0s autopkgtest [23:19:29]: starting date and time: 2024-03-25 23:19:29+0000 0s autopkgtest [23:19:29]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [23:19:29]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rtfartlx/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 --apt-upgrade bali-phy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=bali-phy/3.6.1+dfsg-2build2 boost1.83/1.83.0-2.1ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-22.secgroup --name adt-noble-s390x-bali-phy-20240325-231929-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 138s autopkgtest [23:21:47]: testbed dpkg architecture: s390x 139s autopkgtest [23:21:48]: testbed apt version: 2.7.12 139s autopkgtest [23:21:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 140s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 140s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4039 kB] 142s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 142s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 142s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 142s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 142s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 142s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4136 kB] 143s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 143s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 143s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 144s Fetched 9604 kB in 4s (2481 kB/s) 144s Reading package lists... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Calculating upgrade... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 242 not upgraded. 147s Unknown architecture, assuming PC-style ttyS0 147s sh: Attempting to set up Debian/Ubuntu apt sources automatically 147s sh: Distribution appears to be Ubuntu 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s eatmydata is already the newest version (131-1). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s dbus is already the newest version (1.14.10-4ubuntu1). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s rng-tools-debian is already the newest version (2.4). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s The following packages will be REMOVED: 150s cloud-init* python3-configobj* python3-debconf* 150s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 150s After this operation, 3256 kB disk space will be freed. 150s (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 ... 52170 files and directories currently installed.) 150s Removing cloud-init (24.1.2-0ubuntu1) ... 150s Removing python3-configobj (5.0.8-3) ... 150s Removing python3-debconf (1.5.86) ... 150s Processing triggers for man-db (2.12.0-3) ... 151s (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 ... 51781 files and directories currently installed.) 151s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 151s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 151s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 151s invoke-rc.d: policy-rc.d denied execution of try-restart. 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s linux-generic is already the newest version (6.8.0-11.11+1). 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 152s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 152s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 154s Reading package lists... 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Calculating upgrade... 