0s autopkgtest [00:17:28]: starting date: 2024-03-19 0s autopkgtest [00:17:28]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [00:17:28]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mpjgrmt6/out --timeout-copy=6000 --setup-commands 'sed -i "s/ports.ubuntu.com/ftpmaster.internal/; s/ubuntu-ports/ubuntu/" /etc/apt/sources.list `ls /etc/apt/sources.list.d/*.list 2>/dev/null || true`; ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.44.124.111 lxd-armhf-10.44.124.111:autopkgtest/ubuntu/noble/armhf 62s autopkgtest [00:18:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 66s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3736 kB] 69s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 69s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 69s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 69s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [585 kB] 69s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 69s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 69s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 69s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3609 kB] 70s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 70s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [35.6 kB] 70s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 85s Fetched 8639 kB in 7s (1328 kB/s) 87s Reading package lists... 107s tee: /proc/self/fd/2: Permission denied 144s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 144s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 144s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 144s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease 144s Hit:5 http://ftpmaster.internal/ubuntu noble-security InRelease 144s Hit:6 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 144s Hit:7 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 144s Hit:8 http://ftpmaster.internal/ubuntu noble-proposed InRelease 153s Reading package lists... 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 157s Calculating upgrade... 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 160s Building dependency tree... 160s Reading state information... 163s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s autopkgtest [00:20:15]: rebooting testbed after setup commands that affected boot 203s autopkgtest [00:20:51]: testbed running kernel: Linux 5.4.0-170-generic #188-Ubuntu SMP Wed Jan 10 09:51:10 UTC 2024 208s autopkgtest [00:20:56]: testbed dpkg architecture: armhf 223s autopkgtest [00:21:11]: @@@@@@@@@@@@@@@@@@@@ apt-source garli 232s Get:1 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (dsc) [2047 B] 232s Get:2 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (tar) [1249 kB] 232s Get:3 http://ftpmaster.internal/ubuntu noble/universe garli 2.1-7 (diff) [4788 B] 233s gpgv: Signature made Sun Feb 20 14:34:04 2022 UTC 233s gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 233s gpgv: Can't check signature: No public key 233s dpkg-source: warning: cannot verify inline signature for ./garli_2.1-7.dsc: no acceptable signature found 233s autopkgtest [00:21:21]: testing package garli version 2.1-7 233s autopkgtest [00:21:21]: build not needed 237s autopkgtest [00:21:25]: test run-unit-test: preparing testbed 253s Reading package lists... 255s Building dependency tree... 255s Reading state information... 256s Correcting dependencies...Starting pkgProblemResolver with broken count: 1 256s Starting 2 pkgProblemResolver with broken count: 1 256s Investigating (0) garli-mpi:armhf < none -> 2.1-7 @un uN Ib > 256s Broken garli-mpi:armhf Depends on libopenmpi3:armhf < none | 4.1.6-5ubuntu1 @un uH > (>= 4.1.2) 256s Considering libopenmpi3:armhf 0 as a solution to garli-mpi:armhf 0 256s Holding Back garli-mpi:armhf rather than change libopenmpi3:armhf 256s Investigating (0) autopkgtest-satdep:armhf < 0 @iU K Nb Ib > 256s Broken autopkgtest-satdep:armhf Depends on garli-mpi:armhf < none | 2.1-7 @un uH > 256s Considering garli-mpi:armhf 0 as a solution to autopkgtest-satdep:armhf -2 256s Removing autopkgtest-satdep:armhf rather than change garli-mpi:armhf 256s Done 258s Done 259s Starting pkgProblemResolver with broken count: 0 260s Starting 2 pkgProblemResolver with broken count: 0 260s Done 262s The following packages will be REMOVED: 262s autopkgtest-satdep 263s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 263s 1 not fully installed or removed. 