0s autopkgtest [01:02:43]: starting date and time: 2024-03-19 01:02:43+0000 0s autopkgtest [01:02:43]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [01:02:43]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0up524uw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade garli --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-14.secgroup --name adt-noble-ppc64el-garli-20240319-010243-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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://us.ports.ubuntu.com/ubuntu-ports/ 177s autopkgtest [01:05:40]: testbed dpkg architecture: ppc64el 177s autopkgtest [01:05:40]: testbed apt version: 2.7.12 177s autopkgtest [01:05:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 178s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 179s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 179s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3748 kB] 179s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 179s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 179s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [645 kB] 179s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 179s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 179s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 179s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4015 kB] 180s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 180s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.3 kB] 180s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 183s Fetched 9129 kB in 2s (3745 kB/s) 184s Reading package lists... 186s Reading package lists... 187s Building dependency tree... 187s Reading state information... 187s Calculating upgrade... 187s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 187s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 188s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 188s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 188s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 188s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 189s Reading package lists... 189s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Calculating upgrade... 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s autopkgtest [01:05:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 193s autopkgtest [01:05:56]: @@@@@@@@@@@@@@@@@@@@ apt-source garli 196s Get:1 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (dsc) [2047 B] 196s Get:2 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (tar) [1249 kB] 196s Get:3 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (diff) [4788 B] 196s gpgv: Signature made Sun Feb 20 14:34:04 2022 UTC 196s gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 196s gpgv: Can't check signature: No public key 196s dpkg-source: warning: cannot verify inline signature for ./garli_2.1-7.dsc: no acceptable signature found 197s autopkgtest [01:06:00]: testing package garli version 2.1-7 197s autopkgtest [01:06:00]: build not needed 197s autopkgtest [01:06:00]: 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 garli garli-examples garli-mpi libamd-comgr2 libamdhip64-5 libdrm-amdgpu1 200s libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 libhsakmt1 200s libhwloc-plugins libhwloc15 libllvm17 libmunge2 libncl2 libopenmpi3t64 200s libpciaccess0 libpmix2t64 librdmacm1t64 libucx0 libxnvctrl0 200s ocl-icd-libopencl1 openmpi-bin openmpi-common 200s Suggested packages: 200s opencl-icd gfortran | fortran-compiler 200s The following NEW packages will be installed: 200s autopkgtest-satdep garli garli-examples garli-mpi libamd-comgr2 200s libamdhip64-5 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 200s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 200s libmunge2 libncl2 libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 200s libucx0 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common 200s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 55.8 MB/55.8 MB of archives. 200s After this operation, 259 MB of additional disk space will be used. 200s Get:1 /tmp/autopkgtest.5HBk27/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 201s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libncl2 ppc64el 2.1.21+git20210811.b1213a7-5 [391 kB] 201s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el garli ppc64el 2.1-7 [625 kB] 201s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el garli-examples all 2.1-7 [132 kB] 201s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libevent-pthreads-2.1-7 ppc64el 2.1.12-stable-9 [7844 B] 201s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el librdmacm1t64 ppc64el 50.0-2 [80.9 kB] 201s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfabric1 ppc64el 1.17.0-3 [677 kB] 201s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc15 ppc64el 2.10.0-1 [216 kB] 201s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmunge2 ppc64el 0.5.15-3ubuntu1 [17.6 kB] 201s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libpciaccess0 ppc64el 0.17-3 [20.8 kB] 201s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu1 [11.7 kB] 201s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1 [41.7 kB] 201s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-plugins ppc64el 2.10.0-1 [17.3 kB] 201s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libpmix2t64 ppc64el 5.0.1-4.1 [765 kB] 201s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libllvm17 ppc64el 1:17.0.6-5build1 [27.3 MB] 202s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3 [15.3 MB] 202s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libdrm-amdgpu1 ppc64el 2.4.120-2 [24.5 kB] 202s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsakmt1 ppc64el 5.7.0-1 [76.5 kB] 202s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-1 [330 kB] 202s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamdhip64-5 ppc64el 5.2.3-12 [5004 kB] 203s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el libucx0 ppc64el 1.16.0+ds-4 [1203 kB] 203s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libopenmpi3t64 ppc64el 4.1.6-7ubuntu1 [2721 kB] 203s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-common all 4.1.6-7ubuntu1 [170 kB] 203s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-bin ppc64el 4.1.6-7ubuntu1 [118 kB] 203s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el garli-mpi ppc64el 2.1-7 [615 kB] 203s Fetched 55.8 MB in 2s (23.9 MB/s) 203s Selecting previously unselected package libncl2:ppc64el. 203s (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 ... 