0s autopkgtest [03:40:58]: starting date and time: 2024-03-26 03:40:58+0000 0s autopkgtest [03:40:58]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [03:40:58]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j4ofb7j0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade garli --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-33.secgroup --name adt-noble-amd64-garli-20240326-034058-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 951s autopkgtest [03:56:49]: testbed dpkg architecture: amd64 951s autopkgtest [03:56:49]: testbed apt version: 2.7.12 951s autopkgtest [03:56:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 952s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 952s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4027 kB] 952s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 952s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 952s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 952s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [731 kB] 952s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [483 kB] 952s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 952s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [37.9 kB] 952s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 952s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 952s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4390 kB] 952s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1260 kB] 952s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 952s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [28.6 kB] 952s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.8 kB] 952s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 955s Fetched 11.7 MB in 2s (7502 kB/s) 955s Reading package lists... 956s Reading package lists... 957s Building dependency tree... 957s Reading state information... 957s Calculating upgrade... 957s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 957s Reading package lists... 958s Building dependency tree... 958s Reading state information... 958s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded. 958s sh: Attempting to set up Debian/Ubuntu apt sources automatically 958s sh: Distribution appears to be Ubuntu 959s Reading package lists... 959s Building dependency tree... 959s Reading state information... 960s eatmydata is already the newest version (131-1). 960s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 960s Reading package lists... 960s Building dependency tree... 960s Reading state information... 960s dbus is already the newest version (1.14.10-4ubuntu1). 960s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 960s Reading package lists... 960s Building dependency tree... 960s Reading state information... 961s rng-tools-debian is already the newest version (2.4). 961s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 961s Reading package lists... 961s Building dependency tree... 961s Reading state information... 961s The following packages will be REMOVED: 961s cloud-init* python3-configobj* python3-debconf* 961s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 961s After this operation, 3256 kB disk space will be freed. 962s (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 ... 71864 files and directories currently installed.) 962s Removing cloud-init (24.1.2-0ubuntu1) ... 962s Removing python3-configobj (5.0.8-3) ... 962s Removing python3-debconf (1.5.86) ... 962s Processing triggers for man-db (2.12.0-3) ... 963s (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 ... 71475 files and directories currently installed.) 963s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 963s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 963s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 964s invoke-rc.d: policy-rc.d denied execution of try-restart. 964s Reading package lists... 964s Building dependency tree... 964s Reading state information... 964s linux-generic is already the newest version (6.8.0-11.11+1). 964s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 964s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 964s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 964s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 966s Reading package lists... 966s Reading package lists... 966s Building dependency tree... 966s Reading state information... 967s Calculating upgrade... 967s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 967s Reading package lists... 967s Building dependency tree... 967s Reading state information... 967s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 967s autopkgtest [03:57:05]: rebooting testbed after setup commands that affected boot 1128s autopkgtest [03:59:46]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 1129s autopkgtest [03:59:47]: @@@@@@@@@@@@@@@@@@@@ apt-source garli 1130s Get:1 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (dsc) [2047 B] 1130s Get:2 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (tar) [1249 kB] 1130s Get:3 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (diff) [4788 B] 1130s gpgv: Signature made Sun Feb 20 14:34:04 2022 UTC 1130s gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 1130s gpgv: Can't check signature: No public key 1130s dpkg-source: warning: cannot verify inline signature for ./garli_2.1-7.dsc: no acceptable signature found 1131s autopkgtest [03:59:49]: testing package garli version 2.1-7 1131s autopkgtest [03:59:49]: build not needed 1131s autopkgtest [03:59:49]: test run-unit-test: preparing testbed 1131s Reading package lists... 1131s Building dependency tree... 1131s Reading state information... 1132s Starting pkgProblemResolver with broken count: 0 1132s Starting 2 pkgProblemResolver with broken count: 0 1132s Done 1132s The following additional packages will be installed: 1132s garli garli-examples garli-mpi libamd-comgr2 libamdhip64-5 libatomic1 1132s libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 1132s libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 libmunge2 libncl2 1132s libopenmpi3 libpciaccess0 libpmix2 libpsm-infinipath1 libpsm2-2 1132s librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin 1132s openmpi-common 1132s Suggested packages: 1132s libhwloc-contrib-plugins opencl-icd gfortran | fortran-compiler 1132s The following NEW packages will be installed: 1132s autopkgtest-satdep garli garli-examples garli-mpi libamd-comgr2 1132s libamdhip64-5 libatomic1 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 1132s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 1132s libmunge2 libncl2 libopenmpi3 libpciaccess0 libpmix2 libpsm-infinipath1 1132s libpsm2-2 librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin 1132s openmpi-common 1132s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 1132s Need to get 54.7 MB/54.7 MB of archives. 