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s autopkgtest [23:22:04]: rebooting testbed after setup commands that affected boot 182s autopkgtest [23:22:31]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 185s autopkgtest [23:22:34]: @@@@@@@@@@@@@@@@@@@@ apt-source bali-phy 187s Get:1 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (dsc) [2216 B] 187s Get:2 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (tar) [1124 kB] 187s Get:3 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (diff) [5408 B] 187s gpgv: Signature made Tue Dec 19 15:00:40 2023 UTC 187s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 187s gpgv: Can't check signature: No public key 187s dpkg-source: warning: cannot verify inline signature for ./bali-phy_3.6.1+dfsg-2build1.dsc: no acceptable signature found 187s autopkgtest [23:22:36]: testing package bali-phy version 3.6.1+dfsg-2build1 188s autopkgtest [23:22:37]: build not needed 198s autopkgtest [23:22:47]: test run-unit-test: preparing testbed 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 200s Starting pkgProblemResolver with broken count: 0 200s Starting 2 pkgProblemResolver with broken count: 0 200s Done 200s The following additional packages will be installed: 200s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 200s libboost-chrono1.83.0 libboost-filesystem1.83.0 200s libboost-program-options1.83.0 libboost-random1.83.0 libcairo2 200s libfontconfig1 libfreetype6 libpixman-1-0 libxcb-render0 libxcb-shm0 200s libxrender1 200s Suggested packages: 200s figtree seaview 200s Recommended packages: 200s r-base gnuplot 200s The following NEW packages will be installed: 200s autopkgtest-satdep bali-phy fontconfig-config fonts-dejavu-core 200s fonts-dejavu-mono libboost-chrono1.83.0 libboost-filesystem1.83.0 200s libboost-program-options1.83.0 libboost-random1.83.0 libcairo2 200s libfontconfig1 libfreetype6 libpixman-1-0 libxcb-render0 libxcb-shm0 200s libxrender1 200s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 9090 kB/9090 kB of archives. 200s After this operation, 37.1 MB of additional disk space will be used. 200s Get:1 /tmp/autopkgtest.A8gagA/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 200s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libboost-chrono1.83.0 s390x 1.83.0-2ubuntu1 [323 kB] 201s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libboost-filesystem1.83.0 s390x 1.83.0-2ubuntu1 [372 kB] 201s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2ubuntu1 [418 kB] 201s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libboost-random1.83.0 s390x 1.83.0-2ubuntu1 [320 kB] 201s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 201s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 201s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 201s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 201s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 201s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 201s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 201s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 201s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 201s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 201s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x bali-phy s390x 3.6.1+dfsg-2build1 [4908 kB] 202s Fetched 9090 kB in 2s (6000 kB/s) 202s Selecting previously unselected package libboost-chrono1.83.0:s390x. 202s (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 ... 51726 files and directories currently installed.) 202s Preparing to unpack .../00-libboost-chrono1.83.0_1.83.0-2ubuntu1_s390x.deb ... 202s Unpacking libboost-chrono1.83.0:s390x (1.83.0-2ubuntu1) ... 202s Selecting previously unselected package libboost-filesystem1.83.0:s390x. 202s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_s390x.deb ... 