0s autopkgtest [01:15:08]: starting date and time: 2026-02-05 01:15:08+0000 0s autopkgtest [01:15:08]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:15:08]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5iua0v78/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:chiark-tcl --apt-upgrade bali-phy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 chiark-tcl/1.3.7build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-8.secgroup --name adt-resolute-arm64-bali-phy-20260205-011508-juju-7f2275-prod-proposed-migration-environment-20-93627d22-9dc0-45ff-aa91-68940ed15fd7 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-bali-phy-20260205-011508-juju-7f2275-prod-proposed-migration-environment-20-93627d22-9dc0-45ff-aa91-68940ed15fd7 from image adt/ubuntu-resolute-arm64-server-20260204.img (UUID f58d981d-b271-4157-b9b1-fd704695563c)... 57s autopkgtest [01:16:05]: testbed dpkg architecture: arm64 57s autopkgtest [01:16:05]: testbed apt version: 3.1.14 58s autopkgtest [01:16:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 58s autopkgtest [01:16:06]: testbed release detected to be: None 59s autopkgtest [01:16:07]: updating testbed package index (apt update) 59s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 59s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 59s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 59s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 59s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 59s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 59s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [228 kB] 59s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1768 kB] 60s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [262 kB] 60s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7248 B] 60s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 60s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 60s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1540 kB] 60s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [40.2 kB] 60s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [26.0 kB] 60s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 64s Fetched 4091 kB in 1s (3578 kB/s) 64s Reading package lists... 65s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 65s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 66s Reading package lists... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 67s Calculating upgrade... 67s The following packages will be upgraded: 67s libc-bin libc-gconv-modules-extra libc6 locales python3-linkify-it 67s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 7881 kB of archives. 67s After this operation, 0 B of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-gconv-modules-extra arm64 2.42-2ubuntu5 [1413 kB] 67s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6 arm64 2.42-2ubuntu5 [1594 kB] 67s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-bin arm64 2.42-2ubuntu5 [599 kB] 67s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 locales all 2.42-2ubuntu5 [4255 kB] 67s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 68s dpkg-preconfigure: unable to re-open stdin: No such file or directory 68s Fetched 7881 kB in 0s (18.3 MB/s) 68s (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 ... 89360 files and directories currently installed.) 68s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_arm64.deb ... 68s Unpacking libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 68s Setting up libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) ... 68s (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 ... 89360 files and directories currently installed.) 68s Preparing to unpack .../libc6_2.42-2ubuntu5_arm64.deb ... 69s Unpacking libc6:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 69s Setting up libc6:arm64 (2.42-2ubuntu5) ... 69s (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 ... 89360 files and directories currently installed.) 69s Preparing to unpack .../libc-bin_2.42-2ubuntu5_arm64.deb ... 69s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 69s Setting up libc-bin (2.42-2ubuntu5) ... 69s (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 ... 89360 files and directories currently installed.) 