70095 files and directories currently installed.) 203s Preparing to unpack .../00-libncl2_2.1.21+git20210811.b1213a7-5_ppc64el.deb ... 203s Unpacking libncl2:ppc64el (2.1.21+git20210811.b1213a7-5) ... 204s Selecting previously unselected package garli. 204s Preparing to unpack .../01-garli_2.1-7_ppc64el.deb ... 204s Unpacking garli (2.1-7) ... 204s Selecting previously unselected package garli-examples. 204s Preparing to unpack .../02-garli-examples_2.1-7_all.deb ... 204s Unpacking garli-examples (2.1-7) ... 204s Selecting previously unselected package libevent-pthreads-2.1-7:ppc64el. 204s Preparing to unpack .../03-libevent-pthreads-2.1-7_2.1.12-stable-9_ppc64el.deb ... 204s Unpacking libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 204s Selecting previously unselected package librdmacm1t64:ppc64el. 204s Preparing to unpack .../04-librdmacm1t64_50.0-2_ppc64el.deb ... 204s Unpacking librdmacm1t64:ppc64el (50.0-2) ... 204s Selecting previously unselected package libfabric1:ppc64el. 204s Preparing to unpack .../05-libfabric1_1.17.0-3_ppc64el.deb ... 204s Unpacking libfabric1:ppc64el (1.17.0-3) ... 204s Selecting previously unselected package libhwloc15:ppc64el. 204s Preparing to unpack .../06-libhwloc15_2.10.0-1_ppc64el.deb ... 204s Unpacking libhwloc15:ppc64el (2.10.0-1) ... 204s Selecting previously unselected package libmunge2:ppc64el. 204s Preparing to unpack .../07-libmunge2_0.5.15-3ubuntu1_ppc64el.deb ... 204s Unpacking libmunge2:ppc64el (0.5.15-3ubuntu1) ... 204s Selecting previously unselected package libpciaccess0:ppc64el. 204s Preparing to unpack .../08-libpciaccess0_0.17-3_ppc64el.deb ... 204s Unpacking libpciaccess0:ppc64el (0.17-3) ... 204s Selecting previously unselected package libxnvctrl0:ppc64el. 204s Preparing to unpack .../09-libxnvctrl0_510.47.03-0ubuntu1_ppc64el.deb ... 204s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 204s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 204s Preparing to unpack .../10-ocl-icd-libopencl1_2.3.2-1_ppc64el.deb ... 204s Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 204s Selecting previously unselected package libhwloc-plugins:ppc64el. 204s Preparing to unpack .../11-libhwloc-plugins_2.10.0-1_ppc64el.deb ... 204s Unpacking libhwloc-plugins:ppc64el (2.10.0-1) ... 204s Selecting previously unselected package libpmix2t64:ppc64el. 204s Preparing to unpack .../12-libpmix2t64_5.0.1-4.1_ppc64el.deb ... 204s Unpacking libpmix2t64:ppc64el (5.0.1-4.1) ... 204s Selecting previously unselected package libllvm17:ppc64el. 204s Preparing to unpack .../13-libllvm17_1%3a17.0.6-5build1_ppc64el.deb ... 204s Unpacking libllvm17:ppc64el (1:17.0.6-5build1) ... 205s Selecting previously unselected package libamd-comgr2:ppc64el. 205s Preparing to unpack .../14-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_ppc64el.deb ... 205s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 205s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 205s Preparing to unpack .../15-libdrm-amdgpu1_2.4.120-2_ppc64el.deb ... 205s Unpacking libdrm-amdgpu1:ppc64el (2.4.120-2) ... 205s Selecting previously unselected package libhsakmt1:ppc64el. 205s Preparing to unpack .../16-libhsakmt1_5.7.0-1_ppc64el.deb ... 205s Unpacking libhsakmt1:ppc64el (5.7.0-1) ... 205s Selecting previously unselected package libhsa-runtime64-1. 205s Preparing to unpack .../17-libhsa-runtime64-1_5.7.1-1_ppc64el.deb ... 205s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 205s Selecting previously unselected package libamdhip64-5. 205s Preparing to unpack .../18-libamdhip64-5_5.2.3-12_ppc64el.deb ... 205s Unpacking libamdhip64-5 (5.2.3-12) ... 206s Selecting previously unselected package libucx0:ppc64el. 206s Preparing to unpack .../19-libucx0_1.16.0+ds-4_ppc64el.deb ... 206s Unpacking libucx0:ppc64el (1.16.0+ds-4) ... 206s Selecting previously unselected package libopenmpi3t64:ppc64el. 206s Preparing to unpack .../20-libopenmpi3t64_4.1.6-7ubuntu1_ppc64el.deb ... 206s Unpacking libopenmpi3t64:ppc64el (4.1.6-7ubuntu1) ... 206s Selecting previously unselected package openmpi-common. 206s Preparing to unpack .../21-openmpi-common_4.1.6-7ubuntu1_all.deb ... 206s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 206s Selecting previously unselected package openmpi-bin. 206s Preparing to unpack .../22-openmpi-bin_4.1.6-7ubuntu1_ppc64el.deb ... 206s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 206s Selecting previously unselected package garli-mpi. 206s Preparing to unpack .../23-garli-mpi_2.1-7_ppc64el.deb ... 206s Unpacking garli-mpi (2.1-7) ... 206s Selecting previously unselected package autopkgtest-satdep. 206s Preparing to unpack .../24-1-autopkgtest-satdep.deb ... 206s Unpacking autopkgtest-satdep (0) ... 206s Setting up libpciaccess0:ppc64el (0.17-3) ... 206s Setting up libncl2:ppc64el (2.1.21+git20210811.b1213a7-5) ... 206s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 206s Setting up garli-examples (2.1-7) ... 206s Setting up garli (2.1-7) ... 206s Setting up libmunge2:ppc64el (0.5.15-3ubuntu1) ... 206s Setting up libhwloc15:ppc64el (2.10.0-1) ... 206s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 206s Setting up openmpi-common (4.1.6-7ubuntu1) ... 206s Setting up librdmacm1t64:ppc64el (50.0-2) ... 206s Setting up libllvm17:ppc64el (1:17.0.6-5build1) ... 206s Setting up libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 206s Setting up libdrm-amdgpu1:ppc64el (2.4.120-2) ... 206s Setting up libfabric1:ppc64el (1.17.0-3) ... 206s Setting up libhwloc-plugins:ppc64el (2.10.0-1) ... 206s Setting up libpmix2t64:ppc64el (5.0.1-4.1) ... 206s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 206s Setting up libhsakmt1:ppc64el (5.7.0-1) ... 206s Setting up libhsa-runtime64-1 (5.7.1-1) ... 206s Setting up libamdhip64-5 (5.2.3-12) ... 