202s Unpacking libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 202s Selecting previously unselected package libboost-program-options1.83.0:s390x. 202s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_s390x.deb ... 202s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 202s Selecting previously unselected package libboost-random1.83.0:s390x. 202s Preparing to unpack .../03-libboost-random1.83.0_1.83.0-2ubuntu1_s390x.deb ... 202s Unpacking libboost-random1.83.0:s390x (1.83.0-2ubuntu1) ... 202s Selecting previously unselected package libfreetype6:s390x. 202s Preparing to unpack .../04-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 202s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 202s Selecting previously unselected package fonts-dejavu-mono. 202s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ... 202s Unpacking fonts-dejavu-mono (2.37-8) ... 202s Selecting previously unselected package fonts-dejavu-core. 202s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ... 202s Unpacking fonts-dejavu-core (2.37-8) ... 202s Selecting previously unselected package fontconfig-config. 202s Preparing to unpack .../07-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 202s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 202s Selecting previously unselected package libfontconfig1:s390x. 202s Preparing to unpack .../08-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 202s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 202s Selecting previously unselected package libpixman-1-0:s390x. 202s Preparing to unpack .../09-libpixman-1-0_0.42.2-1_s390x.deb ... 202s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 203s Selecting previously unselected package libxcb-render0:s390x. 203s Preparing to unpack .../10-libxcb-render0_1.15-1_s390x.deb ... 203s Unpacking libxcb-render0:s390x (1.15-1) ... 203s Selecting previously unselected package libxcb-shm0:s390x. 203s Preparing to unpack .../11-libxcb-shm0_1.15-1_s390x.deb ... 203s Unpacking libxcb-shm0:s390x (1.15-1) ... 203s Selecting previously unselected package libxrender1:s390x. 203s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 203s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 203s Selecting previously unselected package libcairo2:s390x. 203s Preparing to unpack .../13-libcairo2_1.18.0-1_s390x.deb ... 203s Unpacking libcairo2:s390x (1.18.0-1) ... 203s Selecting previously unselected package bali-phy. 203s Preparing to unpack .../14-bali-phy_3.6.1+dfsg-2build1_s390x.deb ... 203s Unpacking bali-phy (3.6.1+dfsg-2build1) ... 203s Selecting previously unselected package autopkgtest-satdep. 203s Preparing to unpack .../15-1-autopkgtest-satdep.deb ... 203s Unpacking autopkgtest-satdep (0) ... 203s Setting up libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 203s Setting up libpixman-1-0:s390x (0.42.2-1) ... 203s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 203s Setting up libxcb-render0:s390x (1.15-1) ... 203s Setting up libboost-random1.83.0:s390x (1.83.0-2ubuntu1) ... 203s Setting up libxcb-shm0:s390x (1.15-1) ... 203s Setting up libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 203s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 203s Setting up fonts-dejavu-mono (2.37-8) ... 203s Setting up fonts-dejavu-core (2.37-8) ... 203s Setting up libboost-chrono1.83.0:s390x (1.83.0-2ubuntu1) ... 203s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 203s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 203s Setting up libcairo2:s390x (1.18.0-1) ... 203s Setting up bali-phy (3.6.1+dfsg-2build1) ... 203s Setting up autopkgtest-satdep (0) ... 203s Processing triggers for man-db (2.12.0-3) ... 203s Processing triggers for libc-bin (2.39-0ubuntu6) ... 206s (Reading database ... 52457 files and directories currently installed.) 