1132s After this operation, 228 MB of additional disk space will be used. 1132s Get:1 /tmp/autopkgtest.Po0ufl/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 1132s Get:2 http://ftpmaster.internal/ubuntu noble/universe amd64 libncl2 amd64 2.1.21+git20210811.b1213a7-5 [461 kB] 1132s Get:3 http://ftpmaster.internal/ubuntu noble/universe amd64 garli amd64 2.1-7 [546 kB] 1132s Get:4 http://ftpmaster.internal/ubuntu noble/universe amd64 garli-examples all 2.1-7 [132 kB] 1132s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-9 [7802 B] 1132s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 1132s Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [178 kB] 1132s Get:8 http://ftpmaster.internal/ubuntu noble/universe amd64 libpsm2-2 amd64 11.2.185-2 [196 kB] 1132s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 librdmacm1t64 amd64 50.0-2 [70.7 kB] 1132s Get:10 http://ftpmaster.internal/ubuntu noble/universe amd64 libfabric1 amd64 1.17.0-3build1 [657 kB] 1132s Get:11 http://ftpmaster.internal/ubuntu noble/universe amd64 libhwloc15 amd64 2.10.0-1 [171 kB] 1132s Get:12 http://ftpmaster.internal/ubuntu noble/universe amd64 libmunge2 amd64 0.5.15-3ubuntu1 [14.6 kB] 1132s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libpciaccess0 amd64 0.17-3 [18.9 kB] 1132s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu1 [11.5 kB] 1132s Get:15 http://ftpmaster.internal/ubuntu noble/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1 [38.3 kB] 1132s Get:16 http://ftpmaster.internal/ubuntu noble/universe amd64 libhwloc-plugins amd64 2.10.0-1 [15.8 kB] 1132s Get:17 http://ftpmaster.internal/ubuntu noble/universe amd64 libpmix2 amd64 5.0.1-4 [695 kB] 1132s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libllvm17 amd64 1:17.0.6-5build1 [26.2 MB] 1132s Get:19 http://ftpmaster.internal/ubuntu noble/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3 [14.4 MB] 1133s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [20.4 kB] 1133s Get:21 http://ftpmaster.internal/ubuntu noble/universe amd64 libhsakmt1 amd64 5.7.0-1 [63.0 kB] 1133s Get:22 http://ftpmaster.internal/ubuntu noble/universe amd64 libhsa-runtime64-1 amd64 5.7.1-1 [491 kB] 1133s Get:23 http://ftpmaster.internal/ubuntu noble/universe amd64 libamdhip64-5 amd64 5.2.3-12 [5204 kB] 1133s Get:24 http://ftpmaster.internal/ubuntu noble/universe amd64 libucx0 amd64 1.16.0+ds-4 [1139 kB] 1133s Get:25 http://ftpmaster.internal/ubuntu noble/universe amd64 libopenmpi3 amd64 4.1.6-5ubuntu1 [3177 kB] 1133s Get:26 http://ftpmaster.internal/ubuntu noble/universe amd64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] 1133s Get:27 http://ftpmaster.internal/ubuntu noble/universe amd64 openmpi-bin amd64 4.1.6-5ubuntu1 [124 kB] 1133s Get:28 http://ftpmaster.internal/ubuntu noble/universe amd64 garli-mpi amd64 2.1-7 [537 kB] 1133s Fetched 54.7 MB in 1s (81.0 MB/s) 1133s Selecting previously unselected package libncl2:amd64. 1133s (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 ... 71420 files and directories currently installed.) 1133s Preparing to unpack .../00-libncl2_2.1.21+git20210811.b1213a7-5_amd64.deb ... 1133s Unpacking libncl2:amd64 (2.1.21+git20210811.b1213a7-5) ... 1133s Selecting previously unselected package garli. 1133s Preparing to unpack .../01-garli_2.1-7_amd64.deb ... 1133s Unpacking garli (2.1-7) ... 1133s Selecting previously unselected package garli-examples. 1133s Preparing to unpack .../02-garli-examples_2.1-7_all.deb ... 1133s Unpacking garli-examples (2.1-7) ... 1133s Selecting previously unselected package libevent-pthreads-2.1-7:amd64. 1133s Preparing to unpack .../03-libevent-pthreads-2.1-7_2.1.12-stable-9_amd64.deb ... 1133s Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-9) ... 1133s Selecting previously unselected package libatomic1:amd64. 1133s Preparing to unpack .../04-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 1133s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 1133s Selecting previously unselected package libpsm-infinipath1. 1133s Preparing to unpack .../05-libpsm-infinipath1_3.3+20.604758e7-6.3_amd64.deb ... 1133s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) ... 1133s Selecting previously unselected package libpsm2-2. 1133s Preparing to unpack .../06-libpsm2-2_11.2.185-2_amd64.deb ... 1133s Unpacking libpsm2-2 (11.2.185-2) ... 1133s Selecting previously unselected package librdmacm1t64:amd64. 1133s Preparing to unpack .../07-librdmacm1t64_50.0-2_amd64.deb ... 1133s Unpacking librdmacm1t64:amd64 (50.0-2) ... 1133s Selecting previously unselected package libfabric1:amd64. 1133s Preparing to unpack .../08-libfabric1_1.17.0-3build1_amd64.deb ... 1133s Unpacking libfabric1:amd64 (1.17.0-3build1) ... 1133s Selecting previously unselected package libhwloc15:amd64. 1133s Preparing to unpack .../09-libhwloc15_2.10.0-1_amd64.deb ... 1133s Unpacking libhwloc15:amd64 (2.10.0-1) ... 1133s Selecting previously unselected package libmunge2:amd64. 1133s Preparing to unpack .../10-libmunge2_0.5.15-3ubuntu1_amd64.deb ... 1133s Unpacking libmunge2:amd64 (0.5.15-3ubuntu1) ... 1133s Selecting previously unselected package libpciaccess0:amd64. 1133s Preparing to unpack .../11-libpciaccess0_0.17-3_amd64.deb ... 1133s Unpacking libpciaccess0:amd64 (0.17-3) ... 1133s Selecting previously unselected package libxnvctrl0:amd64. 1133s Preparing to unpack .../12-libxnvctrl0_510.47.03-0ubuntu1_amd64.deb ... 1133s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... 1134s Selecting previously unselected package ocl-icd-libopencl1:amd64. 1134s Preparing to unpack .../13-ocl-icd-libopencl1_2.3.2-1_amd64.deb ... 1134s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1) ... 1134s Selecting previously unselected package libhwloc-plugins:amd64. 1134s Preparing to unpack .../14-libhwloc-plugins_2.10.0-1_amd64.deb ... 1134s Unpacking libhwloc-plugins:amd64 (2.10.0-1) ... 1134s Selecting previously unselected package libpmix2:amd64. 1134s Preparing to unpack .../15-libpmix2_5.0.1-4_amd64.deb ... 1134s Unpacking libpmix2:amd64 (5.0.1-4) ... 1134s Selecting previously unselected package libllvm17:amd64. 1134s Preparing to unpack .../16-libllvm17_1%3a17.0.6-5build1_amd64.deb ... 1134s Unpacking libllvm17:amd64 (1:17.0.6-5build1) ... 1134s Selecting previously unselected package libamd-comgr2:amd64. 1134s Preparing to unpack .../17-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_amd64.deb ... 1134s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3) ... 1134s Selecting previously unselected package libdrm-amdgpu1:amd64. 1134s Preparing to unpack .../18-libdrm-amdgpu1_2.4.120-2_amd64.deb ... 