206s Setting up libucx0:ppc64el (1.16.0+ds-4) ... 206s Setting up libopenmpi3t64:ppc64el (4.1.6-7ubuntu1) ... 206s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 206s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 206s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 206s Setting up garli-mpi (2.1-7) ... 206s Setting up autopkgtest-satdep (0) ... 206s Processing triggers for man-db (2.12.0-3) ... 208s Processing triggers for libc-bin (2.39-0ubuntu2) ... 211s (Reading database ... 70722 files and directories currently installed.) 211s Removing autopkgtest-satdep (0) ... 212s autopkgtest [01:06:15]: test run-unit-test: [----------------------- 212s Running GARLI Version 2.1. () 212s ->Single processor version for 64-bit OS<- 212s ############################################################## 212s This is GARLI 2.1: maximum likelihood phylogenetic inference 212s using nucleotide, amino acid, codon and morphology-like data, 212s as well as partitioned models. 212s General program usage is extensively documented here: 212s http://www.nescent.org/wg/garli/ 212s See this page for details on partitioned model usage: 212s http://www.nescent.org/wg_garli/Using_partitioned_models 212s and this page for details on Mkv mophology model usage: 212s http://www.nescent.org/wg_garli/Mkv_morphology_model 212s PLEASE LET ME KNOW OF ANY PROBLEMS AT: 212s garli.support@gmail.com 212s ############################################################## 212s Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 11.2.0 212s Using NCL version 2.1.17 212s 212s ####################################################### 212s Reading config file garli.conf 212s ################################################### 212s READING OF DATA 212s Attempting to read data file in Nexus format (using NCL): 212s rana.nex ... 212s Reading DATA block... successful 212s 212s ################################################### 212s PARTITIONING OF DATA AND MODELS 212s GARLI data subset 1 212s CHARACTERS block #1 ("Untitled DATA Block 1") 212s Data read as Nucleotide data, 212s modeled as Nucleotide data 212s storing implied block: TAXA 212s storing read block: DATA 212s Summary of data: 212s 64 sequences. 212s 1062 constant characters. 212s 664 parsimony-informative characters. 212s 250 uninformative variable characters. 212s 1976 total characters. 212s 890 unique patterns in compressed data matrix. 212s 212s ################################################### 212s NOTE: Unlike many programs, the amount of system memory that Garli will 212s use can be controlled by the user. 212s (This comes from the availablememory setting in the configuration file. 212s Availablememory should NOT be set to more than the actual amount of 212s physical memory that your computer has installed) 212s 212s For this dataset: 212s Mem level availablememory setting 212s great >= 70 MB 212s good approx 69 MB to 45 MB 212s low approx 44 MB to 19 MB 212s very low approx 18 MB to 15 MB 212s the minimum required availablememory is 15 MB 212s 212s You specified that Garli should use at most 512.0 MB of memory. 212s 212s Garli will actually use approx. 104.2 MB of memory 212s **Your memory level is: great (you don't need to change anything)** 212s 212s ####################################################### 212s Found outgroup specification: 1 212s 212s ####################################################### 212s STARTING RUN 212s 212s >>>Search rep 1 (of 2)<<< 212s MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 212s Model 1 212s Number of states = 4 (nucleotide data) 212s Nucleotide Relative Rate Matrix: 6 rates 212s AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 212s Equilibrium State Frequencies: estimated 212s (ACGT) 0.3381 0.2238 0.1789 0.2592 212s Rate Heterogeneity Model: 212s 4 discrete gamma distributed rate categories, alpha param estimated 212s 0.5000 212s with an invariant (invariable) site category, proportion estimated 212s 0.1344 212s Substitution rate categories under this model: 212s rate proportion 212s 0.0000 0.1344 212s 0.0334 0.2164 212s 0.2519 0.2164 212s 0.8203 0.2164 212s 2.8944 0.2164 212s 212s Starting with seed=966957 212s 212s creating likelihood stepwise addition starting tree... 212s number of taxa added: 213s 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 213s Optimizing parameters... improved 86.555 lnL 213s Optimizing branchlengths... improved 32.871 lnL 215s 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 215s Initial ln Likelihood: -22592.7374 215s optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... 215s pass 1:+ 301.762 (branch= 44.57 scale= 10.78 alpha= 0.04 freqs=129.41 rel rates=109.82 pinv= 7.14) 216s pass 2:+ 53.018 (branch= 4.48 scale= 0.71 alpha= 7.17 freqs= 28.32 rel rates= 7.86 pinv= 4.47) 216s pass 3:+ 18.574 (branch= 3.48 scale= 0.00 alpha= 5.94 freqs= 1.87 rel rates= 5.19 pinv= 2.10) 216s pass 4:+ 12.679 (branch= 1.41 scale= 0.00 alpha= 3.26 freqs= 0.86 rel rates= 5.44 pinv= 1.70) 216s pass 5:+ 7.174 (branch= 0.00 scale= 0.00 alpha= 2.13 freqs= 0.64 rel rates= 3.21 pinv= 1.19) 216s pass 6:+ 5.158 (branch= 0.00 scale= 0.00 alpha= 1.48 freqs= 0.20 rel rates= 2.63 pinv= 0.85) 216s pass 7:+ 4.599 (branch= 0.00 scale= 0.00 alpha= 0.86 freqs= 0.13 rel rates= 3.01 pinv= 0.60) 216s pass 8:+ 1.905 (branch= 0.00 scale= 0.49 alpha= 0.02 freqs= 0.13 rel rates= 1.25 pinv= 0.02) 216s pass 9:+ 0.169 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 0.13 rel rates= 0.01 pinv= 0.01) 216s lnL after optimization: -22187.6995 216s gen current_lnL precision last_tree_imp 216s 0 -22187.6995 0.500 0 217s 100 -22099.1486 0.500 97 217s 200 -22044.7024 0.500 188 218s 300 -21957.8646 0.500 299 218s 400 -21897.9049 0.500 388 218s 500 -21875.2846 0.500 484 219s 600 -21858.4087 0.500 553 219s 700 -21842.6379 0.500 625 220s 800 -21841.7112 0.500 625 220s 900 -21840.4645 0.500 625 221s 1000 -21833.5328 0.500 912 221s 1100 -21833.2076 0.500 912 222s 1200 -21832.4851 0.500 912 222s 1300 -21831.2908 0.500 912 223s 1400 -21830.5234 0.500 912 223s 1500 -21829.3226 0.500 912 223s Optimization precision reduced 223s Optimizing