206s Removing autopkgtest-satdep (0) ... 206s autopkgtest [23:22:55]: test run-unit-test: [----------------------- 206s VERSION: 3.6.1 [3.6.1] 206s BUILD: Dec 19 2023 14:51:09 206s ARCH: linux s390x 206s COMPILER: gcc 13.2.0 s390x 207s Bayesian Inference of Alignment and Phylogeny 207s Usage: bali-phy [ ...] [OPTIONS] 207s Basic options: 207s 207s General options: 207s -h [ --help ] [=arg(=basic)] Print usage information. 207s -v [ --version ] Print version information. 207s -t [ --test ] Analyze the initial values and exit. 207s -c [ --config ] arg Command file to read. 207s 207s MCMC options: 207s -i [ --iterations ] arg The number of iterations to run. 207s -n [ --name ] arg Name for the output directory to create. 207s 207s Parameter options: 207s --align arg Sequence file & initial alignment. 207s -T [ --tree ] arg File with initial tree 207s 207s Model options: 207s -A [ --alphabet ] arg The alphabet. 207s -S [ --smodel ] arg Substitution model. 207s -I [ --imodel ] arg Insertion-deletion model. 207s -R [ --scale ] arg Prior on the scale. 207s -L [ --link ] arg Link partitions. 207s 207s Showing basic command line options. Not all options are shown! 207s * See `bali-phy help advanced` to see more options. 207s 207s See `bali-phy help option` for help on option. For example, 207s * `bali-phy help alphabet` shows help on the --alphabet command. 207s * `bali-phy help normal` shows help on the normal distribution. 207s * `bali-phy help tn93` shows help on the TN93 model. 207s * `bali-phy help log` shows help on the log function. 207s 207s To see help on one of the following topics, run `bali-phy help topic` 207s 207s alphabets/ commands/ distributions/ functions/ models/ 207s parameters/ 207s 209s T:topology ~ uniform on tree topologies 209s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 209s 209s Partition P1: 209s file = sequences/5S-rRNA/5d.fasta 209s alphabet = DNA 209s subst = tn93 (S1) 209s indel = rs07 (I1) 209s scale ~ gamma[0.5,2] (Scale1) 209s 209s Substitution model S1 priors: 209s tn93:kappaPur ~ log_normal[log[2],0.25] 209s tn93:kappaPyr ~ log_normal[log[2],0.25] 209s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 209s 209s Insertion/deletion model I1 priors: 209s rs07:log_rate ~ laplace[-4,0.707] 209s rs07:mean_length ~ shifted_exponential[10,1] 209s 209s 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 209s 209s start time: Mon Mar 25 23:22:56 2024 209s 209s end time: Mon Mar 25 23:22:58 2024 209s 209s total (elapsed) time: 2 seconds 209s total (CPU) time: 1 second 209s Created directory '5d-1/' for output files. 211s T:topology ~ uniform on tree topologies 211s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 211s 211s Partition P1: 211s file = sequences/5S-rRNA/5d.fasta 211s alphabet = DNA 211s subst = tn93 (S1) 211s indel = rs07 (I1) 211s scale ~ gamma[0.5,2] (Scale1) 211s 211s Substitution model S1 priors: 211s tn93:kappaPur ~ log_normal[log[2],0.25] 211s tn93:kappaPyr ~ log_normal[log[2],0.25] 211s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 211s 211s Insertion/deletion model I1 priors: 211s rs07:log_rate ~ laplace[-4,0.707] 211s rs07:mean_length ~ shifted_exponential[10,1] 211s 211s Beginning pre-burnin: 3 iterations. 