0s autopkgtest [11:55:54]: starting date and time: 2024-03-18 11:55:54+0000 0s autopkgtest [11:55:54]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [11:55:54]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f8tn2nsm/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src: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-3@bos01-arm64-10.secgroup --name adt-noble-arm64-garli-20240318-115553-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-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://us.ports.ubuntu.com/ubuntu-ports/ 128s autopkgtest [11:58:02]: testbed dpkg architecture: arm64 128s autopkgtest [11:58:02]: testbed apt version: 2.7.12 128s autopkgtest [11:58:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 129s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 130s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 130s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 130s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3727 kB] 130s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 130s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 130s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 130s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 130s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 130s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4127 kB] 130s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 130s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 130s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 132s Fetched 9270 kB in 2s (5493 kB/s) 133s Reading package lists... 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 136s Calculating upgrade... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s sh: Attempting to set up Debian/Ubuntu apt sources automatically 138s sh: Distribution appears to be Ubuntu 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 140s eatmydata is already the newest version (131-1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s dbus is already the newest version (1.14.10-4ubuntu1). 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s rng-tools-debian is already the newest version (2.4). 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s The following packages will be REMOVED: 142s cloud-init* python3-configobj* python3-debconf* 143s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 143s After this operation, 3252 kB disk space will be freed. 143s (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 ... 75850 files and directories currently installed.) 143s Removing cloud-init (24.1.1-0ubuntu1) ... 143s Removing python3-configobj (5.0.8-3) ... 143s Removing python3-debconf (1.5.86) ... 143s Processing triggers for man-db (2.12.0-3) ... 144s (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 ... 75461 files and directories currently installed.) 144s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 144s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 144s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 144s invoke-rc.d: policy-rc.d denied execution of try-restart. 144s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s linux-generic is already the newest version (6.8.0-11.11+1). 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 146s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 146s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 148s Reading package lists... 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s Calculating upgrade... 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 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [11:58:24]: rebooting testbed after setup commands that affected boot 188s autopkgtest [11:59:02]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 190s autopkgtest [11:59:04]: @@@@@@@@@@@@@@@@@@@@ apt-source garli 193s Get:1 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (dsc) [2047 B] 193s Get:2 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (tar) [1249 kB] 193s Get:3 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (diff) [4788 B] 193s gpgv: Signature made Sun Feb 20 14:34:04 2022 UTC 193s gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 193s gpgv: Can't check signature: No public key 193s dpkg-source: warning: cannot verify inline signature for ./garli_2.1-7.dsc: no acceptable signature found 193s autopkgtest [11:59:07]: testing package garli version 2.1-7 193s autopkgtest [11:59:07]: build not needed 194s autopkgtest [11:59:08]: test run-unit-test: preparing testbed 195s Reading package lists... 195s Building dependency tree... 195s Reading state information... 195s Starting pkgProblemResolver with broken count: 0 195s Starting 2 pkgProblemResolver with broken count: 0 195s Done 196s The following additional packages will be installed: 196s garli garli-examples garli-mpi libamd-comgr2 libamdhip64-5 libatomic1 196s libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 196s libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 libmunge2 libncl2 196s libopenmpi3 libpciaccess0 libpmix2 librdmacm1t64 libucx0 libxnvctrl0 196s ocl-icd-libopencl1 openmpi-bin openmpi-common 196s Suggested packages: 196s opencl-icd gfortran | fortran-compiler 196s The following NEW packages will be installed: 196s autopkgtest-satdep garli garli-examples garli-mpi libamd-comgr2 196s libamdhip64-5 libatomic1 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 196s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 196s libmunge2 libncl2 libopenmpi3 libpciaccess0 libpmix2 librdmacm1t64 libucx0 196s libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common 196s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 196s Need to get 52.2 MB/52.2 MB of archives. 