parameters... improved 0.032 lnL 223s Optimizing branchlengths... improved 1.791 lnL 223s 1600 -21826.3030 0.451 912 224s 1700 -21825.2015 0.451 1658 224s 1800 -21824.4690 0.451 1658 225s 1900 -21823.3714 0.451 1658 225s 2000 -21822.7809 0.451 1658 226s 2100 -21821.3574 0.451 2044 226s 2200 -21820.7601 0.451 2044 227s 2300 -21819.6502 0.451 2207 227s 2400 -21819.4636 0.451 2207 228s 2500 -21819.3637 0.451 2207 228s 2600 -21819.1394 0.451 2207 228s 2700 -21818.8637 0.451 2207 229s 2800 -21818.6255 0.451 2207 229s Optimization precision reduced 229s Optimizing parameters... improved 0.029 lnL 229s Optimizing branchlengths... improved 0.000 lnL 229s 2900 -21818.3673 0.402 2207 230s 3000 -21818.0023 0.402 2207 230s 3100 -21817.8797 0.402 2207 231s 3200 -21817.7895 0.402 2207 231s 3300 -21817.7252 0.402 2207 231s Optimization precision reduced 231s Optimizing parameters... improved 0.018 lnL 231s Optimizing branchlengths... improved 0.471 lnL 232s 3400 -21817.0474 0.353 2207 232s 3500 -21816.8682 0.353 2207 233s 3600 -21816.7773 0.353 2207 233s 3700 -21816.6256 0.353 2207 234s 3800 -21816.4978 0.353 2207 234s Optimization precision reduced 234s Optimizing parameters... improved 0.006 lnL 234s Optimizing branchlengths... improved 0.000 lnL 234s 3900 -21816.4560 0.304 2207 235s 4000 -21816.2132 0.304 2207 235s 4100 -21816.1242 0.304 2207 235s 4200 -21816.0323 0.304 2207 236s 4300 -21815.8948 0.304 2207 236s Optimization precision reduced 236s Optimizing parameters... improved 0.004 lnL 236s Optimizing branchlengths... improved 0.000 lnL 236s 4400 -21815.8308 0.255 2207 237s 4500 -21815.7352 0.255 2207 237s 4600 -21815.7002 0.255 2207 238s 4700 -21815.5924 0.255 2207 238s 4800 -21815.5668 0.255 2207 238s Optimization precision reduced 238s Optimizing parameters... improved 0.004 lnL 238s Optimizing branchlengths... improved 0.000 lnL 239s 4900 -21815.4718 0.206 2207 239s 5000 -21815.4338 0.206 2207 240s 5100 -21815.3357 0.206 5097 240s 5200 -21815.2853 0.206 5097 241s 5300 -21815.2091 0.206 5097 241s 5400 -21815.1728 0.206 5097 242s 5500 -21815.0951 0.206 5097 242s 5600 -21814.9411 0.206 5097 242s Optimization precision reduced 243s Optimizing parameters... improved 0.006 lnL 243s Optimizing branchlengths... improved 0.000 lnL 243s 5700 -21814.8991 0.157 5097 243s 5800 -21814.8018 0.157 5097 244s 5900 -21814.7562 0.157 5097 244s 6000 -21814.7186 0.157 5097 245s 6100 -21814.6930 0.157 5097 245s Optimization precision reduced 245s Optimizing parameters... improved 0.002 lnL 245s Optimizing branchlengths... improved 0.123 lnL 245s 6200 -21814.5636 0.108 5097 246s 6300 -21814.5395 0.108 5097 246s 6400 -21814.5096 0.108 5097 247s 6500 -21814.4868 0.108 5097 247s 6600 -21814.4483 0.108 5097 247s Optimization precision reduced 247s Optimizing parameters... improved 0.001 lnL 247s Optimizing branchlengths... improved 0.424 lnL 248s 6700 -21814.0020 0.059 5097 248s 6800 -21813.9941 0.059 5097 249s 6900 -21813.9447 0.059 5097 249s 7000 -21813.9360 0.059 5097 250s 7100 -21813.9143 0.059 5097 250s Optimization precision reduced 250s Optimizing parameters... improved 0.011 lnL 250s Optimizing branchlengths... improved 0.098 lnL 251s 7200 -21813.7968 0.010 5097 251s 7300 -21813.7952 0.010 5097 252s 7400 -21813.7952 0.010 5097 252s 7500 -21813.7948 0.010 5097 253s 7600 -21813.7941 0.010 5097 254s 7700 -21813.7888 0.010 5097 254s 7800 -21813.7888 0.010 5097 255s 7900 -21813.7830 0.010 5097 255s 8000 -21813.7830 0.010 5097 256s 8100 -21813.7784 0.010 5097 257s 8200 -21813.7760 0.010 5097 257s 8300 -21813.7720 0.010 5097 258s 8400 -21813.7608 0.010 5097 259s 8500 -21813.7551 0.010 5097 259s 8600 -21813.7451 0.010 5097 260s 8700 -21813.7357 0.010 5097 261s 8800 -21813.7348 0.010 5097 261s 8900 -21813.7313 0.010 5097 262s 9000 -21813.7242 0.010 5097 262s 9100 -21813.7235 0.010 5097 263s 9200 -21813.7234 0.010 5097 263s 9300 -21813.6740 0.010 9249 264s 9400 -21813.6425 0.010 9249 265s 9500 -21813.6286 0.010 9249 265s 9600 -21813.2929 0.010 9506 266s 9700 -21813.2820 0.010 9506 267s 9800 -21813.2820 0.010 9506 267s 9900 -21813.2814 0.010 9506 268s 10000 -21813.2790 0.010 9506 268s 10100 -21813.2772 0.010 9506 269s 10200 -21813.2543 0.010 9506 270s 10300 -21812.9402 0.010 10219 270s 10400 -21812.9336 0.010 10219 271s 10500 -21812.9317 0.010 10219 271s 10600 -21812.9317 0.010 10219 272s 10700 -21812.9301 0.010 10219 272s 10800 -21812.9294 0.010 10219 273s 10900 -21812.9242 0.010 10219 274s 11000 -21812.9197 0.010 10219 274s 11100 -21812.9189 0.010 10219 275s 11200 -21812.9189 0.010 10219 276s 11300 -21812.9187 0.010 10219 276s 11400 -21812.9147 0.010 10219 277s 11500 -21812.8958 0.010 10219 278s 11600 -21812.8805 0.010 10219 278s 11700 -21812.8739 0.010 10219 279s 11800 -21812.8689 0.010 10219 279s 11900 -21812.8679 0.010 10219 280s 12000 -21812.8628 0.010 10219 281s 12100 -21812.8532 0.010 10219 281s 12200 -21812.8448 0.010 10219 282s 12300 -21812.8448 0.010 10219 282s 12400 -21812.8341 0.010 10219 283s 12500 -21812.8294 0.010 10219 284s 12600 -21812.8275 0.010 10219 284s 12700 -21812.8254 0.010 10219 285s 12800 -21812.8228 0.010 10219 286s 12900 -21812.8112 0.010 10219 286s 13000 -21812.8112 0.010 10219 287s 13100 -21812.8112 0.010 10219 288s 13200 -21812.8088 0.010 10219 288s 13300 -21812.8055 0.010 10219 289s 13400 -21812.8030 0.010 10219 289s 13500 -21812.7944 0.010 10219 290s 13600 -21812.7944 0.010 10219 291s 13700 -21812.7918 0.010 10219 291s 13800 -21812.7916 0.010 10219 292s 13900 -21812.7914 0.010 10219 293s 14000 -21812.7913 0.010 10219 293s 14100 -21812.7838 0.010 10219 294s 14200 -21812.7809 0.010 10219 294s 14300 -21812.7807 0.010 10219 295s 14400 -21812.7807 0.010 10219 296s 14500 -21812.7787 0.010 10219 296s 14600 -21812.7730 0.010 10219 297s 14700 -21812.7679 0.010 10219 298s 14800 -21812.7665 0.010 10219 298s 14900 -21812.7640 0.010 10219 299s 15000 -21812.7640 0.010 10219 299s Optimizing parameters... improved 0.001 lnL 299s Optimizing branchlengths... improved 0.000 lnL 300s 15100 -21812.7620 0.010 10219 300s 15200 -21812.7620 0.010 10219 301s 15300 -21812.7620 0.010 10219 302s 15400 -21812.7592 0.010 10219 302s 15500 -21812.7529 0.010 10219 