211s Start #1 prior = -33.7907 likelihood = -1483.23 |T| = 0.480025 Scale1*|T| = 0.312887 211s 211s Tree (S)ize #1 prior = -15.3853 likelihood = -918.651 |T| = 0.351153 Scale1*|T| = 13.4823 211s Tree (S)ize #2 prior = -8.67375 likelihood = -921.505 |T| = 0.557146 Scale1*|T| = 11.6476 211s Tree (S)ize #3 prior = -10.9776 likelihood = -916.148 |T| = 1.76036 Scale1*|T| = 17.2445 211s 211s (S)+Branch (L)engths #1 prior = -16.2584 likelihood = -913.26 |T| = 2.47609 Scale1*|T| = 13.0113 211s (S)+Branch (L)engths #2 prior = -16.8078 likelihood = -894.729 |T| = 3.04489 Scale1*|T| = 6.59351 211s (S)+Branch (L)engths #3 prior = -13.1975 likelihood = -886.107 |T| = 2.05444 Scale1*|T| = 5.6581 211s 211s (S)+(L)+(P)arameters #1 prior = -18.8487 likelihood = -843.212 |T| = 1.94953 Scale1*|T| = 5.31078 211s (S)+(L)+(P)arameters #2 prior = -13.6692 likelihood = -799.58 |T| = 1.45035 Scale1*|T| = 5.99899 211s (S)+(L)+(P)arameters #3 prior = -16.2199 likelihood = -794.492 |T| = 1.25891 Scale1*|T| = 6.13717 211s 211s (S)+(L)+(P)+NNI #1 prior = -14.3438 likelihood = -794.463 |T| = 0.950972 Scale1*|T| = 8.25425 211s (S)+(L)+(P)+NNI #2 prior = -13.0194 likelihood = -796.879 |T| = 0.922848 Scale1*|T| = 5.82845 211s (S)+(L)+(P)+NNI #3 prior = -20.7114 likelihood = -793.84 |T| = 2.12375 Scale1*|T| = 5.74906 211s (S)+(L)+(P)+NNI #4 prior = -17.9262 likelihood = -792.257 |T| = 1.86364 Scale1*|T| = 6.4008 211s 211s SPR #1 prior = -17.1706 likelihood = -791.452 |T| = 2.03026 Scale1*|T| = 7.65838 211s 211s (S)+(L)+(P)+NNI #1 prior = -19.9971 likelihood = -792.17 |T| = 2.12702 Scale1*|T| = 8.17853 211s (S)+(L)+(P)+NNI #2 prior = -12.6645 likelihood = -794.309 |T| = 1.28717 Scale1*|T| = 7.80855 211s (S)+(L)+(P)+NNI #3 prior = -14.7901 likelihood = -792.908 |T| = 1.42784 Scale1*|T| = 10.0019 211s 211s Finished pre-burnin in 0.08 seconds. 211s 211s 211s BAli-Phy does NOT detect how many iterations is sufficient: 211s You need to monitor convergence and kill it when done. 211s Maximum number of iterations set to 50. 211s 211s Beginning MCMC computations. 211s - Future screen output sent to '5d-1/C1.out' 211s - Future debugging output sent to '5d-1/C1.err' 211s - Sampled trees logged to '5d-1/C1.trees' 211s - Sampled alignments logged to '5d-1/C1.P.fastas' 211s - Run info written to '5d-1/C1.run.json' 211s - Sampled numerical parameters logged to '5d-1/C1.log' as TSV 211s 211s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 211s See the manual at http://www.bali-phy.org/README.xhtml for further information. 217s Created directory '5d-2/' for output files. 219s Partition #1: 126 columns -> 110 unique patterns. 219s T:topology ~ uniform on tree topologies 219s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 219s 219s Partition P1: 219s file = sequences/5S-rRNA/5d.fasta 219s alphabet = DNA 219s subst = tn93 (S1) 219s indel = none 219s scale ~ gamma[0.5,2] (Scale1) 219s 219s Substitution model S1 priors: 219s tn93:kappaPur ~ log_normal[log[2],0.25] 219s tn93:kappaPyr ~ log_normal[log[2],0.25] 219s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 219s 219s Beginning pre-burnin: 3 iterations. 219s Start #1 prior = 3.66627 likelihood = -1521.58 |T| = 0.596738 Scale1*|T| = 0.388962 219s 219s Tree (S)ize #1 prior = -20.0519 likelihood = -925.895 |T| = 0.882719 Scale1*|T| = 34.6447 219s Tree (S)ize #2 prior = -24.3393 likelihood = -921.384 |T| = 0.882719 Scale1*|T| = 42.0429 219s Tree (S)ize #3 prior = -24.233 likelihood = -921.47 |T| = 0.882719 Scale1*|T| = 41.8591 219s 219s (S)+Branch (L)engths #1 prior = -21.242 likelihood = -918.932 |T| = 2.6265 Scale1*|T| = 54.994 219s (S)+Branch (L)engths #2 prior = -20.0058 likelihood = -915.641 |T| = 2.85599 Scale1*|T| = 52.1019 219s (S)+Branch (L)engths #3 prior = -18.7336 likelihood = -915.654 |T| = 3.4078 Scale1*|T| = 36.1988 219s 219s (S)+(L)+(P)arameters #1 prior = -14.0743 likelihood = -838.854 |T| = 2.16918 Scale1*|T| = 17.0259 219s (S)+(L)+(P)arameters #2 prior = -8.3735 likelihood = -827.845 |T| = 1.26424 Scale1*|T| = 9.98903 219s (S)+(L)+(P)arameters #3 prior = -9.91045 likelihood = -825.447 |T| = 1.00143 Scale1*|T| = 10.5296 