263s After this operation, 0 B of additional disk space will be used. 263s (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 ... 58620 files and directories currently installed.) 263s Removing autopkgtest-satdep (0) ... 270s autopkgtest: WARNING: package garli is not installed though it should be 274s autopkgtest: WARNING: package garli-mpi is not installed though it should be 279s autopkgtest: WARNING: package garli-examples is not installed though it should be 281s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from noble-proposed 292s Reading package lists... 293s Building dependency tree... 293s Reading state information... 295s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 297s Done 298s Starting pkgProblemResolver with broken count: 0 299s Starting 2 pkgProblemResolver with broken count: 0 299s Done 301s The following additional packages will be installed: 301s garli garli-examples garli-mpi libevent-core-2.1-7 libevent-pthreads-2.1-7 301s libfabric1 libhwloc-plugins libhwloc15 libmunge2 libncl2 libopenmpi3t64 301s libpciaccess0 libpmix2t64 librdmacm1t64 libxnvctrl0 ocl-icd-libopencl1 301s openmpi-bin openmpi-common 301s Suggested packages: 301s opencl-icd gfortran | fortran-compiler 301s The following NEW packages will be installed: 301s garli garli-examples garli-mpi libevent-pthreads-2.1-7 libfabric1 301s libhwloc-plugins libhwloc15 libmunge2 libncl2 libopenmpi3t64 libpciaccess0 301s libpmix2t64 librdmacm1t64 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin 301s openmpi-common 301s The following packages will be upgraded: 301s libevent-core-2.1-7 302s 1 upgraded, 17 newly installed, 0 to remove and 226 not upgraded. 302s 1 not fully installed or removed. 302s Need to get 5381 kB of archives. 302s After this operation, 14.0 MB of additional disk space will be used. 302s Get:1 http://ftpmaster.internal/ubuntu noble/universe armhf libncl2 armhf 2.1.21+git20210811.b1213a7-5 [407 kB] 303s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf garli armhf 2.1-7build1 [580 kB] 303s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 303s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-9build1 [7370 B] 303s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librdmacm1t64 armhf 50.0-2build1 [63.0 kB] 303s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libfabric1 armhf 1.17.0-3build1 [419 kB] 303s Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc15 armhf 2.10.0-1 [145 kB] 303s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmunge2 armhf 0.5.15-4 [17.1 kB] 303s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libpciaccess0 armhf 0.17-3 [16.3 kB] 303s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libxnvctrl0 armhf 510.47.03-0ubuntu1 [10.4 kB] 303s Get:11 http://ftpmaster.internal/ubuntu noble/universe armhf ocl-icd-libopencl1 armhf 2.3.2-1 [34.4 kB] 303s Get:12 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc-plugins armhf 2.10.0-1 [13.7 kB] 303s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpmix2t64 armhf 5.0.1-4.1 [616 kB] 303s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libopenmpi3t64 armhf 4.1.6-7ubuntu1 [2041 kB] 303s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-common all 4.1.6-7ubuntu1 [170 kB] 303s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-bin armhf 4.1.6-7ubuntu1 [83.2 kB] 303s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf garli-mpi armhf 2.1-7build1 [554 kB] 304s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf garli-examples all 2.1-7build1 [120 kB] 305s Fetched 5381 kB in 2s (2872 kB/s) 305s Selecting previously unselected package libncl2:armhf. 306s (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 ... 58620 files and directories currently installed.) 306s Preparing to unpack .../00-libncl2_2.1.21+git20210811.b1213a7-5_armhf.deb ... 306s Unpacking libncl2:armhf (2.1.21+git20210811.b1213a7-5) ... 306s Selecting previously unselected package garli. 306s Preparing to unpack .../01-garli_2.1-7build1_armhf.deb ... 306s Unpacking garli (2.1-7build1) ... 