69s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 69s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 70s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 70s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 70s Setting up locales (2.42-2ubuntu5) ... 71s Generating locales (this might take a while)... 72s en_US.UTF-8... done 72s Generation complete. 72s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 72s Processing triggers for man-db (2.13.1-1) ... 74s Processing triggers for systemd (259-1ubuntu3) ... 75s autopkgtest [01:16:23]: upgrading testbed (apt dist-upgrade and autopurge) 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Calculating upgrade... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Solving dependencies... 77s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s autopkgtest [01:16:27]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 79s autopkgtest [01:16:27]: @@@@@@@@@@@@@@@@@@@@ apt-source bali-phy 81s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bali-phy 4.0-1build2 (dsc) [2260 B] 81s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bali-phy 4.0-1build2 (tar) [1449 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bali-phy 4.0-1build2 (diff) [5640 B] 81s gpgv: Signature made Wed Aug 6 15:05:04 2025 UTC 81s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 81s gpgv: Can't check signature: No public key 81s dpkg-source: warning: cannot verify inline signature for ./bali-phy_4.0-1build2.dsc: no acceptable signature found 81s autopkgtest [01:16:29]: testing package bali-phy version 4.0-1build2 81s autopkgtest [01:16:29]: build not needed 83s autopkgtest [01:16:31]: test run-unit-test: preparing testbed 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 84s The following NEW packages will be installed: 84s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 84s libboost-chrono1.88.0 libboost-json1.88.0 libboost-program-options1.88.0 84s libboost-random1.88.0 libcairo2 libfmt10 libfontconfig1 libpixman-1-0 84s libxcb-render0 libxcb-shm0 libxrender1 84s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 11.7 MB of archives. 84s After this operation, 45.1 MB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu resolute/universe arm64 libboost-chrono1.88.0 arm64 1.88.0-1.4ubuntu3 [247 kB] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 libboost-json1.88.0 arm64 1.88.0-1.4ubuntu3 [382 kB] 84s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-program-options1.88.0 arm64 1.88.0-1.4ubuntu3 [326 kB] 84s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 libboost-random1.88.0 arm64 1.88.0-1.4ubuntu3 [245 kB] 84s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 84s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 85s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 85s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 85s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 85s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 85s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 85s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 85s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfmt10 arm64 10.1.1+ds1-4build1 [74.0 kB] 85s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 bali-phy arm64 4.0-1build2 [8146 kB] 86s Fetched 11.7 MB in 1s (14.6 MB/s) 86s Selecting previously unselected package libboost-chrono1.88.0:arm64. 86s (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 ... 89360 files and directories currently installed.) 86s Preparing to unpack .../00-libboost-chrono1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 86s Unpacking libboost-chrono1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 86s Selecting previously unselected package libboost-json1.88.0:arm64. 86s Preparing to unpack .../01-libboost-json1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 86s Unpacking libboost-json1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 86s Selecting previously unselected package libboost-program-options1.88.0:arm64. 86s Preparing to unpack .../02-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 86s Unpacking libboost-program-options1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 86s Selecting previously unselected package libboost-random1.88.0:arm64. 