219s 219s (S)+(L)+(P)+NNI #1 prior = -15.3467 likelihood = -816.19 |T| = 2.26734 Scale1*|T| = 8.40198 219s (S)+(L)+(P)+NNI #2 prior = -8.19633 likelihood = -792.187 |T| = 1.91628 Scale1*|T| = 6.5609 219s (S)+(L)+(P)+NNI #3 prior = -10.4653 likelihood = -794.019 |T| = 2.00651 Scale1*|T| = 7.691 219s (S)+(L)+(P)+NNI #4 prior = -10.5093 likelihood = -794.981 |T| = 1.83101 Scale1*|T| = 8.14948 219s 219s SPR #1 prior = -9.71503 likelihood = -794.17 |T| = 2.01453 Scale1*|T| = 9.01076 219s 219s (S)+(L)+(P)+NNI #1 prior = -7.67389 likelihood = -790.993 |T| = 0.925182 Scale1*|T| = 6.89699 219s (S)+(L)+(P)+NNI #2 prior = -7.38032 likelihood = -793.615 |T| = 1.83607 Scale1*|T| = 6.24615 219s (S)+(L)+(P)+NNI #3 prior = -6.06074 likelihood = -791.981 |T| = 1.24881 Scale1*|T| = 7.05904 219s 219s Finished pre-burnin in 0.07 seconds. 219s 219s 219s BAli-Phy does NOT detect how many iterations is sufficient: 219s You need to monitor convergence and kill it when done. 219s Maximum number of iterations set to 200. 219s 219s Beginning MCMC computations. 219s - Future screen output sent to '5d-2/C1.out' 219s - Future debugging output sent to '5d-2/C1.err' 219s - Sampled trees logged to '5d-2/C1.trees' 219s - Sampled alignments logged to '5d-2/C1.P.fastas' 219s - Run info written to '5d-2/C1.run.json' 219s - Sampled numerical parameters logged to '5d-2/C1.log' as TSV 219s 219s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 219s See the manual at http://www.bali-phy.org/README.xhtml for further information. 221s Created directory '5d-3/' for output files. 223s T:topology ~ uniform on tree topologies 223s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 223s 223s Partition P1: 223s file = sequences/5S-rRNA/5d.fasta 223s alphabet = DNA 223s subst = tn93 (S1) 223s indel = rs07 (I1) 223s scale ~ gamma[0.5,2] (Scale1) 223s 223s Substitution model S1 priors: 223s tn93:kappaPur ~ log_normal[log[2],0.25] 223s tn93:kappaPyr ~ log_normal[log[2],0.25] 223s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 223s 223s Insertion/deletion model I1 priors: 223s rs07:log_rate ~ laplace[-4,0.707] 223s rs07:mean_length ~ shifted_exponential[10,1] 223s 224s Beginning pre-burnin: 3 iterations. 224s Start #1 prior = -42.861 likelihood = -1135.48 |T| = 0.805985 Scale1*|T| = 1.12633 224s 224s Tree (S)ize #1 prior = -9.5097 likelihood = -986.818 |T| = 0.571706 Scale1*|T| = 5.18182 224s Tree (S)ize #2 prior = -19.6502 likelihood = -950.251 |T| = 1.42889 Scale1*|T| = 23.352 224s Tree (S)ize #3 prior = -19.1601 likelihood = -951.122 |T| = 1.82499 Scale1*|T| = 20.5321 224s 224s (S)+Branch (L)engths #1 prior = -10.5107 likelihood = -912.364 |T| = 1.02321 Scale1*|T| = 4.50974 224s (S)+Branch (L)engths #2 prior = -17.3314 likelihood = -887.392 |T| = 2.91355 Scale1*|T| = 10.2121 224s (S)+Branch (L)engths #3 prior = -8.91919 likelihood = -889.749 |T| = 0.863993 Scale1*|T| = 5.48385 224s 224s (S)+(L)+(P)arameters #1 prior = -21.8629 likelihood = -826.173 |T| = 1.53494 Scale1*|T| = 8.87539 224s (S)+(L)+(P)arameters #2 prior = -12.7488 likelihood = -804.794 |T| = 0.926142 Scale1*|T| = 9.75559 224s (S)+(L)+(P)arameters #3 prior = -19.2858 likelihood = -792.452 |T| = 2.19691 Scale1*|T| = 11.2956 224s 224s (S)+(L)+(P)+NNI #1 prior = -14.7899 likelihood = -791.249 |T| = 1.41735 Scale1*|T| = 8.11816 224s (S)+(L)+(P)+NNI #2 prior = -15.8013 likelihood = -792.575 |T| = 2.14293 Scale1*|T| = 7.96297 224s (S)+(L)+(P)+NNI #3 prior = -15.1015 likelihood = -790.616 |T| = 2.03596 Scale1*|T| = 10.94 224s (S)+(L)+(P)+NNI #4 prior = -15.0413 likelihood = -794.052 |T| = 1.81604 Scale1*|T| = 6.93438 224s 224s SPR #1 prior = -16.5044 likelihood = -793.374 |T| = 1.49565 Scale1*|T| = 6.21705 224s 224s (S)+(L)+(P)+NNI #1 prior = -12.819 likelihood = -794.58 |T| = 1.73736 Scale1*|T| = 6.43391 224s (S)+(L)+(P)+NNI #2 prior = -12.4139 likelihood = -798.025 |T| = 1.52596 Scale1*|T| = 6.6099 224s (S)+(L)+(P)+NNI #3 prior = -11.8244 likelihood = -798.058 |T| = 1.32076 Scale1*|T| = 8.35105 224s 224s Finished pre-burnin in 0.09 seconds. 