196s After this operation, 228 MB of additional disk space will be used. 196s Get:1 /tmp/autopkgtest.hlCk2G/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 196s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libncl2 arm64 2.1.21+git20210811.b1213a7-5 [350 kB] 197s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 garli arm64 2.1-7 [544 kB] 197s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 garli-examples all 2.1-7 [132 kB] 197s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 197s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 197s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 197s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 197s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 197s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 197s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 197s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 197s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 197s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 197s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2 arm64 5.0.1-4 [659 kB] 197s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 199s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 200s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 200s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 200s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 200s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 200s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 200s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 200s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] 200s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-bin arm64 4.1.6-5ubuntu1 [123 kB] 200s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 garli-mpi arm64 2.1-7 [533 kB] 201s Fetched 52.2 MB in 4s (12.8 MB/s) 201s Selecting previously unselected package libncl2:arm64. 201s (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 ... 75406 files and directories currently installed.) 201s Preparing to unpack .../00-libncl2_2.1.21+git20210811.b1213a7-5_arm64.deb ... 201s Unpacking libncl2:arm64 (2.1.21+git20210811.b1213a7-5) ... 201s Selecting previously unselected package garli. 201s Preparing to unpack .../01-garli_2.1-7_arm64.deb ... 201s Unpacking garli (2.1-7) ... 201s Selecting previously unselected package garli-examples. 201s Preparing to unpack .../02-garli-examples_2.1-7_all.deb ... 201s Unpacking garli-examples (2.1-7) ... 201s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 201s Preparing to unpack .../03-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 201s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 201s Selecting previously unselected package libatomic1:arm64. 201s Preparing to unpack .../04-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 201s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 201s Selecting previously unselected package librdmacm1t64:arm64. 201s Preparing to unpack .../05-librdmacm1t64_50.0-2_arm64.deb ... 201s Unpacking librdmacm1t64:arm64 (50.0-2) ... 201s Selecting previously unselected package libfabric1:arm64. 201s Preparing to unpack .../06-libfabric1_1.17.0-3_arm64.deb ... 201s Unpacking libfabric1:arm64 (1.17.0-3) ... 201s Selecting previously unselected package libhwloc15:arm64. 201s Preparing to unpack .../07-libhwloc15_2.10.0-1_arm64.deb ... 201s Unpacking libhwloc15:arm64 (2.10.0-1) ... 201s Selecting previously unselected package libmunge2:arm64. 201s Preparing to unpack .../08-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 201s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 201s Selecting previously unselected package libpciaccess0:arm64. 201s Preparing to unpack .../09-libpciaccess0_0.17-3_arm64.deb ... 201s Unpacking libpciaccess0:arm64 (0.17-3) ... 201s Selecting previously unselected package libxnvctrl0:arm64. 201s Preparing to unpack .../10-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 201s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 201s Selecting previously unselected package ocl-icd-libopencl1:arm64. 201s Preparing to unpack .../11-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 201s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 201s Selecting previously unselected package libhwloc-plugins:arm64. 201s Preparing to unpack .../12-libhwloc-plugins_2.10.0-1_arm64.deb ... 201s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 201s Selecting previously unselected package libpmix2:arm64. 201s Preparing to unpack .../13-libpmix2_5.0.1-4_arm64.deb ... 201s Unpacking libpmix2:arm64 (5.0.1-4) ... 201s Selecting previously unselected package libllvm17:arm64. 201s Preparing to unpack .../14-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 201s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 202s Selecting previously unselected package libamd-comgr2:arm64. 202s Preparing to unpack .../15-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 202s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 202s Selecting previously unselected package libdrm-amdgpu1:arm64. 202s Preparing to unpack .../16-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 202s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 202s Selecting previously unselected package libhsakmt1:arm64. 202s Preparing to unpack .../17-libhsakmt1_5.7.0-1_arm64.deb ... 202s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 202s Selecting previously unselected package libhsa-runtime64-1. 202s Preparing to unpack .../18-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 202s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 202s Selecting previously unselected package libamdhip64-5. 202s Preparing to unpack .../19-libamdhip64-5_5.2.3-12_arm64.deb ... 202s Unpacking libamdhip64-5 (5.2.3-12) ... 202s Selecting previously unselected package libucx0:arm64. 202s Preparing to unpack .../20-libucx0_1.16.0+ds-4_arm64.deb ... 202s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 202s Selecting previously unselected package libopenmpi3:arm64. 202s Preparing to unpack .../21-libopenmpi3_4.1.6-5ubuntu1_arm64.deb ... 202s Unpacking libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 202s Selecting previously unselected package openmpi-common. 202s Preparing to unpack .../22-openmpi-common_4.1.6-5ubuntu1_all.deb ... 202s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 202s Selecting previously unselected package openmpi-bin. 202s Preparing to unpack .../23-openmpi-bin_4.1.6-5ubuntu1_arm64.deb ... 