86s Preparing to unpack .../03-libboost-random1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 86s Unpacking libboost-random1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 86s Selecting previously unselected package fonts-dejavu-mono. 86s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8build1_all.deb ... 86s Unpacking fonts-dejavu-mono (2.37-8build1) ... 86s Selecting previously unselected package fonts-dejavu-core. 86s Preparing to unpack .../05-fonts-dejavu-core_2.37-8build1_all.deb ... 86s Unpacking fonts-dejavu-core (2.37-8build1) ... 86s Selecting previously unselected package fontconfig-config. 86s Preparing to unpack .../06-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 86s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 86s Selecting previously unselected package libfontconfig1:arm64. 86s Preparing to unpack .../07-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 86s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 86s Selecting previously unselected package libpixman-1-0:arm64. 86s Preparing to unpack .../08-libpixman-1-0_0.46.4-1_arm64.deb ... 86s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 86s Selecting previously unselected package libxcb-render0:arm64. 86s Preparing to unpack .../09-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 86s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 86s Selecting previously unselected package libxcb-shm0:arm64. 86s Preparing to unpack .../10-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 86s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 86s Selecting previously unselected package libxrender1:arm64. 86s Preparing to unpack .../11-libxrender1_1%3a0.9.12-1_arm64.deb ... 86s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 86s Selecting previously unselected package libcairo2:arm64. 86s Preparing to unpack .../12-libcairo2_1.18.4-3_arm64.deb ... 86s Unpacking libcairo2:arm64 (1.18.4-3) ... 86s Selecting previously unselected package libfmt10:arm64. 86s Preparing to unpack .../13-libfmt10_10.1.1+ds1-4build1_arm64.deb ... 86s Unpacking libfmt10:arm64 (10.1.1+ds1-4build1) ... 86s Selecting previously unselected package bali-phy. 86s Preparing to unpack .../14-bali-phy_4.0-1build2_arm64.deb ... 86s Unpacking bali-phy (4.0-1build2) ... 87s Setting up libboost-program-options1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 87s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 87s Setting up libxrender1:arm64 (1:0.9.12-1) ... 87s Setting up libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 87s Setting up libboost-random1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 87s Setting up libboost-json1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 87s Setting up libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 87s Setting up fonts-dejavu-mono (2.37-8build1) ... 87s Setting up fonts-dejavu-core (2.37-8build1) ... 87s Setting up libboost-chrono1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 87s Setting up libfmt10:arm64 (10.1.1+ds1-4build1) ... 87s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 87s Setting up libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 87s Setting up libcairo2:arm64 (1.18.4-3) ... 87s Setting up bali-phy (4.0-1build2) ... 87s Processing triggers for man-db (2.13.1-1) ... 87s Processing triggers for libc-bin (2.42-2ubuntu5) ... 88s autopkgtest [01:16:36]: test run-unit-test: [----------------------- 88s + pkg=bali-phy 88s + [ /tmp/autopkgtest.IhAlyu/autopkgtest_tmp = ] 88s + 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.IhAlyu/autopkgtest_tmp 88s + cd /tmp/autopkgtest.IhAlyu/autopkgtest_tmp 88s + export HOME=/tmp/autopkgtest.IhAlyu/autopkgtest_tmp 88s + bali-phy --version 88s VERSION: 4.0 [4.0] 88s BUILD: Aug 6 2025 15:05:03 88s ARCH: linux aarch64 88s COMPILER: gcc 15.1.0 aarch64 88s + bali-phy --help 89s + bali-phy 5S-rRNA/5d.fasta --test --seed=0 89s Bayesian Inference of Alignment and Phylogeny 89s Usage: bali-phy [ ...] [OPTIONS] 89s Basic options: 89s 89s General options: 89s -h [ --help ] [=arg(=basic)] Print usage information. 89s -v [ --version ] Print version information. 