1134s Unpacking libdrm-amdgpu1:amd64 (2.4.120-2) ... 1134s Selecting previously unselected package libhsakmt1:amd64. 1134s Preparing to unpack .../19-libhsakmt1_5.7.0-1_amd64.deb ... 1134s Unpacking libhsakmt1:amd64 (5.7.0-1) ... 1134s Selecting previously unselected package libhsa-runtime64-1. 1134s Preparing to unpack .../20-libhsa-runtime64-1_5.7.1-1_amd64.deb ... 1134s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 1134s Selecting previously unselected package libamdhip64-5. 1134s Preparing to unpack .../21-libamdhip64-5_5.2.3-12_amd64.deb ... 1134s Unpacking libamdhip64-5 (5.2.3-12) ... 1135s Selecting previously unselected package libucx0:amd64. 1135s Preparing to unpack .../22-libucx0_1.16.0+ds-4_amd64.deb ... 1135s Unpacking libucx0:amd64 (1.16.0+ds-4) ... 1135s Selecting previously unselected package libopenmpi3:amd64. 1135s Preparing to unpack .../23-libopenmpi3_4.1.6-5ubuntu1_amd64.deb ... 1135s Unpacking libopenmpi3:amd64 (4.1.6-5ubuntu1) ... 1135s Selecting previously unselected package openmpi-common. 1135s Preparing to unpack .../24-openmpi-common_4.1.6-5ubuntu1_all.deb ... 1135s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 1135s Selecting previously unselected package openmpi-bin. 1135s Preparing to unpack .../25-openmpi-bin_4.1.6-5ubuntu1_amd64.deb ... 1135s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 1135s Selecting previously unselected package garli-mpi. 1135s Preparing to unpack .../26-garli-mpi_2.1-7_amd64.deb ... 1135s Unpacking garli-mpi (2.1-7) ... 1135s Selecting previously unselected package autopkgtest-satdep. 1135s Preparing to unpack .../27-1-autopkgtest-satdep.deb ... 1135s Unpacking autopkgtest-satdep (0) ... 1135s Setting up libpciaccess0:amd64 (0.17-3) ... 1135s Setting up libncl2:amd64 (2.1.21+git20210811.b1213a7-5) ... 1135s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... 1135s Setting up garli-examples (2.1-7) ... 1135s Setting up garli (2.1-7) ... 1135s Setting up libmunge2:amd64 (0.5.15-3ubuntu1) ... 1135s Setting up libhwloc15:amd64 (2.10.0-1) ... 1135s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 1135s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1) ... 1135s Setting up libpsm2-2 (11.2.185-2) ... 1135s Setting up openmpi-common (4.1.6-5ubuntu1) ... 1135s Setting up librdmacm1t64:amd64 (50.0-2) ... 1135s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... 1135s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 1135s Setting up libllvm17:amd64 (1:17.0.6-5build1) ... 1135s Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-9) ... 1135s Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... 1135s Setting up libfabric1:amd64 (1.17.0-3build1) ... 1135s Setting up libhwloc-plugins:amd64 (2.10.0-1) ... 1135s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3) ... 1135s Setting up libhsakmt1:amd64 (5.7.0-1) ... 1135s Setting up libpmix2:amd64 (5.0.1-4) ... 1135s Setting up libhsa-runtime64-1 (5.7.1-1) ... 1135s Setting up libamdhip64-5 (5.2.3-12) ... 1135s Setting up libucx0:amd64 (1.16.0+ds-4) ... 1135s Setting up libopenmpi3:amd64 (4.1.6-5ubuntu1) ... 1135s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 1135s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 1135s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 1135s Setting up garli-mpi (2.1-7) ... 1135s Setting up autopkgtest-satdep (0) ... 1135s Processing triggers for man-db (2.12.0-3) ... 1135s Processing triggers for libc-bin (2.39-0ubuntu6) ... 1138s (Reading database ... 72066 files and directories currently installed.) 1138s Removing autopkgtest-satdep (0) ... 1138s autopkgtest [03:59:56]: test run-unit-test: [----------------------- 1138s Running GARLI Version 2.1. () 1138s ->Single processor version for 64-bit OS<- 1138s ############################################################## 1138s This is GARLI 2.1: maximum likelihood phylogenetic inference 1138s using nucleotide, amino acid, codon and morphology-like data, 1138s as well as partitioned models. 1138s General program usage is extensively documented here: 1138s http://www.nescent.org/wg/garli/ 1138s See this page for details on partitioned model usage: 1138s http://www.nescent.org/wg_garli/Using_partitioned_models 1138s and this page for details on Mkv mophology model usage: 1138s http://www.nescent.org/wg_garli/Mkv_morphology_model 1138s PLEASE LET ME KNOW OF ANY PROBLEMS AT: 1138s garli.support@gmail.com 1138s ############################################################## 1138s Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 11.2.0 1138s Using NCL version 2.1.17 1138s 1138s ####################################################### 1138s Reading config file garli.conf 1138s ################################################### 1138s READING OF DATA 1138s Attempting to read data file in Nexus format (using NCL): 1138s rana.nex ... 1138s Reading DATA block... successful 1138s 1138s ################################################### 1138s PARTITIONING OF DATA AND MODELS 1138s GARLI data subset 1 1138s CHARACTERS block #1 ("Untitled DATA Block 1") 1138s Data read as Nucleotide data, 1138s modeled as Nucleotide data 1138s storing implied block: TAXA 1138s storing read block: DATA 1138s Summary of data: 1138s 64 sequences. 1138s 1062 constant characters. 1138s 664 parsimony-informative characters. 1138s 250 uninformative variable characters. 1138s 1976 total characters. 1138s 890 unique patterns in compressed data matrix. 1138s 1138s ################################################### 1138s NOTE: Unlike many programs, the amount of system memory that Garli will 1138s use can be controlled by the user. 1138s (This comes from the availablememory setting in the configuration file. 1138s Availablememory should NOT be set to more than the actual amount of 1138s physical memory that your computer has installed) 1138s 1138s For this dataset: 1138s Mem level availablememory setting 1138s great >= 70 MB 1138s good approx 69 MB to 45 MB 1138s low approx 44 MB to 19 MB 1138s very low approx 18 MB to 15 MB 1138s the minimum required availablememory is 15 MB 1138s 1138s You specified that Garli should use at most 512.0 MB of memory. 1138s 1138s Garli will actually use approx. 