303s 15600 -21812.7519 0.010 10219 304s 15700 -21812.7519 0.010 10219 304s 15800 -21812.7502 0.010 10219 305s 15900 -21812.7499 0.010 10219 305s 16000 -21812.7467 0.010 10219 306s 16100 -21812.7467 0.010 10219 307s 16200 -21812.7467 0.010 10219 307s 16300 -21812.7458 0.010 10219 308s 16400 -21812.7454 0.010 10219 308s 16500 -21812.7411 0.010 10219 309s 16600 -21812.7407 0.010 10219 309s 16700 -21812.7407 0.010 10219 310s 16800 -21812.7407 0.010 10219 311s 16900 -21812.7396 0.010 10219 311s 17000 -21812.7377 0.010 10219 312s 17100 -21812.7377 0.010 10219 312s 17200 -21812.7377 0.010 10219 313s 17300 -21812.7377 0.010 10219 313s 17400 -21812.7349 0.010 10219 314s 17500 -21812.7335 0.010 10219 315s 17600 -21812.7335 0.010 10219 315s 17700 -21812.7328 0.010 10219 316s 17800 -21812.7328 0.010 10219 316s 17900 -21812.7313 0.010 10219 317s 18000 -21812.7313 0.010 10219 318s 18100 -21812.7310 0.010 10219 318s 18200 -21812.7310 0.010 10219 319s 18300 -21812.7310 0.010 10219 320s 18400 -21812.7286 0.010 10219 320s 18500 -21812.7286 0.010 10219 321s 18600 -21812.7286 0.010 10219 322s 18700 -21812.7286 0.010 10219 322s 18800 -21812.7275 0.010 10219 323s 18900 -21812.7275 0.010 10219 324s 19000 -21812.7275 0.010 10219 324s 19100 -21812.7275 0.010 10219 325s 19200 -21812.7275 0.010 10219 325s 19300 -21812.7269 0.010 10219 326s 19400 -21812.7267 0.010 10219 327s 19500 -21812.7264 0.010 10219 327s 19600 -21812.7245 0.010 10219 328s 19700 -21812.7245 0.010 10219 329s 19800 -21812.7245 0.010 10219 329s 19900 -21812.7245 0.010 10219 330s 20000 -21812.7245 0.010 10219 330s Optimizing parameters... improved 0.000 lnL 330s Optimizing branchlengths... improved 0.000 lnL 331s 20100 -21812.7243 0.010 10219 331s 20200 -21812.7243 0.010 10219 332s 20300 -21812.7236 0.010 10219 333s 20400 -21812.7236 0.010 10219 333s 20500 -21812.7235 0.010 10219 334s 20600 -21812.7230 0.010 10219 335s 20700 -21812.7230 0.010 10219 335s 20800 -21812.7230 0.010 10219 336s 20900 -21812.7206 0.010 10219 336s 21000 -21812.7200 0.010 10219 337s 21100 -21812.7200 0.010 10219 338s 21200 -21812.7195 0.010 10219 338s 21300 -21812.7195 0.010 10219 339s 21400 -21812.7195 0.010 10219 340s 21500 -21812.7195 0.010 10219 341s 21600 -21812.7195 0.010 10219 341s 21700 -21812.7195 0.010 10219 342s 21800 -21812.7195 0.010 10219 342s 21900 -21812.7194 0.010 10219 343s 22000 -21812.7191 0.010 10219 344s 22100 -21812.7175 0.010 10219 344s 22200 -21812.7162 0.010 10219 345s 22300 -21812.7162 0.010 10219 345s 22400 -21812.7162 0.010 10219 346s 22500 -21812.7162 0.010 10219 347s 22600 -21812.7162 0.010 10219 347s 22700 -21812.7162 0.010 10219 348s 22800 -21812.7162 0.010 10219 349s 22900 -21812.7157 0.010 10219 349s 23000 -21812.7157 0.010 10219 350s 23100 -21812.7157 0.010 10219 350s 23200 -21812.7155 0.010 10219 351s 23300 -21812.7144 0.010 10219 352s 23400 -21812.7144 0.010 10219 353s 23500 -21812.7143 0.010 10219 353s 23600 -21812.7131 0.010 10219 354s 23700 -21812.7131 0.010 10219 355s 23800 -21812.7131 0.010 10219 355s 23900 -21812.7131 0.010 10219 356s 24000 -21812.7130 0.010 10219 356s 24100 -21812.7130 0.010 10219 357s 24200 -21812.7130 0.010 10219 358s 24300 -21812.7130 0.010 10219 360s 24400 -21812.7130 0.010 10219 360s 24500 -21812.7129 0.010 10219 360s 24600 -21812.7129 0.010 10219 360s 24700 -21812.7123 0.010 10219 361s 24800 -21812.7121 0.010 10219 361s 24900 -21812.7113 0.010 10219 362s 25000 -21812.7113 0.010 10219 362s Optimizing parameters... improved 0.000 lnL 362s Optimizing branchlengths... improved 0.000 lnL 363s 25100 -21812.7110 0.010 10219 363s 25200 -21812.7110 0.010 10219 364s 25300 -21812.7109 0.010 10219 364s 25400 -21812.7109 0.010 10219 365s 25500 -21812.7109 0.010 10219 366s 25600 -21812.7109 0.010 10219 366s 25700 -21812.7109 0.010 10219 367s 25800 -21812.7109 0.010 10219 368s 25900 -21812.7104 0.010 10219 368s 26000 -21812.7104 0.010 10219 369s 26100 -21812.7104 0.010 10219 369s 26200 -21812.7104 0.010 10219 370s 26300 -21812.7104 0.010 10219 371s 26400 -21812.7103 0.010 10219 371s 26500 -21812.7103 0.010 10219 372s 26600 -21812.7102 0.010 10219 373s 26700 -21812.7102 0.010 10219 373s 26800 -21812.7102 0.010 10219 374s 26900 -21812.7093 0.010 10219 374s 27000 -21812.7093 0.010 10219 375s 27100 -21812.7086 0.010 10219 376s 27200 -21812.7081 0.010 10219 376s 27300 -21812.7079 0.010 10219 377s 27400 -21812.7079 0.010 10219 378s 27500 -21812.7079 0.010 10219 378s 27600 -21812.7079 0.010 10219 379s 27700 -21812.7079 0.010 10219 380s 27800 -21812.7079 0.010 10219 380s 27900 -21812.7079 0.010 10219 381s 28000 -21812.7079 0.010 10219 381s 28100 -21812.7079 0.010 10219 382s 28200 -21812.7078 0.010 10219 383s 28300 -21812.7076 0.010 10219 384s 28400 -21812.7076 0.010 10219 384s 28500 -21812.7076 0.010 10219 385s 28600 -21812.7076 0.010 10219 386s 28700 -21812.7075 0.010 10219 386s 28800 -21812.7075 0.010 10219 387s 28900 -21812.7069 0.010 10219 387s 29000 -21812.7069 0.010 10219 388s 29100 -21812.7069 0.010 10219 389s 29200 -21812.7069 0.010 10219 389s 29300 -21812.7069 0.010 10219 390s 29400 -21812.7069 0.010 10219 390s 29500 -21812.7069 0.010 10219 391s 29600 -21812.7069 0.010 10219 392s 29700 -21812.7069 0.010 10219 392s 29800 -21812.7069 0.010 10219 393s 29900 -21812.7069 0.010 10219 393s 30000 -21812.7068 0.010 10219 394s Optimizing parameters... improved 0.000 lnL 394s Optimizing branchlengths... improved 0.000 lnL 394s 30100 -21812.7065 0.010 10219 395s 30200 -21812.7065 0.010 10219 396s 30300 -21812.7065 0.010 10219 396s Reached termination condition! 396s last topological improvement at gen 10219 396s Improvement over last 500 gen = 0.00046 396s Current score = -21812.7065 396s Performing final optimizations... 