89s -t [ --test ] Analyze the initial values and exit. 89s -c [ --config ] arg Command file to read. 89s 89s MCMC options: 89s -i [ --iterations ] arg The number of iterations to run. 89s -n [ --name ] arg Name for the output directory to create. 89s 89s Parameter options: 89s --align arg Sequence file & initial alignment. 89s -T [ --tree ] arg Tree prior: ~uniform_tree(taxa), 89s ~uniform_rooted_tree(taxa), ~yule(taxa), etc. 89s 89s Model options: 89s -A [ --alphabet ] arg The alphabet. 89s -S [ --smodel ] arg Substitution model. 89s -I [ --imodel ] arg Insertion-deletion model. 89s -R [ --scale ] arg Prior on the scale. 89s -F [ --fix ] arg Fix topology,tree,alignment 89s --variables arg Variable definitions 89s -L [ --link ] arg Link partitions. 89s --subst-rates arg (=constant) Subst rates: *constant, relaxed, or an 89s expression. 89s --indel-rates arg (=relaxed) Indel rates: constant, *relaxed, or an 89s expression. 89s 89s Showing basic command line options. Not all options are shown! 89s * See `bali-phy help advanced` to see more options. 89s 89s See `bali-phy help option` for help on option. For example, 89s * `bali-phy help alphabet` shows help on the --alphabet command. 89s * `bali-phy help normal` shows help on the normal distribution. 89s * `bali-phy help tn93` shows help on the TN93 model. 89s * `bali-phy help log` shows help on the log function. 89s 89s To see help on one of the following topics, run `bali-phy help topic` 89s 89s alphabets/ commands/ distributions/ functions/ models/ 89s parameters/ 89s 89s tree ~ uniform_tree(taxa, gamma(0.5, 1/length(@taxa))) 89s subst rates = constant 89s indel rates = map(|x:pow(x, sigma)|, ~iidMap(branches(tree), logNormal(0, 1))) where {sigma ~ logLaplace(-3, 1)} 89s 89s Partition P1: 89s file = 5S-rRNA/5d.fasta 89s alphabet = DNA 89s subst = tn93 (S1) 89s indel = rs07 (I1) 89s scale ~ gamma(0.5, 2) (Scale1) 89s 89s Substitution model S1 priors: 89s tn93:kappaPur ~ logNormal(log(2), 0.25) 89s tn93:kappaPyr ~ logNormal(log(2), 0.25) 89s tn93:pi ~ symmetric_dirichlet_on(letters(@a), 1) 89s 89s Insertion/deletion model I1 priors: 89s rs07:rate ~ logLaplace(-4, 0.707) 89s rs07:mean_length ~ shifted_exponential(10, 1) 89s 105s + bali-phy 5S-rRNA/5d.fasta --iter=50 --seed=0 105s Created directory "5d-1" for output files. 105s 105s iter = 0 prior = -5.823164954659224E1 likelihood = -3.072890587203335E3 posterior = -3.131122236749927E3 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 = -3.072890587203335E3 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 105s tree ~ uniform_tree(taxa, gamma(0.5, 1/length(@taxa))) 105s subst rates = constant 105s indel rates = map(|x:pow(x, sigma)|, ~iidMap(branches(tree), logNormal(0, 1))) where {sigma ~ logLaplace(-3, 1)} 105s 105s Partition P1: 105s file = 5S-rRNA/5d.fasta 105s alphabet = DNA 105s subst = tn93 (S1) 105s indel = rs07 (I1) 105s scale ~ gamma(0.5, 2) (Scale1) 105s 105s Substitution model S1 priors: 105s tn93:kappaPur ~ logNormal(log(2), 0.25) 105s tn93:kappaPyr ~ logNormal(log(2), 0.25) 105s tn93:pi ~ symmetric_dirichlet_on(letters(@a), 1) 105s 105s Insertion/deletion model I1 priors: 105s rs07:rate ~ logLaplace(-4, 0.707) 105s rs07:mean_length ~ shifted_exponential(10, 1) 105s 108s Run info written to "5d-1/C1.run.json" 108s 108s Beginning MCMC computations. 108s - Sampled numerical parameters logged to "5d-1/C1.log" as TSV 108s - Sampled trees logged to "5d-1/C1.trees" 108s - Sampled alignments logged to "5d-1/C1.P.fastas" 108s 108s BAli-Phy does NOT detect how many iterations is sufficient: 108s You need to monitor convergence and kill it when done. 108s Maximum number of iterations set to 50. 108s 108s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 108s See the manual at http://www.bali-phy.org/README.xhtml for further information. 114s 114s Work: 114s start: Thu Feb 5 01:16:53 2026 114s end: Thu Feb 5 01:17:02 2026 114s total (elapsed) time: 5s (5.000s) 114s total (CPU) time: 4s (4.980s) 114s + bali-phy 5S-rRNA/5d.fasta --iter=200 -I rs07tree ~ uniform_tree(taxa, gamma(0.5, 1/length(@taxa))) 114s subst rates = constant 114s indel rates = map(|x:pow(x, sigma)|, ~iidMap(branches(tree), logNormal(0, 1))) where {sigma ~ logLaplace(-3, 1)} 114s 114s Partition P1: 114s file = 5S-rRNA/5d.fasta 114s alphabet = DNA 114s subst = tn93 (S1) 114s indel = rs07 (I1) 114s scale ~ gamma(0.5, 2) (Scale1) 114s 114s --seed=0 114s Created directory "5d-2" for output files. 