202s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 202s Selecting previously unselected package garli-mpi. 202s Preparing to unpack .../24-garli-mpi_2.1-7_arm64.deb ... 202s Unpacking garli-mpi (2.1-7) ... 202s Selecting previously unselected package autopkgtest-satdep. 202s Preparing to unpack .../25-1-autopkgtest-satdep.deb ... 202s Unpacking autopkgtest-satdep (0) ... 203s Setting up libpciaccess0:arm64 (0.17-3) ... 203s Setting up libncl2:arm64 (2.1.21+git20210811.b1213a7-5) ... 203s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 203s Setting up garli-examples (2.1-7) ... 203s Setting up garli (2.1-7) ... 203s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 203s Setting up libhwloc15:arm64 (2.10.0-1) ... 203s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 203s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 203s Setting up openmpi-common (4.1.6-5ubuntu1) ... 203s Setting up librdmacm1t64:arm64 (50.0-2) ... 203s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 203s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 203s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 203s Setting up libfabric1:arm64 (1.17.0-3) ... 203s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 203s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 203s Setting up libhsakmt1:arm64 (5.7.0-1) ... 203s Setting up libpmix2:arm64 (5.0.1-4) ... 203s Setting up libhsa-runtime64-1 (5.7.1-1) ... 203s Setting up libamdhip64-5 (5.2.3-12) ... 203s Setting up libucx0:arm64 (1.16.0+ds-4) ... 203s Setting up libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 203s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 203s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 203s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 203s Setting up garli-mpi (2.1-7) ... 203s Setting up autopkgtest-satdep (0) ... 203s Processing triggers for man-db (2.12.0-3) ... 203s Processing triggers for libc-bin (2.39-0ubuntu2) ... 206s (Reading database ... 76034 files and directories currently installed.) 206s Removing autopkgtest-satdep (0) ... 207s autopkgtest [11:59:21]: test run-unit-test: [----------------------- 207s Running GARLI Version 2.1. () 207s ->Single processor version for 64-bit OS<- 207s ############################################################## 207s This is GARLI 2.1: maximum likelihood phylogenetic inference 207s using nucleotide, amino acid, codon and morphology-like data, 207s as well as partitioned models. 207s General program usage is extensively documented here: 207s http://www.nescent.org/wg/garli/ 207s See this page for details on partitioned model usage: 207s http://www.nescent.org/wg_garli/Using_partitioned_models 207s and this page for details on Mkv mophology model usage: 207s http://www.nescent.org/wg_garli/Mkv_morphology_model 207s PLEASE LET ME KNOW OF ANY PROBLEMS AT: 207s garli.support@gmail.com 207s ############################################################## 207s Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 11.2.0 207s Using NCL version 2.1.17 207s 207s ####################################################### 207s Reading config file garli.conf 207s ################################################### 207s READING OF DATA 207s Attempting to read data file in Nexus format (using NCL): 207s rana.nex ... 207s Reading DATA block... successful 207s 207s ################################################### 207s PARTITIONING OF DATA AND MODELS 207s GARLI data subset 1 207s CHARACTERS block #1 ("Untitled DATA Block 1") 207s Data read as Nucleotide data, 207s modeled as Nucleotide data 207s storing implied block: TAXA 207s storing read block: DATA 207s Summary of data: 207s 64 sequences. 207s 1062 constant characters. 207s 664 parsimony-informative characters. 207s 250 uninformative variable characters. 207s 1976 total characters. 207s 890 unique patterns in compressed data matrix. 207s 207s ################################################### 207s NOTE: Unlike many programs, the amount of system memory that Garli will 207s use can be controlled by the user. 207s (This comes from the availablememory setting in the configuration file. 207s Availablememory should NOT be set to more than the actual amount of 207s physical memory that your computer has installed) 207s 207s For this dataset: 207s Mem level availablememory setting 207s great >= 70 MB 207s good approx 69 MB to 45 MB 207s low approx 44 MB to 19 MB 207s very low approx 18 MB to 15 MB 207s the minimum required availablememory is 15 MB 207s 207s You specified that Garli should use at most 512.0 MB of memory. 207s 207s Garli will actually use approx. 104.2 MB of memory 207s **Your memory level is: great (you don't need to change anything)** 207s 207s ####################################################### 207s Found outgroup specification: 1 207s 207s ####################################################### 207s STARTING RUN 207s 207s >>>Search rep 1 (of 2)<<< 207s MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 207s Model 1 207s Number of states = 4 (nucleotide data) 207s Nucleotide Relative Rate Matrix: 6 rates 207s AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 207s Equilibrium State Frequencies: estimated 207s (ACGT) 0.3381 0.2238 0.1789 0.2592 207s Rate Heterogeneity Model: 207s 4 discrete gamma distributed rate categories, alpha param estimated 207s 0.5000 207s with an invariant (invariable) site category, proportion estimated 207s 0.1344 207s Substitution rate categories under this model: 207s rate proportion 207s 0.0000 0.1344 207s 0.0334 0.2164 207s 0.2519 0.2164 207s 0.8203 0.2164 207s 2.8944 0.2164 207s 207s Starting with seed=896302 207s 207s creating likelihood stepwise addition starting tree... 207s number of taxa added: 208s 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 208s Optimizing parameters... improved 58.303 lnL 208s Optimizing branchlengths... improved 12.034 lnL 210s 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 210s Initial ln Likelihood: -22569.6148 210s optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... 