396s pass 1 : -21812.7064 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) 396s pass 2 : -21812.6989 (branch= 0.0074 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 396s pass 3 : -21812.6939 (branch= 0.0049 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 396s pass 4 : -21812.6864 (branch= 0.0075 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 396s pass 5 : -21812.6769 (branch= 0.0095 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 396s pass 6 : -21812.6728 (branch= 0.0041 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 397s pass 7 : -21812.6711 (branch= 0.0017 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 397s pass 8 : -21812.6702 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 397s pass 9 : -21812.6699 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 397s pass 10: -21812.6697 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 397s pass 11: -21812.6696 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 397s pass 12: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 397s pass 13: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 398s pass 14: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 398s pass 15: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 398s Looking for minimum length branches... 398s Final score = -21812.6695 398s Time used so far = 0 hours, 3 minutes and 6 seconds 398s 398s MODEL REPORT - Parameter values are FINAL 398s Model 1 398s Number of states = 4 (nucleotide data) 398s Nucleotide Relative Rate Matrix: 6 rates 398s AC = 2.215, AG = 8.209, AT = 2.369, CG = 0.914, CT = 16.548, GT = 1.000 398s Equilibrium State Frequencies: estimated 398s (ACGT) 0.3475 0.2133 0.1497 0.2895 398s Rate Heterogeneity Model: 398s 4 discrete gamma distributed rate categories, alpha param estimated 398s 0.5558 398s with an invariant (invariable) site category, proportion estimated 398s 0.3361 398s Substitution rate categories under this model: 398s rate proportion 398s 0.0000 0.3361 398s 0.0441 0.1660 398s 0.2868 0.1660 398s 0.8569 0.1660 398s 2.8122 0.1660 398s 398s NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 398s No branches were short enough to be collapsed. 398s 398s >>>Completed Search rep 1 (of 2)<<< 398s 398s >>>Search rep 2 (of 2)<<< 398s MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 398s Model 1 398s Number of states = 4 (nucleotide data) 398s Nucleotide Relative Rate Matrix: 6 rates 398s AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 398s Equilibrium State Frequencies: estimated 398s (ACGT) 0.3381 0.2238 0.1789 0.2592 398s Rate Heterogeneity Model: 398s 4 discrete gamma distributed rate categories, alpha param estimated 398s 0.5000 398s with an invariant (invariable) site category, proportion estimated 398s 0.1344 398s Substitution rate categories under this model: 398s rate proportion 398s 0.0000 0.1344 398s 0.0334 0.2164 398s 0.2519 0.2164 398s 0.8203 0.2164 398s 2.8944 0.2164 398s 398s Starting with seed=704019873 398s 398s creating likelihood stepwise addition starting tree... 398s number of taxa added: 399s 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 399s Optimizing parameters... improved 46.812 lnL 399s Optimizing branchlengths... improved 17.956 lnL 401s 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 401s Initial ln Likelihood: -23138.7012 401s optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... 401s pass 1:+ 509.466 (branch= 241.54 scale= 9.97 alpha= 0.00 freqs=133.98 rel rates=115.37 pinv= 8.60) 401s pass 2:+ 81.733 (branch= 34.10 scale= 0.00 alpha= 4.05 freqs= 33.00 rel rates= 6.17 pinv= 4.41) 401s pass 3:+ 14.830 (branch= 3.11 scale= 0.00 alpha= 5.26 freqs= 1.85 rel rates= 2.97 pinv= 1.64) 401s pass 4:+ 8.358 (branch= 0.42 scale= 0.00 alpha= 2.57 freqs= 0.87 rel rates= 3.26 pinv= 1.24) 401s pass 5:+ 5.585 (branch= 0.00 scale= 0.00 alpha= 1.64 freqs= 0.92 rel rates= 2.25 pinv= 0.78) 401s pass 6:+ 6.041 (branch= 0.00 scale= 0.00 alpha= 0.93 freqs= 0.14 rel rates= 4.47 pinv= 0.50) 401s pass 7:+ 3.026 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 0.08 rel rates= 2.93 pinv= 0.00) 402s pass 8:+ 0.720 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 0.10 rel rates= 0.60 pinv= 0.00) 402s pass 9:+ 0.085 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 0.04 rel rates= 0.02 pinv= 0.00) 402s lnL after optimization: -22508.8576 402s gen current_lnL precision last_tree_imp 402s 0 -22508.8576 0.500 0 402s 100 -22441.4364 0.500 97 402s 200 -22380.0470 0.500 200 403s 300 -22158.4878 0.500 284 403s 400 -22013.5315 0.500 400 404s 500 -21932.7265 0.500 493 404s 600 -21886.3085 0.500 551 405s 700 -21879.6493 0.500 651 405s 800 -21863.5456 0.500 796 405s 900 -21827.2856 0.500 872 406s 1000 -21826.4829 0.500 872 406s 1100 -21825.4384 0.500 872 407s 1200 -21824.1426 0.500 872 407s 1300 -21822.8538 0.500 872 408s 1400 -21822.2823 0.500 872 408s Optimization precision reduced 408s Optimizing parameters... improved 0.039 lnL 408s Optimizing branchlengths... improved 0.000 lnL 408s 1500 -21821.7339 0.451 1435 409s 1600 -21820.7985 0.451 1435 409s 1700 -21820.3745 0.451 1435 410s 1800 -21819.8256 0.451 1435 410s 1900 -21819.3789 0.451 1435 410s 2000 -21819.2589 0.451 1435 410s Optimization precision reduced 410s Optimizing parameters... improved 0.024 lnL 410s Optimizing branchlengths... improved 0.003 lnL 411s 2100 -21818.9054 0.402 1435 411s 2200 -21818.7813 0.402 1435 412s 2300 -21818.5654 0.402 1435 412s 2400 -21818.3903 0.402 1435 412s 2500 -21818.0135 0.402 1435 412s Optimization precision reduced 413s Optimizing parameters... improved 0.034 lnL 413s Optimizing branchlengths... improved 0.000 lnL 413s 2600 -21817.8827 0.353 1435 413s 2700 -21817.5897 0.353 1435 414s 2800 -21817.4271 0.353 1435 414s 2900 -21817.1192 0.353 1435 415s 3000 -21817.0442 0.353 1435 415s Optimization precision reduced 415s Optimizing parameters... improved 0.013 lnL 415s Optimizing branchlengths... improved 0.414 lnL 415s 3100 -21816.4122 0.304 1435 416s 3200 -21815.8293 0.304 3144 416s 3300 -21815.7109 0.304 3144 417s 3400 -21815.5899 0.304 3144 417s 3500 -21815.5576 0.304 3144 417s 3600 -21815.3643 0.304 3144 418s 3700 -21815.2428 0.304 3144 418s Optimization precision reduced 418s Optimizing parameters... improved 0.008 lnL 418s Optimizing branchlengths... improved 0.000 lnL 418s 3800 -21815.1783 0.255 3144 419s 3900 -21815.0882 0.255 3144 419s 4000 -21815.0402 0.255 3144 420s 4100 -21814.9134 0.255 3144 420s 4200 -21814.7612 0.255 3144 420s Optimization precision reduced 420s Optimizing parameters... improved 0.003 lnL 420s Optimizing branchlengths... improved 