104.2 MB of memory 1138s **Your memory level is: great (you don't need to change anything)** 1138s 1138s ####################################################### 1138s Found outgroup specification: 1 1138s 1138s ####################################################### 1138s STARTING RUN 1138s 1138s >>>Search rep 1 (of 2)<<< 1138s MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 1138s Model 1 1138s Number of states = 4 (nucleotide data) 1138s Nucleotide Relative Rate Matrix: 6 rates 1138s AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 1138s Equilibrium State Frequencies: estimated 1138s (ACGT) 0.3381 0.2238 0.1789 0.2592 1138s Rate Heterogeneity Model: 1138s 4 discrete gamma distributed rate categories, alpha param estimated 1138s 0.5000 1138s with an invariant (invariable) site category, proportion estimated 1138s 0.1344 1138s Substitution rate categories under this model: 1138s rate proportion 1138s 0.0000 0.1344 1138s 0.0334 0.2164 1138s 0.2519 0.2164 1138s 0.8203 0.2164 1138s 2.8944 0.2164 1138s 1138s Starting with seed=490834 1138s 1138s creating likelihood stepwise addition starting tree... 1138s number of taxa added: 1139s 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 1139s Optimizing parameters... improved 71.877 lnL 1139s Optimizing branchlengths... improved 27.536 lnL 1140s 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 1140s Initial ln Likelihood: -22986.0102 1140s optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... 1141s pass 1:+ 347.753 (branch= 84.27 scale= 6.03 alpha= 0.63 freqs=135.24 rel rates=114.42 pinv= 7.16) 1141s pass 2:+ 71.914 (branch= 27.04 scale= 0.84 alpha= 4.78 freqs= 29.11 rel rates= 5.91 pinv= 4.24) 1141s pass 3:+ 17.902 (branch= 5.26 scale= 0.00 alpha= 4.79 freqs= 1.50 rel rates= 4.51 pinv= 1.84) 1141s pass 4:+ 11.734 (branch= 0.50 scale= 0.53 alpha= 1.87 freqs= 2.06 rel rates= 4.95 pinv= 1.81) 1141s pass 5:+ 6.230 (branch= 0.00 scale= 0.00 alpha= 2.04 freqs= 0.20 rel rates= 3.06 pinv= 0.94) 1141s pass 6:+ 6.011 (branch= 0.00 scale= 0.00 alpha= 1.00 freqs= 0.15 rel rates= 4.21 pinv= 0.65) 1141s pass 7:+ 3.229 (branch= 0.00 scale= 0.00 alpha= 0.63 freqs= 0.56 rel rates= 2.02 pinv= 0.03) 1141s pass 8:+ 1.262 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.11 rel rates= 1.12 pinv= 0.03) 1141s pass 9:+ 1.551 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 1.43 pinv= 0.02) 1141s pass10:+ 0.882 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.82 pinv= 0.03) 1141s pass11:+ 0.124 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.08 rel rates= 0.02 pinv= 0.02) 1141s lnL after optimization: -22517.4176 1141s gen current_lnL precision last_tree_imp 1141s 0 -22517.4176 0.500 0 1142s 100 -22260.6387 0.500 93 1142s 200 -22040.2755 0.500 195 1143s 300 -21997.4198 0.500 295 1143s 400 -21952.5929 0.500 375 1144s 500 -21873.8042 0.500 496 1144s 600 -21853.2297 0.500 588 1144s 700 -21849.0506 0.500 641 1145s 800 -21847.6652 0.500 726 1145s 900 -21843.1568 0.500 894 1146s 1000 -21836.2144 0.500 920 1146s 1100 -21834.5875 0.500 920 1147s 1200 -21833.3860 0.500 1127 1147s 1300 -21831.2458 0.500 1230 1148s 1400 -21830.3474 0.500 1230 1148s 1500 -21826.7034 0.500 1493 1148s 1600 -21824.1469 0.500 1493 1149s 1700 -21823.4909 0.500 1493 1149s 1800 -21822.6757 0.500 1493 1150s 1900 -21822.0570 0.500 1493 1150s 2000 -21821.0704 0.500 1493 1150s Optimization precision reduced 1150s Optimizing parameters... improved 0.065 lnL 1150s Optimizing branchlengths... improved 0.000 lnL 1151s 2100 -21820.6653 0.451 1493 1151s 2200 -21820.3185 0.451 1493 1151s 2300 -21819.9782 0.451 1493 1152s 2400 -21819.5103 0.451 1493 1152s 2500 -21819.4204 0.451 1493 1152s Optimization precision reduced 1152s Optimizing parameters... improved 0.026 lnL 1152s Optimizing branchlengths... improved 0.000 lnL 1153s 2600 -21818.9749 0.402 1493 1153s 2700 -21818.8516 0.402 1493 1154s 2800 -21818.4945 0.402 1493 1154s 2900 -21818.3994 0.402 1493 1155s 3000 -21817.9878 0.402 1493 1155s Optimization precision reduced 1155s Optimizing parameters... improved 0.023 lnL 1155s Optimizing branchlengths... improved 0.000 lnL 1155s 3100 -21817.7213 0.353 1493 1155s 3200 -21817.4237 0.353 1493 1156s 3300 -21817.1888 0.353 1493 1156s 3400 -21817.0854 0.353 1493 1157s 3500 -21816.9816 0.353 1493 1157s Optimization precision reduced 1157s Optimizing parameters... improved 0.010 lnL 1157s Optimizing branchlengths... improved 0.443 lnL 1157s 3600 -21816.3800 0.304 1493 1158s 3700 -21816.2382 0.304 1493 1158s 3800 -21816.1220 0.304 1493 1159s 3900 -21815.9926 0.304 1493 1159s 4000 -21815.8421 0.304 1493 1159s Optimization precision reduced 1159s Optimizing parameters... improved 0.006 lnL 1159s Optimizing branchlengths... improved 0.000 lnL 1160s 4100 -21815.7895 0.255 1493 1160s 4200 -21815.7713 0.255 1493 1161s 4300 -21815.6481 0.255 1493 1161s 4400 -21815.5313 0.255 1493 1161s 4500 -21815.4288 0.255 1493 1161s Optimization precision reduced 1162s Optimizing parameters... improved 0.003 lnL 1162s Optimizing branchlengths... improved 0.440 lnL 1162s 4600 -21814.8623 0.206 4554 1162s 4700 -21814.7432 0.206 4554 1163s 4800 -21814.6696 0.206 4554 1163s 4900 -21814.6264 0.206 4554 1164s 5000 -21814.4147 0.206 4554 1164s 5100 -21814.3445 0.206 4554 1164s Optimization precision reduced 1164s Optimizing parameters... improved 0.007 lnL 1164s Optimizing branchlengths... improved 0.000 lnL 1165s 5200 -21814.2952 0.157 4554 1165s 5300 -21814.2337 0.157 4554 1166s 5400 -21814.1867 0.157 4554 1166s 5500 -21814.1171 0.157 4554 1167s 5600 -21814.0777 0.157 4554 1167s Optimization precision reduced 1167s Optimizing parameters... improved 0.001 lnL 1167s Optimizing branchlengths... improved 0.131 lnL 1167s 5700 -21813.8725 0.108 4554 1168s 5800 -21813.8149 0.108 4554 1168s 5900 -21813.7881 0.108 4554 1169s 6000 -21813.7737 0.108 4554 1169s 6100 -21813.7556 0.108 4554 1169s Optimization precision reduced 1169s Optimizing parameters... improved 0.001 lnL 1169s Optimizing branchlengths... improved 0.133 lnL 1170s 6200 -21813.5757 0.059 4554 1170s 6300 -21813.5508 0.059 4554 1171s 6400 -21813.4979 0.059 4554 1171s 6500 -21813.4348 0.059 4554 1172s 6600 -21813.3695 0.059 4554 1172s Optimization precision reduced 1172s Optimizing parameters... improved 0.033 lnL 1172s Optimizing branchlengths... improved 0.401 lnL 1173s 6700 -21812.9287 0.010 4554 1173s 6800 -21812.9249 0.010 4554 1174s 6900 -21812.9115 0.010 4554 1174s 7000 -21812.9114 0.010 4554 1175s 7100 -21812.9086 0.010 4554 1176s 7200 -21812.9025 0.010 4554 1176s 7300 -21812.8902 0.010 4554 1177s 7400 -21812.8902 0.010 4554 1178s 7500 -21812.8866 0.010 4554 1178s 7600 -21812.8866 0.010 4554 1179s 7700 -21812.8840 0.010 4554 1180s 7800 -21812.8757 0.010 4554 1180s 7900 -21812.8757 0.010 4554 1181s 8000 -21812.8649 0.010 4554 1181s 8100 -21812.8551 0.010 4554 1182s 8200 -21812.8509 0.010 4554 1183s 8300 -21812.8333 0.010 4554 1183s 8400 -21812.8333 0.010 4554 1184s 8500 -21812.8323 0.010 4554 1185s 8600 -21812.8312 0.010 4554 1185s 8700 -21812.8298 0.010 4554 1186s 8800 -21812.8288 0.010 4554 1186s 8900 -21812.8276 0.010 4554 1187s 9000 -21812.8234 0.010 4554 1188s 9100 -21812.8200 0.010 4554 1188s 9200 -21812.8200 0.010 4554 1189s 9300 -21812.8176 0.010 4554 1190s 9400 -21812.8176 0.010 4554 1190s 9500 -21812.8148 0.010 4554 1191s 9600 -21812.8148 0.010 4554 1191s 9700 -21812.8142 0.010 4554 1192s 9800 -21812.8132 0.010 4554 1193s 9900 -21812.8132 0.010 4554 1193s 10000 -21812.8121 0.010 4554 1194s 10100 -21812.8069 0.010 4554 1195s 10200 -21812.8069 0.010 4554 1195s 10300 -21812.8060 0.010 4554 1196s 10400 -21812.8026 0.010 4554 1197s 10500 -21812.8006 0.010 4554 1197s 10600 -21812.8006 0.010 4554 1198s 10700 -21812.7959 0.010 4554 1198s 10800 -21812.7959 0.010 4554 1199s 10900 -21812.7959 0.010 4554 1200s 11000 -21812.7941 0.010 4554 1200s 11100 -21812.7941 0.010 4554 1201s 11200 -21812.7939 0.010 4554 1202s 11300 -21812.7937 0.010 4554 1202s 11400 -21812.7856 0.010 4554 1203s 11500 -21812.7784 0.010 4554 1204s 11600 -21812.7771 0.010 4554 1204s 11700 -21812.7731 0.010 4554 1205s 11800 -21812.7731 0.010 4554 1206s 11900 -21812.7729 0.010 4554 1206s 12000 -21812.7729 0.010 4554 1207s 12100 -21812.7706 0.010 4554 1207s 12200 -21812.7705 0.010 4554 1208s 12300 -21812.7578 0.010 4554 1209s 12400 -21812.7572 0.010 4554 1209s 12500 -21812.7568 0.010 4554 1210s 12600 -21812.7568 0.010 4554 1211s 12700 -21812.7537 0.010 4554 1211s 12800 -21812.7537 0.010 4554 1212s 12900 -21812.7537 0.010 4554 1213s 13000 -21812.7537 0.010 4554 1213s 13100 -21812.7537 0.010 4554 1214s 13200 -21812.7521 0.010 4554 1214s 13300 -21812.7430 0.010 4554 1215s 13400 -21812.7422 0.010 4554 1216s 13500 -21812.7422 0.010 4554 1216s 13600 -21812.7419 0.010 4554 1217s 13700 -21812.7400 0.010 4554 1218s 13800 -21812.7400 0.010 4554 1218s 13900 -21812.7399 0.010 4554 1219s 14000 -21812.7394 0.010 4554 1220s 14100 -21812.7393 0.010 4554 1220s 14200 -21812.7339 0.010 4554 1221s 14300 -21812.7286 0.010 4554 1221s 14400 -21812.7273 0.010 4554 1222s 14500 -21812.7272 0.010 4554 1223s 14600 -21812.7229 0.010 4554 1223s 14700 -21812.7195 0.010 4554 1224s 14800 -21812.7190 0.010 4554 1224s 14900 -21812.7175 0.010 4554 1225s 15000 -21812.7165 0.010 4554 1225s Optimizing parameters... improved 0.000 lnL 1225s Optimizing branchlengths... improved 0.000 lnL 1226s 15100 -21812.7160 0.010 4554 1227s 15200 -21812.7160 0.010 4554 1227s 15300 -21812.7160 0.010 4554 1228s 15400 -21812.7160 0.010 4554 1229s 15500 -21812.7160 0.010 4554 1229s 15600 -21812.7151 0.010 4554 1230s 15700 -21812.7151 0.010 4554 1231s 15800 -21812.7151 0.010 4554 1231s 15900 -21812.7151 0.010 4554 1232s 16000 -21812.7142 0.010 4554 1232s 16100 -21812.7142 0.010 4554 1233s 16200 -21812.7137 0.010 4554 1234s 16300 -21812.7137 0.010 4554 1234s 16400 -21812.7130 0.010 4554 1235s 16500 -21812.7114 0.010 4554 1236s 16600 -21812.7107 0.010 4554 1236s 16700 -21812.7090 0.010 4554 1237s 16800 -21812.7085 0.010 4554 1238s 16900 -21812.7082 0.010 4554 1238s 17000 -21812.7082 0.010 4554 1239s 17100 -21812.7077 0.010 4554 1240s 17200 -21812.7070 0.010 4554 1240s 17300 -21812.7067 0.010 4554 1241s 17400 -21812.7067 0.010 4554 1242s 17500 -21812.7067 0.010 4554 1242s 17600 -21812.7067 0.010 4554 1243s 17700 -21812.7067 0.010 4554 1244s 17800 -21812.7058 0.010 4554 1244s 17900 -21812.7054 0.010 4554 1245s 18000 -21812.7053 0.010 4554 1245s 18100 -21812.7053 0.010 4554 1246s 18200 -21812.7051 0.010 4554 1247s 18300 -21812.7051 0.010 4554 1247s 18400 -21812.7051 0.010 4554 1248s 18500 -21812.7051 0.010 4554 1249s 18600 -21812.7051 0.010 4554 1249s 18700 -21812.7051 0.010 4554 1250s 18800 -21812.7021 0.010 4554 1251s 18900 -21812.7013 0.010 4554 1251s 19000 -21812.7013 0.010 4554 1252s 19100 -21812.7013 0.010 4554 1253s 19200 -21812.7013 0.010 4554 1253s 19300 -21812.7010 0.010 4554 1254s 19400 -21812.6990 0.010 4554 1255s 19500 -21812.6988 0.010 4554 1255s 19600 -21812.6982 0.010 4554 1256s 19700 -21812.6982 0.010 4554 1257s 19800 -21812.6982 0.010 4554 1257s 19900 -21812.6976 0.010 4554 1258s 20000 -21812.6976 0.010 4554 1258s Optimizing parameters... improved 0.000 lnL 1258s Optimizing branchlengths... improved 0.000 lnL 1259s 20100 -21812.6967 0.010 4554 1259s 20200 -21812.6967 0.010 4554 1260s 20300 -21812.6948 0.010 4554 1260s 20400 -21812.6945 0.010 4554 1261s 20500 -21812.6945 0.010 4554 1262s 20600 -21812.6892 0.010 4554 1262s 20700 -21812.6889 0.010 4554 1263s 20800 -21812.6869 0.010 4554 1263s 20900 -21812.6850 0.010 4554 1264s 21000 -21812.6850 0.010 4554 1265s 21100 -21812.6850 0.010 4554 1265s 21200 -21812.6849 0.010 4554 1266s 21300 -21812.6849 0.010 4554 1267s 21400 -21812.6849 0.010 4554 1267s 21500 -21812.6849 0.010 4554 1268s 21600 -21812.6849 0.010 4554 1268s 21700 -21812.6849 0.010 4554 1269s 21800 -21812.6849 0.010 4554 1270s 21900 -21812.6840 0.010 4554 1270s 22000 -21812.6837 0.010 4554 1271s 22100 -21812.6837 0.010 4554 1272s 22200 -21812.6826 0.010 4554 1272s 22300 -21812.6826 0.010 4554 1273s 22400 -21812.6826 0.010 4554 1274s 22500 -21812.6826 0.010 4554 1274s 22600 -21812.6826 0.010 4554 1275s 22700 -21812.6822 0.010 4554 1276s 22800 -21812.6822 0.010 4554 1276s 22900 -21812.6822 0.010 4554 1277s 23000 -21812.6822 0.010 4554 1277s 23100 -21812.6819 0.010 4554 1278s 23200 -21812.6819 0.010 4554 1279s 23300 -21812.6809 0.010 4554 1279s 23400 -21812.6809 0.010 4554 1280s 23500 -21812.6809 0.010 4554 1281s 23600 -21812.6808 0.010 4554 1281s 23700 -21812.6808 0.010 4554 1282s 23800 -21812.6808 0.010 4554 1283s 23900 -21812.6808 0.010 4554 1283s 24000 -21812.6801 0.010 4554 1284s 24100 -21812.6801 0.010 4554 1285s 24200 -21812.6801 0.010 4554 1285s 24300 -21812.6801 0.010 4554 1286s 24400 -21812.6795 0.010 4554 1287s 24500 -21812.6795 0.010 4554 1287s 24600 -21812.6795 0.010 4554 1288s 24700 -21812.6795 0.010 4554 1288s 24800 -21812.6795 0.010 4554 1289s 24900 -21812.6795 0.010 4554 1290s 25000 -21812.6795 0.010 4554 1290s Optimizing parameters... improved 0.000 lnL 1290s Optimizing branchlengths... improved 0.000 lnL 1290s 25100 -21812.6792 0.010 4554 1291s 25200 -21812.6792 0.010 4554 1292s 25300 -21812.6792 0.010 4554 1292s 25400 -21812.6791 0.010 4554 1293s 25500 -21812.6791 0.010 4554 1294s 25600 -21812.6791 0.010 4554 1294s 25700 -21812.6786 0.010 4554 1295s 25800 -21812.6786 0.010 4554 1296s 25900 -21812.6786 0.010 4554 1296s 26000 -21812.6785 0.010 4554 1297s 26100 -21812.6785 0.010 4554 1297s 26200 -21812.6785 0.010 4554 1298s 26300 -21812.6785 0.010 4554 1299s 26400 -21812.6784 0.010 4554 1299s 26500 -21812.6782 0.010 4554 1300s 26600 -21812.6782 0.010 4554 1301s 26700 -21812.6782 0.010 4554 1301s Reached termination condition! 1301s last topological improvement at gen 4554 1301s Improvement over last 500 gen = 0.00026 1301s Current score = -21812.6782 1301s Performing final optimizations... 