210s pass 1:+ 333.821 (branch= 75.81 scale= 8.70 alpha= 0.03 freqs=131.56 rel rates=110.34 pinv= 7.38) 210s pass 2:+ 56.888 (branch= 13.46 scale= 0.54 alpha= 3.15 freqs= 28.83 rel rates= 7.59 pinv= 3.33) 210s pass 3:+ 14.844 (branch= 2.71 scale= 0.00 alpha= 3.71 freqs= 1.81 rel rates= 5.05 pinv= 1.57) 210s pass 4:+ 8.719 (branch= 1.82 scale= 0.00 alpha= 2.39 freqs= 0.68 rel rates= 2.54 pinv= 1.28) 210s pass 5:+ 6.362 (branch= 0.42 scale= 0.00 alpha= 1.55 freqs= 0.79 rel rates= 2.52 pinv= 1.08) 210s pass 6:+ 6.940 (branch= 0.00 scale= 0.00 alpha= 1.25 freqs= 0.21 rel rates= 4.67 pinv= 0.80) 210s pass 7:+ 5.014 (branch= 0.34 scale= 0.00 alpha= 0.76 freqs= 0.16 rel rates= 3.15 pinv= 0.61) 210s pass 8:+ 1.581 (branch= 0.00 scale= 0.00 alpha= 0.61 freqs= 0.17 rel rates= 0.77 pinv= 0.03) 210s pass 9:+ 0.161 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.11 rel rates= 0.02 pinv= 0.03) 210s lnL after optimization: -22135.2852 210s gen current_lnL precision last_tree_imp 210s 0 -22135.2852 0.500 0 211s 100 -22015.2562 0.500 88 211s 200 -21951.1331 0.500 187 211s 300 -21903.7783 0.500 290 212s 400 -21848.5315 0.500 399 212s 500 -21842.3249 0.500 474 213s 600 -21840.3508 0.500 474 213s 700 -21834.2860 0.500 474 213s 800 -21831.8369 0.500 719 214s 900 -21830.5685 0.500 719 214s 1000 -21825.0619 0.500 926 214s 1100 -21822.7928 0.500 926 215s 1200 -21822.2116 0.500 926 215s 1300 -21821.4972 0.500 926 215s 1400 -21820.8631 0.500 926 216s 1500 -21820.3117 0.500 926 216s Optimization precision reduced 216s Optimizing parameters... improved 0.143 lnL 216s Optimizing branchlengths... improved 0.000 lnL 216s 1600 -21819.9258 0.451 926 217s 1700 -21819.2246 0.451 926 217s 1800 -21818.9194 0.451 926 217s 1900 -21818.6633 0.451 926 218s 2000 -21818.4052 0.451 926 218s Optimization precision reduced 218s Optimizing parameters... improved 0.018 lnL 218s Optimizing branchlengths... improved 0.479 lnL 218s 2100 -21816.6927 0.402 926 218s 2200 -21816.4397 0.402 926 219s 2300 -21816.3003 0.402 926 219s 2400 -21816.1198 0.402 926 220s 2500 -21815.8504 0.402 926 220s Optimization precision reduced 220s Optimizing parameters... improved 0.028 lnL 220s Optimizing branchlengths... improved 0.003 lnL 220s 2600 -21815.7916 0.353 926 220s 2700 -21815.6514 0.353 926 221s 2800 -21815.4884 0.353 926 221s 2900 -21815.3886 0.353 926 221s 3000 -21815.3412 0.353 926 221s Optimization precision reduced 221s Optimizing parameters... improved 0.006 lnL 221s Optimizing branchlengths... improved 0.004 lnL 222s 3100 -21815.2974 0.304 926 222s 3200 -21815.1265 0.304 926 223s 3300 -21814.9998 0.304 926 223s 3400 -21814.9712 0.304 926 223s 3500 -21814.8448 0.304 926 223s Optimization precision reduced 223s Optimizing parameters... improved 0.027 lnL 223s Optimizing branchlengths... improved 0.000 lnL 224s 3600 -21814.7257 0.255 926 224s 3700 -21814.7077 0.255 926 225s 3800 -21814.6616 0.255 926 225s 3900 -21814.5601 0.255 926 225s 4000 -21814.5408 0.255 926 225s Optimization precision reduced 225s Optimizing parameters... improved 0.007 lnL 225s Optimizing branchlengths... improved 0.257 lnL 226s 4100 -21814.2685 0.206 926 226s 4200 -21814.2273 0.206 926 227s 4300 -21814.2235 0.206 926 227s 4400 -21814.1552 0.206 926 227s 4500 -21814.0289 0.206 926 227s Optimization precision reduced 227s Optimizing parameters... improved 0.004 lnL 227s Optimizing branchlengths... improved 0.000 lnL 228s 4600 -21813.9245 0.157 926 228s 4700 -21813.8251 0.157 926 229s 4800 -21813.8108 0.157 926 229s 4900 -21813.7264 0.157 926 229s 5000 -21813.7065 0.157 926 229s Optimization precision reduced 229s Optimizing parameters... improved 0.002 lnL 229s Optimizing branchlengths... improved 0.146 lnL 230s 5100 -21813.4846 0.108 926 230s 5200 -21813.4490 0.108 926 231s 5300 -21813.4440 0.108 926 231s 5400 -21813.4343 0.108 926 231s 5500 -21813.4015 0.108 926 231s Optimization precision reduced 232s Optimizing parameters... improved 0.001 lnL 232s Optimizing branchlengths... improved 0.199 lnL 232s 5600 -21813.1861 0.059 926 232s 5700 -21813.1604 0.059 926 233s 5800 -21813.1526 0.059 926 233s 5900 -21813.1341 0.059 926 234s 6000 -21813.1148 0.059 926 234s Optimization precision reduced 234s Optimizing parameters... improved 0.023 lnL 234s Optimizing branchlengths... improved 0.196 lnL 234s 6100 -21812.8917 0.010 926 235s 6200 -21812.8852 0.010 926 235s 6300 -21812.8852 0.010 926 236s 6400 -21812.8841 0.010 926 236s 6500 -21812.8814 0.010 926 237s 6600 -21812.8724 0.010 926 237s 6700 -21812.8723 0.010 926 238s 6800 -21812.8695 0.010 926 238s 6900 -21812.8632 0.010 926 239s 7000 -21812.8597 0.010 926 239s 7100 -21812.8535 0.010 926 240s 7200 -21812.8475 0.010 926 240s 7300 -21812.8472 0.010 926 241s 7400 -21812.8471 0.010 926 241s 7500 -21812.8434 0.010 926 242s 7600 -21812.8426 0.010 926 242s 7700 -21812.8375 0.010 926 243s 7800 -21812.8375 0.010 926 243s 7900 -21812.8356 0.010 926 244s 8000 -21812.8351 0.010 926 244s 8100 -21812.8310 0.010 926 245s 8200 -21812.8299 0.010 926 245s 8300 -21812.8256 0.010 926 246s 8400 -21812.8225 0.010 926 247s 8500 -21812.8225 0.010 926 247s 8600 -21812.8217 0.010 926 248s 8700 -21812.8174 0.010 926 248s 8800 -21812.8060 0.010 926 249s 8900 -21812.8048 0.010 926 249s 9000 -21812.8018 0.010 926 250s 9100 -21812.8018 0.010 926 250s 9200 -21812.8011 0.010 926 251s 9300 -21812.7995 0.010 926 251s 9400 -21812.7995 0.010 926 252s 9500 -21812.7995 0.010 926 252s 9600 -21812.7941 0.010 926 253s 9700 -21812.7935 0.010 926 253s 9800 -21812.7935 0.010 926 254s 9900 -21812.7866 0.010 926 254s 10000 -21812.7866 0.010 926 255s 10100 -21812.7829 0.010 926 255s 10200 -21812.7827 0.010 926 256s 10300 -21812.7827 0.010 926 256s 10400 -21812.7817 0.010 926 257s 10500 -21812.7787 0.010 926 257s 10600 -21812.7780 0.010 926 258s 10700 -21812.7780 0.010 926 258s 10800 -21812.7774 0.010 926 259s 10900 -21812.7774 0.010 926 259s 11000 -21812.7774 0.010 926 260s 11100 -21812.7748 0.010 926 260s 11200 -21812.7741 0.010 926 261s 11300 -21812.7706 0.010 926 261s 11400 -21812.7706 0.010 926 263s 11500 -21812.7704 