114s 114s Substitution model S1 priors: 114s tn93:kappaPur ~ logNormal(log(2), 0.25) 114s tn93:kappaPyr ~ logNormal(log(2), 0.25) 114s tn93:pi ~ symmetric_dirichlet_on(letters(@a), 1) 114s 114s Insertion/deletion model I1 priors: 114s rs07:rate ~ logLaplace(-4, 0.707) 114s rs07:mean_length ~ shifted_exponential(10, 1) 114s 122s Run info written to "5d-2/C1.run.json" 122s 122s Beginning MCMC computations. 122s - Sampled numerical parameters logged to "5d-2/C1.log" as TSV 122s - Sampled trees logged to "5d-2/C1.trees" 122s - Sampled alignments logged to "5d-2/C1.P.fastas" 122s 122s BAli-Phy does NOT detect how many iterations is sufficient: 122s You need to monitor convergence and kill it when done. 122s Maximum number of iterations set to 200. 122s 122s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 122s See the manual at http://www.bali-phy.org/README.xhtml for further information. 134s 134s Work: 134s start: Thu Feb 5 01:17:02 2026 134s end: Thu Feb 5 01:17:22 2026 134s total (elapsed) time: 17s (17.097s) 134s total (CPU) time: 17s (17.050s) 134s tree ~ uniform_tree(taxa, gamma(0.5, 1/length(@taxa))) 134s subst rates = constant 134s indel rates = map(|x:pow(x, sigma)|, ~iidMap(branches(tree), logNormal(0, 1))) where {sigma ~ logLaplace(-3, 1)} 134s 134s Partition P1: 134s file = 5S-rRNA/5d.fasta 134s alphabet = DNA 134s subst = tn93 (S1) 134s indel = rs07 (I1) 134s scale ~ gamma(0.5, 2) (Scale1) 134s 134s Substitution model S1 priors: 134s tn93:kappaPur ~ logNormal(log(2), 0.25) 134s tn93:kappaPyr ~ logNormal(log(2), 0.25) 134s tn93:pi ~ symmetric_dirichlet_on(letters(@a), 1) 134s 134s Insertion/deletion model I1 priors: 134s rs07:rate ~ logLaplace(-4, 0.707) 134s rs07:mean_length ~ shifted_exponential(10, 1) 134s 134s + bali-phy 5S-rRNA/5d.fasta --iter=100 134s Created directory "5d-3" for output files. 134s 137s Run info written to "5d-3/C1.run.json" 137s 137s Beginning MCMC computations. 137s - Sampled numerical parameters logged to "5d-3/C1.log" as TSV 137s - Sampled trees logged to "5d-3/C1.trees" 137s - Sampled alignments logged to "5d-3/C1.P.fastas" 137s 137s BAli-Phy does NOT detect how many iterations is sufficient: 137s You need to monitor convergence and kill it when done. 137s Maximum number of iterations set to 100. 137s 137s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 137s See the manual at http://www.bali-phy.org/README.xhtml for further information. 147s 147s Work: 147s start: Thu Feb 5 01:17:22 2026 147s end: Thu Feb 5 01:17:35 2026 147s total (elapsed) time: 9s (9.319s) 147s total (CPU) time: 9s (9.290s) 147s + bp-analyze 5d-1 147s Program 'gnuplot' not found: Some graphs will not be generated. 147s 147s Program 'R' not found: Some mixing graphs will not be generated. 147s 147s Can't find fourmolu, ormolu or hindent -- not formatting Haskell code. 147s Creating new directory 'Results' for summary files. 147s Summarizing distribution of numerical parameters: done. 147s Analyzing scalar variables: done. 147s 147s Summarizing topology distribution: done. 147s Drawing trees: c50 c66 c80 c90 c95 c99 c100 greedy MAP . done. 147s 147s Generate mixing diagnostics for topologies ... done. 147s Generate SRQ plot for partitions: done. 147s Generate SRQ plot for c50 tree: done. 147s Computing initial alignments: done. 147s 147s Computing WPD alignments: done. 147s Computing ancestral state alignment: done. 147s Drawing alignments: **** done. 147s Generating AU values for 'P1.initial'... done. 147s Generating AU values for 'P1.max'... done. 147s 147s NOTE: burnin (scalar) <= Not Converged! 147s NOTE: min_ESS (scalar) = 5.181 147s NOTE: min_ESS (partition) = 19.826 147s NOTE: ASDSF = NA 147s NOTE: MSDSF = NA 147s NOTE: PSRF-80%CI = NA 147s NOTE: PSRF-RCF = NA 147s 147s RUN 1: directory = 5d-1 iterations = 50 burnin = 5 147s 147s Report written to 'Results/index.html 147s autopkgtest [01:17:35]: test run-unit-test: -----------------------] 148s autopkgtest [01:17:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 148s run-unit-test PASS 148s autopkgtest [01:17:36]: @@@@@@@@@@@@@@@@@@@@ summary 148s run-unit-test PASS