1301s pass 1 : -21812.6779 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0001) 1301s pass 2 : -21812.6778 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) 1301s pass 3 : -21812.6722 (branch= 0.0053 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0001) 1301s pass 4 : -21812.6623 (branch= 0.0089 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0000) 1301s pass 5 : -21812.6510 (branch= 0.0101 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0000) 1301s pass 6 : -21812.6468 (branch= 0.0034 alpha= 0.0004 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0000) 1301s pass 7 : -21812.6437 (branch= 0.0026 alpha= 0.0003 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 8 : -21812.6425 (branch= 0.0009 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 9 : -21812.6420 (branch= 0.0004 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 10: -21812.6417 (branch= 0.0001 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 11: -21812.6416 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 12: -21812.6415 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 13: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 14: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 15: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1302s pass 16: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1302s Looking for minimum length branches... 1302s Final score = -21812.6414 1302s Time used so far = 0 hours, 2 minutes and 44 seconds 1302s 1302s MODEL REPORT - Parameter values are FINAL 1302s Model 1 1302s Number of states = 4 (nucleotide data) 1302s Nucleotide Relative Rate Matrix: 6 rates 1302s AC = 2.214, AG = 8.157, AT = 2.357, CG = 0.918, CT = 16.508, GT = 1.000 1302s Equilibrium State Frequencies: estimated 1302s (ACGT) 0.3476 0.2126 0.1499 0.2898 1302s Rate Heterogeneity Model: 1302s 4 discrete gamma distributed rate categories, alpha param estimated 1302s 0.5605 1302s with an invariant (invariable) site category, proportion estimated 1302s 0.3385 1302s Substitution rate categories under this model: 1302s rate proportion 1302s 0.0000 0.3385 1302s 0.0451 0.1654 1302s 0.2896 0.1654 1302s 0.8597 0.1654 1302s 2.8056 0.1654 1302s 1302s NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1302s No branches were short enough to be collapsed. 1302s 1302s >>>Completed Search rep 1 (of 2)<<< 1302s 1302s >>>Search rep 2 (of 2)<<< 1302s MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 1302s Model 1 1302s Number of states = 4 (nucleotide data) 1302s Nucleotide Relative Rate Matrix: 6 rates 1302s AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 1302s Equilibrium State Frequencies: estimated 1302s (ACGT) 0.3381 0.2238 0.1789 0.2592 1302s Rate Heterogeneity Model: 1302s 4 discrete gamma distributed rate categories, alpha param estimated 1302s 0.5000 1302s with an invariant (invariable) site category, proportion estimated 1302s 0.1344 1302s Substitution rate categories under this model: 1302s rate proportion 1302s 0.0000 0.1344 1302s 0.0334 0.2164 1302s 0.2519 0.2164 1302s 0.8203 0.2164 1302s 2.8944 0.2164 1302s 1302s Starting with seed=1338674031 1302s 1302s creating likelihood stepwise addition starting tree... 1302s number of taxa added: 1303s 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 1303s Optimizing parameters... improved 62.093 lnL 1303s Optimizing branchlengths... improved 15.567 lnL 1305s 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 1305s Initial ln Likelihood: -22566.1510 1305s optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... 1305s pass 1:+ 332.150 (branch= 74.43 scale= 10.51 alpha= 0.00 freqs=125.25 rel rates=113.82 pinv= 8.14) 1305s pass 2:+ 52.144 (branch= 7.57 scale= 0.63 alpha= 4.80 freqs= 28.29 rel rates= 7.47 pinv= 3.38) 1305s pass 3:+ 15.467 (branch= 2.91 scale= 0.00 alpha= 4.10 freqs= 1.85 rel rates= 5.07 pinv= 1.54) 1306s pass 4:+ 8.562 (branch= 1.21 scale= 0.00 alpha= 2.18 freqs= 0.76 rel rates= 3.29 pinv= 1.12) 1306s pass 5:+ 5.141 (branch= 0.00 scale= 0.00 alpha= 1.36 freqs= 0.66 rel rates= 2.34 pinv= 0.78) 1306s pass 6:+ 4.255 (branch= 0.00 scale= 0.48 alpha= 0.02 freqs= 0.13 rel rates= 3.61 pinv= 0.02) 1306s pass 7:+ 2.905 (branch= 0.00 scale= 0.00 alpha= 0.03 freqs= 0.62 rel rates= 2.24 pinv= 0.01) 1306s pass 8:+ 2.300 (branch= 0.00 scale= 0.00 alpha= 0.03 freqs= 0.06 rel rates= 2.20 pinv= 0.01) 1306s pass 9:+ 1.560 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 0.04 rel rates= 1.48 pinv= 0.01) 1306s pass10:+ 0.091 (branch= 0.00 scale= 0.00 alpha= 0.03 freqs= 0.04 rel rates= 0.01 pinv= 0.01) 1306s lnL after optimization: -22141.5762 1306s gen current_lnL precision last_tree_imp 1306s 0 -22141.5762 0.500 0 1306s 100 -22046.6395 0.500 85 1307s 200 -21970.0356 0.500 182 1307s 300 -21916.6513 0.500 279 1308s 400 -21899.0892 0.500 399 1308s 500 -21895.2106 0.500 401 1309s 600 -21892.3480 0.500 600 1309s 700 -21888.8385 0.500 638 1310s 800 -21886.7599 0.500 774 1310s 900 -21883.7499 0.500 887 1310s 1000 -21882.4296 0.500 887 1311s 1100 -21876.0055 0.500 1053 1311s 1200 -21874.2489 0.500 1146 1312s 1300 -21869.3218 0.500 1206 1312s 1400 -21861.4304 0.500 1366 1313s 1500 -21860.1350 0.500 1411 1313s 1600 -21836.7269 0.500 1584 1313s 1700 -21834.8726 0.500 1646 1314s 1800 -21833.8532 0.500 1791 1314s 1900 -21833.1770 0.500 1791 1315s 2000 -21830.2260 0.500 1961 1315s 2100 -21829.4158 0.500 2087 1316s 2200 -21828.8918 0.500 2087 1316s 2300 -21827.7404 0.500 2087 1316s 2400 -21825.5605 0.500 2310 1317s 2500 -21825.1677 0.500 2310 1317s 2600 -21824.7216 0.500 2310 1318s 2700 -21824.0212 0.500 2310 1318s 2800 -21823.7544 0.500 2310 1319s 2900 -21823.4048 0.500 2310 1319s Optimization precision reduced 1319s Optimizing parameters... improved 0.022 lnL 1319s Optimizing branchlengths... improved 0.703 lnL 1319s 3000 -21822.3847 0.451 2310 1319s 3100 -21822.1483 0.451 2310 1320s 3200 -21822.0345 0.451 2310 1320s 3300 -21821.8346 0.451 2310 1321s 3400 -21818.8729 0.451 3357 1321s 3500 -21818.6120 0.451 3433 1322s 3600 -21818.3439 0.451 3433 1322s 3700 -21817.8649 0.451 3433 1323s 3800 -21817.6748 0.451 3433 1323s 3900 -21817.3859 0.451 3433 1323s 4000 -21817.1732 0.451 3433 1323s Optimization precision reduced 1323s Optimizing parameters... improved 0.014 lnL 1323s Optimizing branchlengths... improved 0.000 lnL 1324s 4100 -21816.9224 0.402 3433 1324s 4200 -21816.7608 0.402 3433 1325s 4300 -21816.7094 0.402 3433 1325s 4400 -21816.4776 0.402 3433 1326s 4500 -21816.4010 0.402 3433 1326s Optimization precision reduced 1326s Optimizing parameters... improved 0.011 lnL 1326s Optimizing branchlengths... improved 0.000 lnL 1326s 4600 -21816.2854 0.353 3433 1327s 4700 -21816.2040 0.353 3433 1327s 4800 -21816.0652 0.353 3433 1327s 4900 -21815.9287 0.353 3433 1328s 5000 -21815.7679 0.353 3433 1328s Optimization precision reduced 