0.010 926 263s 11600 -21812.7704 0.010 926 263s 11700 -21812.7704 0.010 926 263s 11800 -21812.7704 0.010 926 264s 11900 -21812.7679 0.010 926 264s 12000 -21812.7671 0.010 926 265s 12100 -21812.7671 0.010 926 266s 12200 -21812.7656 0.010 926 266s 12300 -21812.7641 0.010 926 267s 12400 -21812.7641 0.010 926 269s 12500 -21812.7609 0.010 926 269s 12600 -21812.7590 0.010 926 269s 12700 -21812.7590 0.010 926 269s 12800 -21812.7571 0.010 926 269s 12900 -21812.7536 0.010 926 270s 13000 -21812.7510 0.010 926 270s 13100 -21812.7510 0.010 926 271s 13200 -21812.7507 0.010 926 271s 13300 -21812.7507 0.010 926 272s 13400 -21812.7500 0.010 926 272s 13500 -21812.7471 0.010 926 273s 13600 -21812.7400 0.010 926 273s 13700 -21812.7361 0.010 926 274s 13800 -21812.7359 0.010 926 274s 13900 -21812.7359 0.010 926 275s 14000 -21812.7359 0.010 926 275s 14100 -21812.7338 0.010 926 276s 14200 -21812.7338 0.010 926 276s 14300 -21812.7262 0.010 926 277s 14400 -21812.7262 0.010 926 277s 14500 -21812.7222 0.010 926 278s 14600 -21812.7222 0.010 926 278s 14700 -21812.7211 0.010 926 279s 14800 -21812.7211 0.010 926 279s 14900 -21812.7211 0.010 926 280s 15000 -21812.7191 0.010 926 280s Optimizing parameters... improved 0.000 lnL 280s Optimizing branchlengths... improved 0.000 lnL 281s 15100 -21812.7133 0.010 926 281s 15200 -21812.7133 0.010 926 282s 15300 -21812.7133 0.010 926 282s 15400 -21812.7133 0.010 926 283s 15500 -21812.7107 0.010 926 283s 15600 -21812.7105 0.010 926 284s 15700 -21812.7060 0.010 926 284s 15800 -21812.7058 0.010 926 285s 15900 -21812.7058 0.010 926 285s 16000 -21812.7058 0.010 926 286s 16100 -21812.7051 0.010 926 286s 16200 -21812.7051 0.010 926 287s 16300 -21812.7024 0.010 926 287s 16400 -21812.7024 0.010 926 288s 16500 -21812.7021 0.010 926 288s 16600 -21812.7021 0.010 926 289s 16700 -21812.7016 0.010 926 289s 16800 -21812.7016 0.010 926 290s 16900 -21812.6995 0.010 926 290s 17000 -21812.6993 0.010 926 291s 17100 -21812.6992 0.010 926 291s 17200 -21812.6992 0.010 926 292s 17300 -21812.6992 0.010 926 292s 17400 -21812.6984 0.010 926 293s 17500 -21812.6984 0.010 926 293s 17600 -21812.6984 0.010 926 294s 17700 -21812.6958 0.010 926 294s 17800 -21812.6958 0.010 926 295s 17900 -21812.6944 0.010 926 295s 18000 -21812.6944 0.010 926 296s 18100 -21812.6944 0.010 926 296s 18200 -21812.6944 0.010 926 297s 18300 -21812.6944 0.010 926 297s 18400 -21812.6944 0.010 926 298s 18500 -21812.6944 0.010 926 298s 18600 -21812.6932 0.010 926 299s 18700 -21812.6925 0.010 926 299s 18800 -21812.6912 0.010 926 300s 18900 -21812.6909 0.010 926 300s 19000 -21812.6904 0.010 926 301s 19100 -21812.6904 0.010 926 301s 19200 -21812.6904 0.010 926 302s 19300 -21812.6868 0.010 926 302s 19400 -21812.6868 0.010 926 303s 19500 -21812.6868 0.010 926 303s 19600 -21812.6861 0.010 926 304s 19700 -21812.6861 0.010 926 304s 19800 -21812.6861 0.010 926 305s 19900 -21812.6860 0.010 926 305s 20000 -21812.6860 0.010 926 305s Optimizing parameters... improved 0.000 lnL 305s Optimizing branchlengths... improved 0.000 lnL 306s 20100 -21812.6857 0.010 926 306s 20200 -21812.6857 0.010 926 308s 20300 -21812.6857 0.010 926 308s 20400 -21812.6857 0.010 926 308s 20500 -21812.6857 0.010 926 308s 20600 -21812.6845 0.010 926 309s 20700 -21812.6845 0.010 926 309s 20800 -21812.6845 0.010 926 310s 20900 -21812.6845 0.010 926 310s 21000 -21812.6845 0.010 926 311s 21100 -21812.6845 0.010 926 311s 21200 -21812.6842 0.010 926 312s 21300 -21812.6842 0.010 926 312s 21400 -21812.6823 0.010 926 313s 21500 -21812.6823 0.010 926 313s 21600 -21812.6823 0.010 926 314s 21700 -21812.6823 0.010 926 314s 21800 -21812.6814 0.010 926 315s 21900 -21812.6814 0.010 926 315s 22000 -21812.6814 0.010 926 316s 22100 -21812.6814 0.010 926 316s 22200 -21812.6806 0.010 926 317s 22300 -21812.6806 0.010 926 317s 22400 -21812.6805 0.010 926 318s 22500 -21812.6805 0.010 926 319s 22600 -21812.6805 0.010 926 319s 22700 -21812.6802 0.010 926 320s 22800 -21812.6800 0.010 926 320s 22900 -21812.6795 0.010 926 321s 23000 -21812.6795 0.010 926 321s 23100 -21812.6795 0.010 926 322s 23200 -21812.6795 0.010 926 322s 23300 -21812.6786 0.010 926 323s 23400 -21812.6786 0.010 926 323s 23500 -21812.6786 0.010 926 324s 23600 -21812.6786 0.010 926 324s 23700 -21812.6785 0.010 926 325s 23800 -21812.6785 0.010 926 325s 23900 -21812.6785 0.010 926 326s 24000 -21812.6785 0.010 926 326s 24100 -21812.6785 0.010 926 327s 24200 -21812.6785 0.010 926 327s 24300 -21812.6784 0.010 926 328s 24400 -21812.6784 0.010 926 328s 24500 -21812.6782 0.010 926 329s 24600 -21812.6782 0.010 926 329s 24700 -21812.6782 0.010 926 330s 24800 -21812.6778 0.010 926 330s 24900 -21812.6777 0.010 926 331s 25000 -21812.6777 0.010 926 331s Optimizing parameters... improved 0.000 lnL 331s Optimizing branchlengths... improved 0.000 lnL 331s 25100 -21812.6754 0.010 926 332s 25200 -21812.6754 0.010 926 332s 25300 -21812.6749 0.010 926 333s 25400 -21812.6749 0.010 926 333s 25500 -21812.6738 0.010 926 334s 25600 -21812.6738 0.010 926 334s 25700 -21812.6738 0.010 926 335s 25800 -21812.6738 0.010 926 335s 25900 -21812.6738 0.010 926 336s 26000 -21812.6727 0.010 926 336s 26100 -21812.6727 0.010 926 336s Reached termination condition! 336s last topological improvement at gen 926 336s Improvement over last 500 gen = 0.00108 336s Current score = -21812.6727 336s Performing final optimizations... 336s pass 1 : -21812.6726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 2 : -21812.6725 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 3 : -21812.6668 (branch= 0.0057 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 4 : -21812.6554 (branch= 0.0113 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 5 : -21812.6500 (branch= 0.0049 alpha= 0.0004 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 6 : -21812.6459 (branch= 0.0038 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 7 : -21812.6436 (branch= 0.0019 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 8 : -21812.6425 (branch= 0.0009 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 9 : -21812.6419 (branch= 0.0004 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 337s pass 10: -21812.6417 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s pass 11: -21812.6416 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s pass 12: -21812.6415 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s pass 13: -21812.6414 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s pass 14: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s pass 15: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s pass 16: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s pass 17: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s pass 18: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 338s Looking for minimum length branches... 