0.000 lnL 421s 4300 -21814.6946 0.206 3144 421s 4400 -21814.6317 0.206 3144 422s 4500 -21814.5682 0.206 3144 422s 4600 -21814.4534 0.206 3144 422s 4700 -21814.4217 0.206 3144 422s Optimization precision reduced 422s Optimizing parameters... improved 0.003 lnL 423s Optimizing branchlengths... improved 0.000 lnL 423s 4800 -21814.3157 0.157 3144 423s 4900 -21814.3094 0.157 3144 424s 5000 -21814.2668 0.157 3144 424s 5100 -21814.2266 0.157 3144 425s 5200 -21814.1975 0.157 3144 425s Optimization precision reduced 425s Optimizing parameters... improved 0.004 lnL 425s Optimizing branchlengths... improved 0.142 lnL 425s 5300 -21814.0046 0.108 3144 426s 5400 -21813.9866 0.108 3144 426s 5500 -21813.9295 0.108 3144 427s 5600 -21813.8871 0.108 3144 427s 5700 -21813.8624 0.108 3144 427s Optimization precision reduced 427s Optimizing parameters... improved 0.002 lnL 427s Optimizing branchlengths... improved 0.445 lnL 428s 5800 -21813.3602 0.059 3144 428s 5900 -21813.3462 0.059 3144 429s 6000 -21813.3067 0.059 3144 429s 6100 -21813.3000 0.059 3144 430s 6200 -21813.2895 0.059 3144 430s Optimization precision reduced 430s Optimizing parameters... improved 0.024 lnL 430s Optimizing branchlengths... improved 0.243 lnL 430s 6300 -21813.0067 0.010 3144 431s 6400 -21813.0062 0.010 3144 432s 6500 -21813.0062 0.010 3144 432s 6600 -21812.9997 0.010 3144 433s 6700 -21812.9969 0.010 3144 433s 6800 -21812.9961 0.010 3144 434s 6900 -21812.9884 0.010 3144 435s 7000 -21812.9764 0.010 3144 435s 7100 -21812.9697 0.010 3144 436s 7200 -21812.9660 0.010 3144 436s 7300 -21812.9607 0.010 3144 437s 7400 -21812.9492 0.010 3144 438s 7500 -21812.9437 0.010 3144 438s 7600 -21812.9384 0.010 3144 439s 7700 -21812.9384 0.010 3144 439s 7800 -21812.9327 0.010 3144 440s 7900 -21812.9326 0.010 3144 440s 8000 -21812.9320 0.010 3144 441s 8100 -21812.8989 0.010 3144 442s 8200 -21812.8966 0.010 3144 442s 8300 -21812.8922 0.010 3144 443s 8400 -21812.8853 0.010 3144 443s 8500 -21812.8821 0.010 3144 444s 8600 -21812.8782 0.010 3144 445s 8700 -21812.8618 0.010 3144 446s 8800 -21812.8618 0.010 3144 446s 8900 -21812.8604 0.010 3144 447s 9000 -21812.8604 0.010 3144 447s 9100 -21812.8601 0.010 3144 448s 9200 -21812.8601 0.010 3144 448s 9300 -21812.8467 0.010 3144 449s 9400 -21812.8360 0.010 3144 450s 9500 -21812.8326 0.010 3144 450s 9600 -21812.8304 0.010 3144 451s 9700 -21812.8294 0.010 3144 451s 9800 -21812.8277 0.010 3144 452s 9900 -21812.8277 0.010 3144 453s 10000 -21812.8259 0.010 3144 453s 10100 -21812.8243 0.010 3144 454s 10200 -21812.8243 0.010 3144 454s 10300 -21812.8212 0.010 3144 455s 10400 -21812.8208 0.010 3144 455s 10500 -21812.8206 0.010 3144 456s 10600 -21812.8196 0.010 3144 456s 10700 -21812.8177 0.010 3144 457s 10800 -21812.8175 0.010 3144 458s 10900 -21812.8146 0.010 3144 458s 11000 -21812.8127 0.010 3144 459s 11100 -21812.8123 0.010 3144 459s 11200 -21812.8121 0.010 3144 460s 11300 -21812.8121 0.010 3144 461s 11400 -21812.8102 0.010 3144 461s 11500 -21812.8023 0.010 3144 462s 11600 -21812.8023 0.010 3144 462s 11700 -21812.8023 0.010 3144 463s 11800 -21812.8023 0.010 3144 464s 11900 -21812.8021 0.010 3144 464s 12000 -21812.8021 0.010 3144 465s 12100 -21812.7996 0.010 3144 465s 12200 -21812.7996 0.010 3144 466s 12300 -21812.7996 0.010 3144 467s 12400 -21812.7993 0.010 3144 467s 12500 -21812.7986 0.010 3144 468s 12600 -21812.7984 0.010 3144 468s 12700 -21812.7984 0.010 3144 469s 12800 -21812.7980 0.010 3144 470s 12900 -21812.7980 0.010 3144 470s 13000 -21812.7980 0.010 3144 471s 13100 -21812.7972 0.010 3144 471s 13200 -21812.7949 0.010 3144 472s 13300 -21812.7949 0.010 3144 473s 13400 -21812.7949 0.010 3144 473s 13500 -21812.7909 0.010 3144 474s 13600 -21812.7909 0.010 3144 474s 13700 -21812.7908 0.010 3144 475s 13800 -21812.7908 0.010 3144 476s 13900 -21812.7907 0.010 3144 476s 14000 -21812.7907 0.010 3144 477s 14100 -21812.7907 0.010 3144 477s 14200 -21812.7907 0.010 3144 478s 14300 -21812.7907 0.010 3144 479s 14400 -21812.7862 0.010 3144 479s 14500 -21812.7834 0.010 3144 480s 14600 -21812.7788 0.010 3144 480s 14700 -21812.7788 0.010 3144 481s 14800 -21812.7788 0.010 3144 482s 14900 -21812.7788 0.010 3144 482s 15000 -21812.7788 0.010 3144 482s Optimizing parameters... improved 0.000 lnL 482s Optimizing branchlengths... improved 0.000 lnL 483s 15100 -21812.7786 0.010 3144 483s 15200 -21812.7786 0.010 3144 484s 15300 -21812.7786 0.010 3144 485s 15400 -21812.7786 0.010 3144 485s 15500 -21812.7777 0.010 3144 486s 15600 -21812.7762 0.010 3144 486s 15700 -21812.7762 0.010 3144 487s 15800 -21812.7753 0.010 3144 488s 15900 -21812.7717 0.010 3144 488s 16000 -21812.7717 0.010 3144 489s 16100 -21812.7705 0.010 3144 489s 16200 -21812.7689 0.010 3144 490s 16300 -21812.7666 0.010 3144 490s 16400 -21812.7660 0.010 3144 491s 16500 -21812.7655 0.010 3144 492s 16600 -21812.7604 0.010 3144 492s 16700 -21812.7604 0.010 3144 493s 16800 -21812.7585 0.010 3144 493s 16900 -21812.7565 0.010 3144 494s 17000 -21812.7523 0.010 3144 494s 17100 -21812.7523 0.010 3144 495s 17200 -21812.7459 0.010 3144 496s 17300 -21812.7459 0.010 3144 496s 17400 -21812.7448 0.010 3144 497s 17500 -21812.7436 0.010 3144 497s 17600 -21812.7424 0.010 3144 498s 17700 -21812.7421 0.010 3144 499s 17800 -21812.7420 0.010 3144 499s 17900 -21812.7420 0.010 3144 500s 18000 -21812.7401 0.010 3144 500s 18100 -21812.7399 0.010 3144 501s 18200 -21812.7396 0.010 3144 502s 18300 -21812.7396 0.010 3144 502s 18400 -21812.7385 0.010 3144 503s 18500 -21812.7310 0.010 3144 503s 18600 -21812.7309 0.010 3144 504s 18700 -21812.7301 0.010 3144 504s 18800 -21812.7301 0.010 3144 505s 18900 -21812.7277 0.010 3144 506s 19000 -21812.7272 0.010 3144 506s 19100 -21812.7272 0.010 3144 507s 19200 -21812.7272 0.010 3144 507s 19300 -21812.7272 0.010 3144 508s 19400 -21812.7272 0.010 3144 509s 19500 -21812.7237 0.010 3144 509s 19600 -21812.7237 0.010 3144 510s 19700 -21812.7212 0.010 3144 510s 19800 -21812.7212 0.010 3144 511s 19900 -21812.7212 0.010 3144 511s 20000 -21812.7212 0.010 3144 511s Optimizing parameters... improved 0.000 lnL 511s Optimizing branchlengths... improved 0.000 lnL 512s 20100 -21812.7206 0.010 3144 513s 20200 -21812.7206 0.010 3144 