1328s Optimizing parameters... improved 0.007 lnL 1328s Optimizing branchlengths... improved 0.000 lnL 1328s 5100 -21815.6606 0.304 3433 1329s 5200 -21815.6414 0.304 3433 1329s 5300 -21815.5269 0.304 3433 1330s 5400 -21815.4991 0.304 3433 1330s 5500 -21815.3804 0.304 3433 1330s Optimization precision reduced 1330s Optimizing parameters... improved 0.014 lnL 1330s Optimizing branchlengths... improved 0.362 lnL 1331s 5600 -21814.9290 0.255 3433 1331s 5700 -21814.9003 0.255 3433 1332s 5800 -21814.8393 0.255 3433 1332s 5900 -21814.7837 0.255 3433 1333s 6000 -21814.7171 0.255 3433 1333s Optimization precision reduced 1333s Optimizing parameters... improved 0.011 lnL 1333s Optimizing branchlengths... improved 0.000 lnL 1333s 6100 -21814.6779 0.206 3433 1334s 6200 -21814.6231 0.206 3433 1334s 6300 -21814.5497 0.206 3433 1334s 6400 -21814.4964 0.206 3433 1335s 6500 -21814.4545 0.206 3433 1335s Optimization precision reduced 1335s Optimizing parameters... improved 0.007 lnL 1335s Optimizing branchlengths... improved 0.207 lnL 1335s 6600 -21814.2290 0.157 3433 1336s 6700 -21814.1729 0.157 3433 1336s 6800 -21814.1353 0.157 3433 1337s 6900 -21814.0848 0.157 3433 1337s 7000 -21814.0807 0.157 3433 1337s Optimization precision reduced 1337s Optimizing parameters... improved 0.005 lnL 1337s Optimizing branchlengths... improved 0.252 lnL 1338s 7100 -21813.8026 0.108 3433 1338s 7200 -21813.7886 0.108 3433 1339s 7300 -21813.7470 0.108 3433 1339s 7400 -21813.6988 0.108 3433 1340s 7500 -21813.6696 0.108 3433 1340s Optimization precision reduced 1340s Optimizing parameters... improved 0.101 lnL 1340s Optimizing branchlengths... improved 0.247 lnL 1341s 7600 -21813.3064 0.059 3433 1341s 7700 -21813.2741 0.059 3433 1342s 7800 -21813.2134 0.059 3433 1342s 7900 -21813.2115 0.059 3433 1343s 8000 -21813.1878 0.059 3433 1343s Optimization precision reduced 1343s Optimizing parameters... improved 0.012 lnL 1343s Optimizing branchlengths... improved 0.210 lnL 1343s 8100 -21812.9599 0.010 3433 1344s 8200 -21812.9507 0.010 3433 1345s 8300 -21812.9369 0.010 3433 1345s 8400 -21812.9332 0.010 3433 1346s 8500 -21812.9319 0.010 3433 1347s 8600 -21812.9260 0.010 3433 1347s 8700 -21812.9196 0.010 3433 1348s 8800 -21812.9188 0.010 3433 1349s 8900 -21812.9179 0.010 3433 1349s 9000 -21812.9131 0.010 3433 1350s 9100 -21812.9091 0.010 3433 1351s 9200 -21812.9063 0.010 3433 1351s 9300 -21812.9063 0.010 3433 1352s 9400 -21812.9027 0.010 3433 1352s 9500 -21812.8991 0.010 3433 1353s 9600 -21812.8991 0.010 3433 1354s 9700 -21812.8978 0.010 3433 1355s 9800 -21812.8971 0.010 3433 1355s 9900 -21812.8966 0.010 3433 1356s 10000 -21812.8941 0.010 3433 1357s 10100 -21812.8854 0.010 3433 1357s 10200 -21812.8826 0.010 3433 1358s 10300 -21812.8826 0.010 3433 1358s 10400 -21812.8815 0.010 3433 1359s 10500 -21812.8660 0.010 3433 1360s 10600 -21812.8615 0.010 3433 1360s 10700 -21812.8572 0.010 3433 1361s 10800 -21812.8572 0.010 3433 1362s 10900 -21812.8463 0.010 3433 1362s 11000 -21812.8418 0.010 3433 1363s 11100 -21812.8418 0.010 3433 1364s 11200 -21812.8354 0.010 3433 1364s 11300 -21812.8354 0.010 3433 1365s 11400 -21812.8311 0.010 3433 1366s 11500 -21812.8309 0.010 3433 1366s 11600 -21812.8280 0.010 3433 1367s 11700 -21812.8236 0.010 3433 1367s 11800 -21812.8236 0.010 3433 1368s 11900 -21812.8236 0.010 3433 1369s 12000 -21812.8175 0.010 3433 1369s 12100 -21812.8175 0.010 3433 1370s 12200 -21812.8162 0.010 3433 1371s 12300 -21812.8127 0.010 3433 1371s 12400 -21812.8112 0.010 3433 1372s 12500 -21812.8112 0.010 3433 1373s 12600 -21812.8093 0.010 3433 1373s 12700 -21812.8060 0.010 3433 1374s 12800 -21812.8029 0.010 3433 1375s 12900 -21812.7974 0.010 3433 1375s 13000 -21812.7974 0.010 3433 1376s 13100 -21812.7964 0.010 3433 1377s 13200 -21812.7896 0.010 3433 1377s 13300 -21812.7885 0.010 3433 1378s 13400 -21812.7885 0.010 3433 1378s 13500 -21812.7885 0.010 3433 1379s 13600 -21812.7885 0.010 3433 1380s 13700 -21812.7884 0.010 3433 1380s 13800 -21812.7884 0.010 3433 1381s 13900 -21812.7884 0.010 3433 1382s 14000 -21812.7855 0.010 3433 1382s 14100 -21812.7855 0.010 3433 1383s 14200 -21812.7850 0.010 3433 1384s 14300 -21812.7850 0.010 3433 1384s 14400 -21812.7850 0.010 3433 1385s 14500 -21812.7838 0.010 3433 1386s 14600 -21812.7838 0.010 3433 1386s 14700 -21812.7830 0.010 3433 1387s 14800 -21812.7827 0.010 3433 1388s 14900 -21812.7802 0.010 3433 1388s 15000 -21812.7802 0.010 3433 1388s Optimizing parameters... improved 0.000 lnL 1388s Optimizing branchlengths... improved 0.000 lnL 1389s 15100 -21812.7787 0.010 3433 1390s 15200 -21812.7780 0.010 3433 1390s 15300 -21812.7777 0.010 3433 1391s 15400 -21812.7761 0.010 3433 1392s 15500 -21812.7716 0.010 3433 1392s 15600 -21812.7671 0.010 3433 1393s 15700 -21812.7647 0.010 3433 1394s 15800 -21812.7611 0.010 3433 1394s 15900 -21812.7586 0.010 3433 1395s 16000 -21812.7561 0.010 3433 1396s 16100 -21812.7561 0.010 3433 1396s 16200 -21812.7561 0.010 3433 1397s 16300 -21812.7554 0.010 3433 1398s 16400 -21812.7508 0.010 3433 1398s 16500 -21812.7503 0.010 3433 1399s 16600 -21812.7466 0.010 3433 1400s 16700 -21812.7464 0.010 3433 1400s 16800 -21812.7462 0.010 3433 1401s 16900 -21812.7451 0.010 3433 1402s 17000 -21812.7450 0.010 3433 1402s 17100 -21812.7450 0.010 3433 1403s 17200 -21812.7447 0.010 3433 1403s 17300 -21812.7447 0.010 3433 1404s 17400 -21812.7447 0.010 3433 1405s 17500 -21812.7445 0.010 3433 1405s 17600 -21812.7445 0.010 3433 1406s 17700 -21812.7443 0.010 3433 1407s 17800 -21812.7443 0.010 3433 1407s 17900 -21812.7427 0.010 3433 1408s 18000 -21812.7424 0.010 3433 1409s 18100 -21812.7405 0.010 3433 1409s 18200 -21812.7405 0.010 3433 1410s 18300 -21812.7405 0.010 3433 1411s 18400 -21812.7403 0.010 3433 1411s 18500 -21812.7399 0.010 3433 1412s 18600 -21812.7390 0.010 3433 1412s 18700 -21812.7381 0.010 3433 1413s 18800 -21812.7366 0.010 3433 1414s 18900 -21812.7366 0.010 3433 1414s 19000 -21812.7366 0.010 3433 1415s 19100 -21812.7348 0.010 3433 1416s 19200 -21812.7342 0.010 3433 1416s 19300 -21812.7342 0.010 3433 1417s 19400 -21812.7336 0.010 3433 1418s 19500 -21812.7336 0.010 3433 1418s 19600 -21812.7336 0.010 3433 1419s 19700 -21812.7336 0.010 3433 1420s 19800 -21812.7336 0.010 3433 1420s 19900 -21812.7336 0.010 3433 1421s 20000 -21812.7245 0.010 3433 1421s Optimizing parameters... improved 0.000 lnL 1421s Optimizing branchlengths... improved 0.000 lnL 1422s 20100 -21812.7226 0.010 3433 1422s 20200 -21812.7226 0.010 3433 1423s 20300 -21812.7222 0.010 3433 1424s 20400 -21812.7210 0.010 3433 1424s 20500 -21812.7192 0.010 3433 1425s 20600 -21812.7169 0.010 3433 1426s 20700 -21812.7148 0.010 3433 1426s 20800 -21812.7132 0.010 3433 1427s 20900 -21812.7130 0.010 3433 1428s 21000 -21812.7130 0.010 3433 1428s 21100 -21812.7130 0.010 3433 1429s 21200 -21812.7130 0.010 3433 1429s 21300 -21812.7108 0.010 3433 1430s 21400 -21812.7107 0.010 3433 1431s 21500 -21812.7095 0.010 3433 1431s 21600 -21812.7095 0.010 3433 1432s 21700 -21812.7095 0.010 3433 1433s 21800 -21812.7095 0.010 3433 1433s 21900 -21812.7086 0.010 3433 1434s 22000 -21812.7086 0.010 3433 1435s 22100 -21812.7086 0.010 3433 1435s 22200 -21812.7085 0.010 3433 1436s 22300 -21812.7085 0.010 3433 1436s 22400 -21812.7085 0.010 3433 1437s 22500 -21812.7071 0.010 3433 1438s 22600 -21812.7071 0.010 3433 1438s 22700 -21812.7043 0.010 3433 1439s 22800 -21812.7043 0.010 3433 1440s 22900 -21812.7025 0.010 3433 1440s 23000 -21812.7024 0.010 3433 1441s 23100 -21812.7024 0.010 3433 1441s 23200 -21812.7024 0.010 3433 1442s 23300 -21812.7024 0.010 3433 1443s 23400 -21812.7024 0.010 3433 1443s 23500 -21812.7024 0.010 3433 1444s 23600 -21812.7024 0.010 3433 1445s 23700 -21812.7019 0.010 3433 1445s 23800 -21812.7019 0.010 3433 1446s 23900 -21812.7017 0.010 3433 1447s 24000 -21812.7017 0.010 3433 1447s 24100 -21812.7017 0.010 3433 1448s 24200 -21812.7017 0.010 3433 1448s 24300 -21812.6999 0.010 3433 1449s 24400 -21812.6999 0.010 3433 1450s 24500 -21812.6997 0.010 3433 1450s 24600 -21812.6997 0.010 3433 1451s 24700 -21812.6994 0.010 3433 1452s 24800 -21812.6994 0.010 3433 1452s 24900 -21812.6994 0.010 3433 1453s 25000 -21812.6994 0.010 3433 1453s Optimizing parameters... improved 0.000 lnL 1453s Optimizing branchlengths... improved 0.000 lnL 1454s 25100 -21812.6977 0.010 3433 1454s 25200 -21812.6977 0.010 3433 1455s 25300 -21812.6977 0.010 3433 1455s 25400 -21812.6961 0.010 3433 1456s 25500 -21812.6957 0.010 3433 1457s 25600 -21812.6953 0.010 3433 1457s 25700 -21812.6953 0.010 3433 1458s 25800 -21812.6953 0.010 3433 1459s 25900 -21812.6953 0.010 3433 1459s 26000 -21812.6953 0.010 3433 1460s 26100 -21812.6953 0.010 3433 1461s 26200 -21812.6930 0.010 3433 1461s 26300 -21812.6893 0.010 3433 1462s 26400 -21812.6893 0.010 3433 1463s 26500 -21812.6893 0.010 3433 1463s 26600 -21812.6893 0.010 3433 1464s 26700 -21812.6893 0.010 3433 1465s 26800 -21812.6878 0.010 3433 1465s 26900 -21812.6878 0.010 3433 1466s 27000 -21812.6878 0.010 3433 1467s 27100 -21812.6873 0.010 3433 1467s 27200 -21812.6873 0.010 3433 1468s 27300 -21812.6867 0.010 3433 1469s 27400 -21812.6866 0.010 3433 1469s 27500 -21812.6866 0.010 3433 1470s 27600 -21812.6866 0.010 3433 1470s 27700 -21812.6864 0.010 3433 1471s 27800 -21812.6864 0.010 3433 1472s 27900 -21812.6864 0.010 3433 1472s 28000 -21812.6864 0.010 3433 1473s 28100 -21812.6864 0.010 3433 1473s Reached termination condition! 1473s last topological improvement at gen 3433 1473s Improvement over last 500 gen = 0.00023 1473s Current score = -21812.6864 1473s Performing final optimizations... 1473s pass 1 : -21812.6860 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0002) 1473s pass 2 : -21812.6746 (branch= 0.0110 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0002) 1473s pass 3 : -21812.6727 (branch= 0.0015 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0001) 1473s pass 4 : -21812.6626 (branch= 0.0099 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0001) 1473s pass 5 : -21812.6530 (branch= 0.0085 alpha= 0.0005 pinv= 0.0003 eq freqs= 0.0001 rel rates= 0.0001) 1474s pass 6 : -21812.6468 (branch= 0.0050 alpha= 0.0003 pinv= 0.0002 eq freqs= 0.0003 rel rates= 0.0003) 1474s pass 7 : -21812.6438 (branch= 0.0025 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0001) 1474s pass 8 : -21812.6427 (branch= 0.0008 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0001) 1474s pass 9 : -21812.6422 (branch= 0.0002 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0001) 1474s pass 10: -21812.6418 (branch= 0.0003 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1474s pass 11: -21812.6416 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1474s pass 12: -21812.6415 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1474s pass 13: -21812.6415 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1474s pass 14: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1475s pass 15: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1475s pass 16: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1475s pass 17: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1475s Looking for minimum length branches... 1475s Final score = -21812.6414 1475s Time used = 0 hours, 5 minutes and 37 seconds 1475s 1475s MODEL REPORT - Parameter values are FINAL 1475s Model 1 1475s Number of states = 4 (nucleotide data) 1475s Nucleotide Relative Rate Matrix: 6 rates 1475s AC = 2.214, AG = 8.155, AT = 2.356, CG = 0.918, CT = 16.505, GT = 1.000 1475s Equilibrium State Frequencies: estimated 1475s (ACGT) 0.3476 0.2126 0.1499 0.2899 1475s Rate Heterogeneity Model: 1475s 4 discrete gamma distributed rate categories, alpha param estimated 1475s 0.5605 1475s with an invariant (invariable) site category, proportion estimated 1475s 0.3385 1475s Substitution rate categories under this model: 1475s rate proportion 1475s 0.0000 0.3385 1475s 0.0451 0.1654 1475s 0.2896 0.1654 1475s 0.8597 0.1654 1475s 2.8056 0.1654 1475s 1475s NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1475s No branches were short enough to be collapsed. 1475s 1475s >>>Completed Search rep 2 (of 2)<<< 1475s 1475s ####################################################### 1475s 1475s Completed 2 replicate search(es) (of 2). 1475s 1475s NOTE: Unless the following output indicates that search replicates found the 1475s same topology, you should assume that they found different topologies. 1475s Results: 1475s Replicate 1 : -21812.6414 (best) 1475s Replicate 2 : -21812.6414 (same topology as 1) 1475s 1475s Parameter estimates across search replicates: 1475s r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv 1475s rep 1: 2.214 8.157 2.357 0.9181 16.51 1 0.348 0.213 0.150 0.290 0.560 0.338 1475s rep 2: 2.214 8.155 2.356 0.918 16.5 1 0.348 0.213 0.150 0.290 0.561 0.338 1475s 1475s Treelengths: 1475s TL 1475s rep 1: 2.940 1475s rep 2: 2.941 1475s 1475s Saving final trees from all search reps to rana.nuc.GTRIG.best.all.tre 1475s 1475s Saving final tree from best search rep (#1) to rana.nuc.GTRIG.best.tre 1475s ####################################################### 1475s autopkgtest [04:05:33]: test run-unit-test: -----------------------] 1475s autopkgtest [04:05:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1475s run-unit-test PASS 1476s autopkgtest [04:05:34]: @@@@@@@@@@@@@@@@@@@@ summary 1476s run-unit-test PASS 1486s Creating nova instance adt-noble-amd64-garli-20240326-034058-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240325.img (UUID ba43860b-557a-4db2-b3f0-378a99bca08c)...