338s Final score = -21812.6414 338s Time used so far = 0 hours, 2 minutes and 11 seconds 338s 338s MODEL REPORT - Parameter values are FINAL 338s Model 1 338s Number of states = 4 (nucleotide data) 338s Nucleotide Relative Rate Matrix: 6 rates 338s AC = 2.215, AG = 8.160, AT = 2.358, CG = 0.919, CT = 16.516, GT = 1.000 338s Equilibrium State Frequencies: estimated 338s (ACGT) 0.3476 0.2126 0.1499 0.2899 338s Rate Heterogeneity Model: 338s 4 discrete gamma distributed rate categories, alpha param estimated 338s 0.5605 338s with an invariant (invariable) site category, proportion estimated 338s 0.3385 338s Substitution rate categories under this model: 338s rate proportion 338s 0.0000 0.3385 338s 0.0451 0.1654 338s 0.2896 0.1654 338s 0.8597 0.1654 338s 2.8056 0.1654 338s 338s NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 338s No branches were short enough to be collapsed. 338s 338s >>>Completed Search rep 1 (of 2)<<< 338s 338s >>>Search rep 2 (of 2)<<< 338s MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 338s Model 1 338s Number of states = 4 (nucleotide data) 338s Nucleotide Relative Rate Matrix: 6 rates 338s AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 338s Equilibrium State Frequencies: estimated 338s (ACGT) 0.3381 0.2238 0.1789 0.2592 338s Rate Heterogeneity Model: 338s 4 discrete gamma distributed rate categories, alpha param estimated 338s 0.5000 338s with an invariant (invariable) site category, proportion estimated 338s 0.1344 338s Substitution rate categories under this model: 338s rate proportion 338s 0.0000 0.1344 338s 0.0334 0.2164 338s 0.2519 0.2164 338s 0.8203 0.2164 338s 2.8944 0.2164 338s 338s Starting with seed=2055833184 338s 338s creating likelihood stepwise addition starting tree... 338s number of taxa added: 339s 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 339s Optimizing parameters... improved 100.668 lnL 339s Optimizing branchlengths... improved 13.407 lnL 341s 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 341s Initial ln Likelihood: -22652.1306 341s optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... 341s pass 1:+ 329.765 (branch= 72.28 scale= 6.17 alpha= 0.01 freqs=130.12 rel rates=111.16 pinv= 10.03) 341s pass 2:+ 53.165 (branch= 4.40 scale= 0.00 alpha= 6.16 freqs= 29.78 rel rates= 7.79 pinv= 5.04) 341s pass 3:+ 17.646 (branch= 1.42 scale= 0.64 alpha= 5.14 freqs= 2.15 rel rates= 5.39 pinv= 2.90) 341s pass 4:+ 12.536 (branch= 0.58 scale= 0.00 alpha= 4.19 freqs= 0.68 rel rates= 5.46 pinv= 1.63) 341s pass 5:+ 7.490 (branch= 0.00 scale= 0.00 alpha= 2.28 freqs= 0.69 rel rates= 3.28 pinv= 1.24) 341s pass 6:+ 5.204 (branch= 0.00 scale= 0.00 alpha= 1.56 freqs= 0.19 rel rates= 2.59 pinv= 0.87) 341s pass 7:+ 4.679 (branch= 0.00 scale= 0.00 alpha= 0.88 freqs= 0.12 rel rates= 3.08 pinv= 0.60) 341s pass 8:+ 2.291 (branch= 0.45 scale= 0.00 alpha= 0.54 freqs= 0.12 rel rates= 1.15 pinv= 0.03) 342s pass 9:+ 0.161 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.12 rel rates= 0.01 pinv= 0.02) 342s lnL after optimization: -22219.1951 342s gen current_lnL precision last_tree_imp 342s 0 -22219.1951 0.500 0 342s 100 -22117.5387 0.500 98 342s 200 -22086.9207 0.500 183 343s 300 -22082.8558 0.500 252 343s 400 -22010.0811 0.500 387 343s 500 -21928.8336 0.500 464 344s 600 -21837.2108 0.500 540 344s 700 -21834.9313 0.500 540 344s 800 -21833.6884 0.500 540 345s 900 -21830.7835 0.500 540 345s 1000 -21827.7860 0.500 932 346s 1100 -21827.4450 0.500 932 346s 1200 -21826.5068 0.500 932 346s 1300 -21825.3966 0.500 932 347s 1400 -21824.6459 0.500 932 347s 1500 -21823.9168 0.500 932 347s Optimization precision reduced 347s Optimizing parameters... improved 0.048 lnL 347s Optimizing branchlengths... improved 0.000 lnL 347s 1600 -21823.2944 0.451 932 348s 1700 -21822.1589 0.451 932 348s 1800 -21821.9694 0.451 932 349s 1900 -21821.6608 0.451 932 349s 2000 -21821.4529 0.451 932 349s Optimization precision reduced 349s Optimizing parameters... improved 0.044 lnL 349s Optimizing branchlengths... improved 0.000 lnL 349s 2100 -21820.9844 0.402 932 350s 2200 -21820.7353 0.402 932 350s 2300 -21820.2472 0.402 932 350s 2400 -21819.7960 0.402 2381 351s 2500 -21819.6082 0.402 2381 351s 2600 -21819.3255 0.402 2381 352s 2700 -21818.8865 0.402 2381 352s 2800 -21818.5687 0.402 2381 352s 2900 -21818.4060 0.402 2381 352s Optimization precision reduced 352s Optimizing parameters... improved 0.011 lnL 352s Optimizing branchlengths... improved 0.000 lnL 353s 3000 -21816.8308 0.353 2928 353s 3100 -21816.4812 0.353 2928 353s 3200 -21816.4097 0.353 2928 354s 3300 -21816.3467 0.353 2928 354s 3400 -21816.1150 0.353 2928 354s 3500 -21815.9747 0.353 2928 354s Optimization precision reduced 355s Optimizing parameters... improved 0.011 lnL 355s Optimizing branchlengths... improved 0.000 lnL 355s 3600 -21815.9320 0.304 2928 355s 3700 -21815.7580 0.304 2928 356s 3800 -21815.5794 0.304 2928 356s 3900 -21815.3187 0.304 2928 356s 4000 -21815.1999 0.304 2928 356s Optimization precision reduced 356s Optimizing parameters... improved 0.002 lnL 356s Optimizing branchlengths... improved 0.000 lnL 357s 4100 -21815.0975 0.255 2928 357s 4200 -21815.0014 0.255 2928 358s 4300 -21814.9739 0.255 2928 358s 4400 -21814.9287 0.255 2928 358s 4500 -21814.9001 0.255 2928 358s Optimization precision reduced 358s Optimizing parameters... improved 0.003 lnL 358s Optimizing branchlengths... improved 0.000 lnL 359s 4600 -21814.8561 0.206 2928 359s 4700 -21814.8559 0.206 2928 360s 4800 -21814.7555 0.206 2928 360s 4900 -21814.6139 0.206 2928 360s 5000 -21814.5305 0.206 2928 360s Optimization precision reduced 360s Optimizing parameters... improved 0.001 lnL 360s Optimizing branchlengths... improved 0.217 lnL 361s 5100 -21814.2530 0.157 2928 361s 5200 -21814.2096 0.157 2928 362s 5300 -21814.1076 0.157 2928 362s 5400 -21814.0990 0.157 2928 362s 5500 -21814.0491 0.157 2928 362s Optimization precision reduced 362s Optimizing parameters... improved 0.001 lnL 362s Optimizing branchlengths... improved 0.473 lnL 363s 5600 -21813.5668 0.108 2928 363s 5700 -21813.5425 0.108 2928 364s 5800 -21813.5106 0.108 2928 364s 5900 -21813.4819 0.108 2928 365s 6000 -21813.4494 0.108 2928 365s Optimization precision reduced 365s Optimizing parameters... improved 0.001 lnL 365s Optimizing branchlengths... improved 0.117 lnL 365s 6100 -21813.2650 0.059 2928 365s 6200 -21813.2413 0.059 2928 366s 6300 -21813.2146 0.059 2928 366s 6400 -21813.2092 0.059 2928 367s 6500 -21813.2030 0.059 2928 367s Optimization precision reduced 367s Optimizing parameters... improved 0.000 lnL 367s Optimizing branchlengths... improved 0.291 lnL 367s 6600 -21812.8990 0.010 2928 368s 6700 -21812.8962 0.010 2928 368s 6800 -21812.8781 0.010 2928 369s 6900 -21812.8763 0.010 2928 370s 7000 -21812.8680 0.010 2928 370s 7100 -21812.8546 0.010 2928 371s 7200 -21812.8453 0.010 2928 371s 7300 -21812.8452 0.010 2928 372s 7400 -21812.8409 0.010 2928 372s 7500 -21812.8405 0.010 2928 373s 7600 -21812.8328 0.010 2928 373s 7700 -21812.8305 0.010 2928 374s 7800 -21812.8305 0.010 2928 374s 7900 -21812.8305 0.010 2928 375s 8000 -21812.8302 0.010 2928 375s 8100 -21812.8301 0.010 2928 376s 8200 -21812.8282 0.010 2928 376s 8300 -21812.8280 0.010 2928 377s 8400 -21812.8275 0.010 2928 377s 8500 -21812.8233 0.010 2928 378s 8600 -21812.8218 0.010 2928 378s 8700 -21812.8218 0.010 2928 379s 8800 -21812.8205 0.010 2928 379s 8900 -21812.8202 0.010 2928 380s 9000 -21812.8184 0.010 2928 381s 9100 -21812.8155 0.010 2928 381s 9200 -21812.8146 0.010 2928 382s 9300 -21812.8084 0.010 2928 382s 9400 -21812.8076 0.010 2928 383s 9500 -21812.8074 0.010 2928 383s 9600 -21812.7992 0.010 2928 384s 9700 -21812.7984 0.010 2928 384s 9800 -21812.7984 0.010 2928 385s 9900 -21812.7954 0.010 2928 385s 10000 -21812.7908 0.010 2928 386s 10100 -21812.7879 0.010 2928 386s 10200 -21812.7879 0.010 2928 387s 10300 -21812.7861 0.010 2928 387s 10400 -21812.7861 0.010 2928 388s 10500 -21812.7851 0.010 2928 388s 10600 -21812.7844 0.010 2928 389s 10700 -21812.7844 0.010 2928 389s 10800 -21812.7838 0.010 2928 390s 10900 -21812.7838 0.010 2928 390s 11000 -21812.7793 0.010 2928 391s 11100 -21812.7739 0.010 2928 391s 11200 -21812.7704 0.010 2928 392s 11300 -21812.7658 0.010 2928 393s 11400 -21812.7639 0.010 2928 393s 11500 -21812.7632 0.010 2928 394s 11600 -21812.7619 0.010 2928 394s 11700 -21812.7618 0.010 2928 395s 11800 -21812.7615 0.010 2928 395s 11900 -21812.7615 0.010 2928 396s 12000 -21812.7609 0.010 2928 396s 12100 -21812.7609 0.010 2928 397s 12200 -21812.7570 0.010 2928 397s 12300 -21812.7547 0.010 2928 398s 12400 -21812.7528 0.010 2928 398s 12500 -21812.7528 0.010 2928 399s 12600 -21812.7511 0.010 2928 399s 12700 -21812.7511 0.010 2928 400s 12800 -21812.7511 0.010 2928 400s 12900 -21812.7511 0.010 2928 401s 13000 -21812.7511 0.010 2928 401s 13100 -21812.7505 0.010 2928 402s 13200 -21812.7491 0.010 2928 402s 13300 -21812.7490 0.010 2928 403s 13400 -21812.7490 0.010 2928 403s 13500 -21812.7477 0.010 2928 404s 13600 -21812.7477 0.010 2928 404s 13700 -21812.7471 0.010 2928 405s 13800 -21812.7434 0.010 2928 405s 13900 -21812.7405 0.010 2928 406s 14000 -21812.7405 0.010 2928 407s 14100 -21812.7396 0.010 2928 407s 14200 -21812.7396 0.010 2928 408s 14300 -21812.7387 0.010 2928 408s 14400 -21812.7387 0.010 2928 409s 14500 -21812.7387 0.010 2928 409s 14600 -21812.7387 0.010 2928 410s 14700 -21812.7376 0.010 2928 410s 14800 -21812.7376 0.010 2928 411s 14900 -21812.7371 0.010 2928 411s 15000 -21812.7363 0.010 2928 411s Optimizing parameters... improved 0.000 lnL 411s Optimizing branchlengths... improved 0.000 lnL 412s 15100 -21812.7360 0.010 2928 412s 15200 -21812.7360 0.010 2928 413s 15300 -21812.7348 0.010 2928 413s 15400 -21812.7298 0.010 2928 414s 15500 -21812.7295 0.010 2928 414s 15600 -21812.7292 0.010 2928 415s 15700 -21812.7292 0.010 2928 415s 15800 -21812.7271 0.010 2928 416s 15900 -21812.7266 0.010 2928 417s 16000 -21812.7264 0.010 2928 417s 16100 -21812.7264 0.010 2928 418s 16200 -21812.7264 0.010 2928 418s 16300 -21812.7264 0.010 2928 419s 16400 -21812.7264 0.010 2928 419s 16500 -21812.7261 0.010 2928 420s 16600 -21812.7254 0.010 2928 420s 16700 -21812.7254 0.010 2928 421s 16800 -21812.7254 0.010 2928 421s 16900 -21812.7239 0.010 2928 422s 17000 -21812.7239 0.010 2928 422s 17100 -21812.7234 0.010 2928 423s 17200 -21812.7215 0.010 2928 423s 17300 -21812.7215 0.010 2928 424s 17400 -21812.7210 0.010 2928 424s 17500 -21812.7210 0.010 2928 425s 17600 -21812.7210 0.010 2928 425s 17700 -21812.7210 0.010 2928 426s 17800 -21812.7210 0.010 2928 426s 17900 -21812.7200 0.010 2928 427s 18000 -21812.7198 0.010 2928 427s 18100 -21812.7198 0.010 2928 428s 18200 -21812.7198 0.010 2928 428s 18300 -21812.7198 0.010 2928 429s 18400 -21812.7198 0.010 2928 429s 18500 -21812.7198 0.010 2928 430s 18600 -21812.7198 0.010 2928 430s 18700 -21812.7198 0.010 2928 431s 18800 -21812.7198 0.010 2928 431s 18900 -21812.7198 0.010 2928 432s 19000 -21812.7198 0.010 2928 432s 19100 -21812.7198 0.010 2928 433s 19200 -21812.7198 0.010 2928 434s 19300 -21812.7190 0.010 2928 434s 19400 -21812.7190 0.010 2928 435s 19500 -21812.7190 0.010 2928 435s 19600 -21812.7190 0.010 2928 436s 19700 -21812.7180 0.010 2928 436s 19800 -21812.7180 0.010 2928 437s 19900 -21812.7149 0.010 2928 437s 20000 -21812.7149 0.010 2928 437s Optimizing parameters... improved 0.000 lnL 437s Optimizing branchlengths... improved 0.000 lnL 438s 20100 -21812.7147 0.010 2928 438s 20200 -21812.7147 0.010 2928 439s 20300 -21812.7147 0.010 2928 439s 20400 -21812.7147 0.010 