306s Preparing to unpack .../02-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 306s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 307s Selecting previously unselected package libevent-pthreads-2.1-7:armhf. 307s Preparing to unpack .../03-libevent-pthreads-2.1-7_2.1.12-stable-9build1_armhf.deb ... 307s Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 307s Selecting previously unselected package librdmacm1t64:armhf. 307s Preparing to unpack .../04-librdmacm1t64_50.0-2build1_armhf.deb ... 307s Unpacking librdmacm1t64:armhf (50.0-2build1) ... 307s Selecting previously unselected package libfabric1:armhf. 307s Preparing to unpack .../05-libfabric1_1.17.0-3build1_armhf.deb ... 307s Unpacking libfabric1:armhf (1.17.0-3build1) ... 307s Selecting previously unselected package libhwloc15:armhf. 307s Preparing to unpack .../06-libhwloc15_2.10.0-1_armhf.deb ... 307s Unpacking libhwloc15:armhf (2.10.0-1) ... 307s Selecting previously unselected package libmunge2:armhf. 307s Preparing to unpack .../07-libmunge2_0.5.15-4_armhf.deb ... 307s Unpacking libmunge2:armhf (0.5.15-4) ... 307s Selecting previously unselected package libpciaccess0:armhf. 307s Preparing to unpack .../08-libpciaccess0_0.17-3_armhf.deb ... 307s Unpacking libpciaccess0:armhf (0.17-3) ... 308s Selecting previously unselected package libxnvctrl0:armhf. 308s Preparing to unpack .../09-libxnvctrl0_510.47.03-0ubuntu1_armhf.deb ... 308s Unpacking libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 308s Selecting previously unselected package ocl-icd-libopencl1:armhf. 308s Preparing to unpack .../10-ocl-icd-libopencl1_2.3.2-1_armhf.deb ... 308s Unpacking ocl-icd-libopencl1:armhf (2.3.2-1) ... 308s Selecting previously unselected package libhwloc-plugins:armhf. 308s Preparing to unpack .../11-libhwloc-plugins_2.10.0-1_armhf.deb ... 308s Unpacking libhwloc-plugins:armhf (2.10.0-1) ... 308s Selecting previously unselected package libpmix2t64:armhf. 308s Preparing to unpack .../12-libpmix2t64_5.0.1-4.1_armhf.deb ... 308s Unpacking libpmix2t64:armhf (5.0.1-4.1) ... 308s Selecting previously unselected package libopenmpi3t64:armhf. 308s Preparing to unpack .../13-libopenmpi3t64_4.1.6-7ubuntu1_armhf.deb ... 308s Unpacking libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 309s Selecting previously unselected package openmpi-common. 309s Preparing to unpack .../14-openmpi-common_4.1.6-7ubuntu1_all.deb ... 309s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 309s Selecting previously unselected package openmpi-bin. 309s Preparing to unpack .../15-openmpi-bin_4.1.6-7ubuntu1_armhf.deb ... 309s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 310s Selecting previously unselected package garli-mpi. 310s Preparing to unpack .../16-garli-mpi_2.1-7build1_armhf.deb ... 310s Unpacking garli-mpi (2.1-7build1) ... 310s Selecting previously unselected package garli-examples. 310s Preparing to unpack .../17-garli-examples_2.1-7build1_all.deb ... 310s Unpacking garli-examples (2.1-7build1) ... 310s Setting up libpciaccess0:armhf (0.17-3) ... 310s Setting up libncl2:armhf (2.1.21+git20210811.b1213a7-5) ... 310s Setting up libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 310s Setting up garli-examples (2.1-7build1) ... 310s Setting up garli (2.1-7build1) ... 310s Setting up libmunge2:armhf (0.5.15-4) ... 310s Setting up libhwloc15:armhf (2.10.0-1) ... 310s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 310s Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ... 310s Setting up openmpi-common (4.1.6-7ubuntu1) ... 310s Setting up librdmacm1t64:armhf (50.0-2build1) ... 310s Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 310s Setting up libfabric1:armhf (1.17.0-3build1) ... 310s Setting up libhwloc-plugins:armhf (2.10.0-1) ... 310s Setting up libpmix2t64:armhf (5.0.1-4.1) ... 310s Setting up libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 310s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 310s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 310s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 310s Setting up garli-mpi (2.1-7build1) ... 310s Setting up autopkgtest-satdep (0) ... 310s Processing triggers for man-db (2.12.0-3) ... 314s Processing triggers for libc-bin (2.39-0ubuntu2) ... 341s (Reading database ... 59147 files and directories currently installed.) 