224s 224s 224s BAli-Phy does NOT detect how many iterations is sufficient: 224s You need to monitor convergence and kill it when done. 224s Maximum number of iterations set to 100. 224s 224s Beginning MCMC computations. 224s - Future screen output sent to '5d-3/C1.out' 224s - Future debugging output sent to '5d-3/C1.err' 224s - Sampled trees logged to '5d-3/C1.trees' 224s - Sampled alignments logged to '5d-3/C1.P.fastas' 224s - Run info written to '5d-3/C1.run.json' 224s - Sampled numerical parameters logged to '5d-3/C1.log' as TSV 224s 224s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 224s See the manual at http://www.bali-phy.org/README.xhtml for further information. 234s /usr/bin/bp-analyze:452: SyntaxWarning: invalid escape sequence '\s' 234s self.version = self.find_header_attribute("VERSION").split('\s+')[0] 234s /usr/bin/bp-analyze:1118: SyntaxWarning: invalid escape sequence '\s' 234s m = re.search('([^\s]+) ~ ([^\s]+)\s+\((.+),(.+)\)',line) 234s /usr/bin/bp-analyze:1126: SyntaxWarning: invalid escape sequence '\s' 234s m = re.search('t @ (.+)\s+Ne = ([^ ]+)\s+burnin = (Not Converged!|[^ ]+)', lines[i]) 234s /usr/bin/bp-analyze:1135: SyntaxWarning: invalid escape sequence '\s' 234s m = re.search('PSRF-80%CI = ([^ ]+)\s+PSRF-RCF = ([^ ]+)',lines[i]) 234s /usr/bin/bp-analyze:1142: SyntaxWarning: invalid escape sequence '\s' 234s m = re.search('\s+(.+) = (.+)', line) 234s Program 'gnuplot' not found: Some graphs will not be generated. 234s 234s Program 'R' not found: Some mixing graphs will not be generated. 234s 234s Creating new directory Results/ for summary files. 234s Summarizing distribution of numerical parameters: done. 234s Analyzing scalar variables: /usr/bin/bp-analyze:1227: SyntaxWarning: invalid escape sequence '\(' 234s m = re.search(' const.: ([^ ]+) \(([^ ]+)\%\)', line) 234s /usr/bin/bp-analyze:1232: SyntaxWarning: invalid escape sequence '\(' 234s m = re.search('inform.: ([^ ]+) \(([^ ]+)\%\)', line) 234s /usr/bin/bp-analyze:2092: SyntaxWarning: invalid escape sequence '\[' 234s asdsf = self.get_value_from_file('Results/partitions.bs','ASDSF\[min=0.100\] =') 234s done. 234s 234s Summarizing topology distribution: done. 234s Drawing trees: c50 c66 c80 c90 c95 c99 c100 greedy MAP . done. 234s 234s Generate mixing diagnostics for topologies ... done. 234s Generate SRQ plot for partitions: done. 234s Generate SRQ plot for c50 tree: done. 234s Computing initial alignments: done. 234s 234s Computing WPD alignments: done. 234s Computing ancestral state alignment: done. 234s Drawing alignments: **** done. 234s Generating AU values for 'P1.initial'... done. 234s Generating AU values for 'P1.max'... done. 234s 234s NOTE: burnin (scalar) <= Not Converged! 234s NOTE: min_ESS (scalar) = 8.008 234s NOTE: min_ESS (partition) = 0.000 234s NOTE: ASDSF = NA 234s NOTE: MSDSF = NA 234s NOTE: PSRF-80%CI = NA 234s NOTE: PSRF-RCF = NA 234s 234s Report written to 'Results/index.html 234s autopkgtest [23:23:23]: test run-unit-test: -----------------------] 235s autopkgtest [23:23:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 235s run-unit-test PASS 235s autopkgtest [23:23:24]: @@@@@@@@@@@@@@@@@@@@ summary 235s run-unit-test PASS 257s Creating nova instance adt-noble-s390x-bali-phy-20240325-231929-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...