2928 441s 20500 -21812.7145 0.010 2928 441s 20600 -21812.7145 0.010 2928 441s 20700 -21812.7144 0.010 2928 441s 20800 -21812.7140 0.010 2928 442s 20900 -21812.7140 0.010 2928 442s 21000 -21812.7140 0.010 2928 443s 21100 -21812.7140 0.010 2928 444s 21200 -21812.7129 0.010 2928 444s 21300 -21812.7128 0.010 2928 444s 21400 -21812.7128 0.010 2928 445s 21500 -21812.7128 0.010 2928 446s 21600 -21812.7124 0.010 2928 446s 21700 -21812.7124 0.010 2928 447s 21800 -21812.7124 0.010 2928 447s 21900 -21812.7123 0.010 2928 448s 22000 -21812.7123 0.010 2928 448s 22100 -21812.7123 0.010 2928 448s 22200 -21812.7123 0.010 2928 449s 22300 -21812.7123 0.010 2928 450s 22400 -21812.7117 0.010 2928 450s 22500 -21812.7117 0.010 2928 451s 22600 -21812.7117 0.010 2928 451s 22700 -21812.7117 0.010 2928 452s 22800 -21812.7117 0.010 2928 452s 22900 -21812.7113 0.010 2928 453s 23000 -21812.7113 0.010 2928 453s 23100 -21812.7113 0.010 2928 454s 23200 -21812.7113 0.010 2928 454s 23300 -21812.7111 0.010 2928 455s 23400 -21812.7111 0.010 2928 455s 23500 -21812.7111 0.010 2928 456s 23600 -21812.7103 0.010 2928 456s 23700 -21812.7103 0.010 2928 457s 23800 -21812.7103 0.010 2928 457s 23900 -21812.7098 0.010 2928 458s 24000 -21812.7098 0.010 2928 458s 24100 -21812.7096 0.010 2928 459s 24200 -21812.7096 0.010 2928 459s 24300 -21812.7096 0.010 2928 460s 24400 -21812.7096 0.010 2928 460s 24500 -21812.7096 0.010 2928 461s 24600 -21812.7096 0.010 2928 461s 24700 -21812.7096 0.010 2928 462s 24800 -21812.7093 0.010 2928 463s 24900 -21812.7093 0.010 2928 463s 25000 -21812.7093 0.010 2928 463s Optimizing parameters... improved 0.000 lnL 463s Optimizing branchlengths... improved 0.000 lnL 464s 25100 -21812.7080 0.010 2928 464s 25200 -21812.7080 0.010 2928 465s 25300 -21812.7080 0.010 2928 465s 25400 -21812.7080 0.010 2928 466s 25500 -21812.7080 0.010 2928 466s 25600 -21812.7073 0.010 2928 467s 25700 -21812.7073 0.010 2928 467s 25800 -21812.7073 0.010 2928 468s 25900 -21812.7064 0.010 2928 468s 26000 -21812.7064 0.010 2928 469s 26100 -21812.7064 0.010 2928 469s 26200 -21812.7064 0.010 2928 470s 26300 -21812.7064 0.010 2928 470s 26400 -21812.7064 0.010 2928 471s 26500 -21812.7061 0.010 2928 471s 26600 -21812.7059 0.010 2928 471s Reached termination condition! 471s last topological improvement at gen 2928 471s Improvement over last 500 gen = 0.00049 471s Current score = -21812.7059 471s Performing final optimizations... 472s pass 1 : -21812.7058 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 472s pass 2 : -21812.6999 (branch= 0.0059 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 472s pass 3 : -21812.6984 (branch= 0.0014 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 472s pass 4 : -21812.6874 (branch= 0.0110 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 472s pass 5 : -21812.6789 (branch= 0.0079 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0000) 472s pass 6 : -21812.6741 (branch= 0.0042 alpha= 0.0003 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0000) 472s pass 7 : -21812.6716 (branch= 0.0021 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0000) 472s pass 8 : -21812.6704 (branch= 0.0009 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 473s pass 9 : -21812.6700 (branch= 0.0003 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 473s pass 10: -21812.6698 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 473s pass 11: -21812.6696 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 473s pass 12: -21812.6695 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 473s pass 13: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 473s pass 14: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 473s pass 15: -21812.6695 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 473s Looking for minimum length branches... 473s Final score = -21812.6695 473s Time used = 0 hours, 4 minutes and 26 seconds 473s 473s MODEL REPORT - Parameter values are FINAL 473s Model 1 473s Number of states = 4 (nucleotide data) 473s Nucleotide Relative Rate Matrix: 6 rates 473s AC = 2.212, AG = 8.203, AT = 2.367, CG = 0.913, CT = 16.531, GT = 1.000 473s Equilibrium State Frequencies: estimated 473s (ACGT) 0.3475 0.2133 0.1496 0.2895 473s Rate Heterogeneity Model: 473s 4 discrete gamma distributed rate categories, alpha param estimated 473s 0.5551 473s with an invariant (invariable) site category, proportion estimated 473s 0.3357 473s Substitution rate categories under this model: 473s rate proportion 473s 0.0000 0.3357 473s 0.0440 0.1661 473s 0.2864 0.1661 473s 0.8566 0.1661 473s 2.8131 0.1661 473s 473s NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 473s No branches were short enough to be collapsed. 473s 473s >>>Completed Search rep 2 (of 2)<<< 473s 473s ####################################################### 473s 473s Completed 2 replicate search(es) (of 2). 473s 473s NOTE: Unless the following output indicates that search replicates found the 473s same topology, you should assume that they found different topologies. 473s Results: 473s Replicate 1 : -21812.6414 (best) 473s Replicate 2 : -21812.6695 473s 473s Parameter estimates across search replicates: 473s r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv 473s rep 1: 2.215 8.16 2.358 0.9186 16.52 1 0.348 0.213 0.150 0.290 0.560 0.338 473s rep 2: 2.212 8.203 2.367 0.9127 16.53 1 0.348 0.213 0.150 0.290 0.555 0.336 473s 473s Treelengths: 473s TL 473s rep 1: 2.941 473s rep 2: 2.935 473s 473s Saving final trees from all search reps to rana.nuc.GTRIG.best.all.tre 473s 473s Saving final tree from best search rep (#1) to rana.nuc.GTRIG.best.tre 473s ####################################################### 474s autopkgtest [12:03:48]: test run-unit-test: -----------------------] 474s autopkgtest [12:03:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 474s run-unit-test PASS 475s autopkgtest [12:03:49]: @@@@@@@@@@@@@@@@@@@@ summary 475s run-unit-test PASS 541s Creating nova instance adt-noble-arm64-garli-20240318-115553-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240317.img (UUID 7a23b7f2-4731-4803-bcc6-08355044298e)...