513s 20300 -21812.7205 0.010 3144 514s 20400 -21812.7205 0.010 3144 514s 20500 -21812.7205 0.010 3144 515s 20600 -21812.7201 0.010 3144 515s 20700 -21812.7201 0.010 3144 516s 20800 -21812.7201 0.010 3144 516s 20900 -21812.7201 0.010 3144 517s 21000 -21812.7201 0.010 3144 518s 21100 -21812.7174 0.010 3144 518s 21200 -21812.7174 0.010 3144 519s 21300 -21812.7174 0.010 3144 519s 21400 -21812.7174 0.010 3144 520s 21500 -21812.7174 0.010 3144 520s 21600 -21812.7159 0.010 3144 521s 21700 -21812.7139 0.010 3144 522s 21800 -21812.7139 0.010 3144 522s 21900 -21812.7139 0.010 3144 523s 22000 -21812.7133 0.010 3144 523s 22100 -21812.7133 0.010 3144 524s 22200 -21812.7133 0.010 3144 525s 22300 -21812.7133 0.010 3144 525s 22400 -21812.7122 0.010 3144 526s 22500 -21812.7121 0.010 3144 526s 22600 -21812.7121 0.010 3144 527s 22700 -21812.7121 0.010 3144 527s 22800 -21812.7115 0.010 3144 528s 22900 -21812.7114 0.010 3144 529s 23000 -21812.7114 0.010 3144 529s 23100 -21812.7114 0.010 3144 530s 23200 -21812.7114 0.010 3144 530s 23300 -21812.7114 0.010 3144 531s 23400 -21812.7114 0.010 3144 532s 23500 -21812.7114 0.010 3144 532s 23600 -21812.7114 0.010 3144 533s 23700 -21812.7114 0.010 3144 533s 23800 -21812.7114 0.010 3144 534s 23900 -21812.7114 0.010 3144 534s 24000 -21812.7114 0.010 3144 535s 24100 -21812.7114 0.010 3144 535s 24200 -21812.7114 0.010 3144 536s 24300 -21812.7114 0.010 3144 537s 24400 -21812.7114 0.010 3144 537s 24500 -21812.7114 0.010 3144 538s 24600 -21812.7113 0.010 3144 538s 24700 -21812.7113 0.010 3144 539s 24800 -21812.7113 0.010 3144 539s 24900 -21812.7113 0.010 3144 540s 25000 -21812.7113 0.010 3144 540s Optimizing parameters... improved 0.000 lnL 540s Optimizing branchlengths... improved 0.000 lnL 541s 25100 -21812.7111 0.010 3144 541s 25200 -21812.7111 0.010 3144 542s 25300 -21812.7111 0.010 3144 542s 25400 -21812.7111 0.010 3144 543s 25500 -21812.7111 0.010 3144 543s 25600 -21812.7111 0.010 3144 544s 25700 -21812.7111 0.010 3144 545s 25800 -21812.7109 0.010 3144 545s 25900 -21812.7109 0.010 3144 546s 26000 -21812.7106 0.010 3144 546s 26100 -21812.7086 0.010 3144 547s 26200 -21812.7083 0.010 3144 547s 26300 -21812.7083 0.010 3144 547s Reached termination condition! 547s last topological improvement at gen 3144 547s Improvement over last 500 gen = 0.00257 547s Current score = -21812.7083 547s Performing final optimizations... 547s pass 1 : -21812.7081 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0001) 548s pass 2 : -21812.7048 (branch= 0.0032 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0000) 548s pass 3 : -21812.6982 (branch= 0.0065 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 548s pass 4 : -21812.6877 (branch= 0.0104 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 548s pass 5 : -21812.6793 (branch= 0.0072 alpha= 0.0007 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0000) 548s pass 6 : -21812.6739 (branch= 0.0047 alpha= 0.0004 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0000) 548s pass 7 : -21812.6715 (branch= 0.0021 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0000) 548s pass 8 : -21812.6706 (branch= 0.0008 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 549s pass 9 : -21812.6701 (branch= 0.0004 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 549s pass 10: -21812.6699 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 549s pass 11: -21812.6697 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 549s pass 12: -21812.6696 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 549s pass 13: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 549s pass 14: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 549s pass 15: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 550s pass 16: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 550s Looking for minimum length branches... 550s Final score = -21812.6695 550s Time used = 0 hours, 5 minutes and 38 seconds 550s 550s MODEL REPORT - Parameter values are FINAL 550s Model 1 550s Number of states = 4 (nucleotide data) 550s Nucleotide Relative Rate Matrix: 6 rates 550s AC = 2.210, AG = 8.197, AT = 2.366, CG = 0.912, CT = 16.520, GT = 1.000 550s Equilibrium State Frequencies: estimated 550s (ACGT) 0.3475 0.2133 0.1496 0.2895 550s Rate Heterogeneity Model: 550s 4 discrete gamma distributed rate categories, alpha param estimated 550s 0.5552 550s with an invariant (invariable) site category, proportion estimated 550s 0.3358 550s Substitution rate categories under this model: 550s rate proportion 550s 0.0000 0.3358 550s 0.0440 0.1660 550s 0.2864 0.1660 550s 0.8566 0.1660 550s 2.8130 0.1660 550s 550s NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 550s No branches were short enough to be collapsed. 550s 550s >>>Completed Search rep 2 (of 2)<<< 550s 550s ####################################################### 550s 550s Completed 2 replicate search(es) (of 2). 550s 550s NOTE: Unless the following output indicates that search replicates found the 550s same topology, you should assume that they found different topologies. 550s Results: 550s Replicate 1 : -21812.6695 550s Replicate 2 : -21812.6695 (best) (same topology as 1) 550s 550s Parameter estimates across search replicates: 550s r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv 550s rep 1: 2.215 8.209 2.369 0.9139 16.55 1 0.348 0.213 0.150 0.290 0.556 0.336 550s rep 2: 2.21 8.197 2.366 0.9122 16.52 1 0.348 0.213 0.150 0.290 0.555 0.336 550s 550s Treelengths: 550s TL 550s rep 1: 2.935 550s rep 2: 2.935 550s 550s Saving final trees from all search reps to rana.nuc.GTRIG.best.all.tre 550s 550s Saving final tree from best search rep (#2) to rana.nuc.GTRIG.best.tre 550s ####################################################### 550s autopkgtest [01:11:53]: test run-unit-test: -----------------------] 551s autopkgtest [01:11:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 551s run-unit-test PASS 551s autopkgtest [01:11:54]: @@@@@@@@@@@@@@@@@@@@ summary 551s run-unit-test PASS 586s Creating nova instance adt-noble-ppc64el-garli-20240319-010243-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240316.img (UUID 1492b190-05c5-462d-b1de-84bc330afe32)...