient: 171s You need to monitor convergence and kill it when done. 171s Maximum number of iterations set to 50. 171s 171s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 171s See the manual at http://www.bali-phy.org/README.xhtml for further information. 176s 176s Work: 176s start: Thu Feb 5 02:27:21 2026 176s end: Thu Feb 5 02:27:29 2026 176s total (elapsed) time: 4s (4.795s) 176s total (CPU) time: 4s (4.780s) 176s + bali-phy 5S-rRNA/5d.fasta --iter=200 -I rs07 --seed=0 176s Created directory "5d-2" for output files. 176s 176s tree ~ uniform_tree(taxa, gamma(0.5, 1/length(@taxa))) 176s subst rates = constant 176s indel rates = map(|x:pow(x, sigma)|, ~iidMap(branches(tree), logNormal(0, 1))) where {sigma ~ logLaplace(-3, 1)} 176s 176s Partition P1: 176s file = 5S-rRNA/5d.fasta 176s alphabet = DNA 176s subst = tn93 (S1) 176s indel = rs07 (I1) 176s scale ~ gamma(0.5, 2) (Scale1) 176s 176s Substitution model S1 priors: 176s tn93:kappaPur ~ logNormal(log(2), 0.25) 176s tn93:kappaPyr ~ logNormal(log(2), 0.25) 176s tn93:pi ~ symmetric_dirichlet_on(letters(@a), 1) 176s 176s Insertion/deletion model I1 priors: 176s rs07:rate ~ logLaplace(-4, 0.707) 176s rs07:mean_length ~ shifted_exponential(10, 1) 176s 179s Run info written to "5d-2/C1.run.json" 179s 179s Beginning MCMC computations. 179s - Sampled numerical parameters logged to "5d-2/C1.log" as TSV 179s - Sampled trees logged to "5d-2/C1.trees" 179s - Sampled alignments logged to "5d-2/C1.P.fastas" 179s 179s BAli-Phy does NOT detect how many iterations is sufficient: 179s You need to monitor convergence and kill it when done. 179s Maximum number of iterations set to 200. 179s 179s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 179s See the manual at http://www.bali-phy.org/README.xhtml for further information. 196s 196s Work: 196s start: Thu Feb 5 02:27:29 2026 196s end: Thu Feb 5 02:27:48 2026 196s total (elapsed) time: 16s (16.926s) 196s total (CPU) time: 16s (16.900s) 196s + bali-phy 5S-rRNA/5d.fasta --iter=100 196s Created directory "5d-3" for output files. 196s 196s tree ~ uniform_tree(taxa, gamma(0.5, 1/length(@taxa))) 196s subst rates = constant 196s indel rates = map(|x:pow(x, sigma)|, ~iidMap(branches(tree), logNormal(0, 1))) where {sigma ~ logLaplace(-3, 1)} 196s 196s Partition P1: 196s file = 5S-rRNA/5d.fasta 196s alphabet = DNA 196s subst = tn93 (S1) 196s indel = rs07 (I1) 196s scale ~ gamma(0.5, 2) (Scale1) 196s 196s Substitution model S1 priors: 196s tn93:kappaPur ~ logNormal(log(2), 0.25) 196s tn93:kappaPyr ~ logNormal(log(2), 0.25) 196s tn93:pi ~ symmetric_dirichlet_on(letters(@a), 1) 196s 196s Insertion/deletion model I1 priors: 196s rs07:rate ~ logLaplace(-4, 0.707) 196s rs07:mean_length ~ shifted_exponential(10, 1) 196s 199s Run info written to "5d-3/C1.run.json" 199s 199s Beginning MCMC computations. 199s - Sampled numerical parameters logged to "5d-3/C1.log" as TSV 199s - Sampled trees logged to "5d-3/C1.trees" 199s - Sampled alignments logged to "5d-3/C1.P.fastas" 199s 199s BAli-Phy does NOT detect how many iterations is sufficient: 199s You need to monitor convergence and kill it when done. 199s Maximum number of iterations set to 100. 199s 199s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 199s See the manual at http://www.bali-phy.org/README.xhtml for further information. 208s 208s Work: 208s start: Thu Feb 5 02:27:48 2026 208s end: Thu Feb 5 02:28:00 2026 208s total (elapsed) time: 8s (8.857s) 208s total (CPU) time: 8s (8.850s) 208s + bp-analyze 5d-1 208s Program 'gnuplot' not found: Some graphs will not be generated. 208s 208s Program 'R' not found: Some mixing graphs will not be generated. 208s 208s Can't find fourmolu, ormolu or hindent -- not formatting Haskell code. 208s Creating new directory 'Results' for summary files. 208s Summarizing distribution of numerical parameters: done. 208s Analyzing scalar variables: done. 208s 208s Summarizing topology distribution: done. 208s Drawing trees: c50 c66 c80 c90 c95 c99 c100 greedy MAP . done. 208s 208s Generate mixing diagnostics for topologies ... done. 208s Generate SRQ plot for partitions: done. 208s Generate SRQ plot for c50 tree: done. 208s Computing initial alignments: done. 208s 208s Computing WPD alignments: done. 208s Computing ancestral state alignment: done. 208s Drawing alignments: **** done. 208s Generating AU values for 'P1.initial'... done. 208s Generating AU values for 'P1.max'... done. 208s 208s NOTE: burnin (scalar) <= Not Converged! 208s NOTE: min_ESS (scalar) = 5.181 208s NOTE: min_ESS (partition) = 19.826 208s NOTE: ASDSF = NA 208s NOTE: MSDSF = NA 208s NOTE: PSRF-80%CI = NA 208s NOTE: PSRF-RCF = NA 208s 208s RUN 1: directory = 5d-1 iterations = 50 burnin = 5 208s 208s Report written to 'Results/index.html 209s autopkgtest [02:28:02]: test run-unit-test: -----------------------] 209s autopkgtest [02:28:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 209s run-unit-test PASS 210s autopkgtest [02:28:03]: @@@@@@@@@@@@@@@@@@@@ summary 210s run-unit-test PASS