341s Removing autopkgtest-satdep (0) ... 353s autopkgtest [00:23:21]: test run-unit-test: [----------------------- 356s Running GARLI Version 2.1. () 356s ->Single processor version for 32-bit OS<- 356s ############################################################## 356s This is GARLI 2.1: maximum likelihood phylogenetic inference 356s using nucleotide, amino acid, codon and morphology-like data, 356s as well as partitioned models. 356s General program usage is extensively documented here: 356s http://www.nescent.org/wg/garli/ 356s See this page for details on partitioned model usage: 356s http://www.nescent.org/wg_garli/Using_partitioned_models 356s and this page for details on Mkv mophology model usage: 356s http://www.nescent.org/wg_garli/Mkv_morphology_model 356s PLEASE LET ME KNOW OF ANY PROBLEMS AT: 356s garli.support@gmail.com 356s ############################################################## 356s Compiled Mar 13 2024 18:25:21 using GNU gcc compiler version 13.2.0 356s Using NCL version 2.1.17 356s 356s ####################################################### 356s Reading config file garli.conf 356s ################################################### 356s READING OF DATA 356s Attempting to read data file in Nexus format (using NCL): 356s rana.nex ... 356s storing implied block: TAXA 356s storing read block: DATA 356s Reading DATA block... successful 356s 356s ################################################### 356s PARTITIONING OF DATA AND MODELS 356s GARLI data subset 1 356s CHARACTERS block #1 ("Untitled DATA Block 1") 356s Data read as Nucleotide data, 356s modeled as Nucleotide data 356s Summary of data: 356s 64 sequences. 356s 1062 constant characters. 356s 664 parsimony-informative characters. 356s 250 uninformative variable characters. 356s 1976 total characters. 356s 890 unique patterns in compressed data matrix. 356s 356s ################################################### 356s NOTE: Unlike many programs, the amount of system memory that Garli will 356s use can be controlled by the user. 356s (This comes from the availablememory setting in the configuration file. 356s Availablememory should NOT be set to more than the actual amount of 356s physical memory that your computer has installed) 356s 356s For this dataset: 356s Mem level availablememory setting 356s great >= 70 MB 356s good approx 69 MB to 45 MB 356s low approx 44 MB to 19 MB 356s very low approx 18 MB to 15 MB 356s the minimum required availablememory is 15 MB 356s 356s You specified that Garli should use at most 512.0 MB of memory. 356s 356s Garli will actually use approx. 104.2 MB of memory 356s **Your memory level is: great (you don't need to change anything)** 356s 356s ####################################################### 356s Found outgroup specification: 1 356s 356s ####################################################### 356s STARTING RUN 356s 356s >>>Search rep 1 (of 2)<<< 356s MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 356s Model 1 356s Number of states = 4 (nucleotide data) 356s Nucleotide Relative Rate Matrix: 6 rates 356s AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 356s Equilibrium State Frequencies: estimated 356s (ACGT) 0.3381 0.2238 0.1789 0.2592 356s Rate Heterogeneity Model: 356s 4 discrete gamma distributed rate categories, alpha param estimated 356s 0.5000 356s with an invariant (invariable) site category, proportion estimated 356s 0.1344 356s Substitution rate categories under this model: 356s rate proportion 356s 0.0000 0.1344 356s 0.0334 0.2164 356s 0.2519 0.2164 356s 0.8203 0.2164 356s 2.8944 0.2164 356s 356s Starting with seed=116033 356s 356s creating likelihood stepwise addition starting tree... 356s number of taxa added: 361s 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 361s Optimizing parameters... improved 37.552 lnL 361s Optimizing branchlengths... improved 16.042 lnL 371s 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 371s Initial ln Likelihood: -22742.0173 371s optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... 372s pass 1:+ 339.462 (branch= 83.47 scale= 7.10 alpha= 0.01 freqs=126.10 rel rates=115.48 pinv= 7.30) 373s pass 2:+ 53.163 (branch= 8.28 scale= 0.00 alpha= 3.16 freqs= 30.16 rel rates= 7.60 pinv= 3.96) 373s pass 3:+ 16.038 (branch= 2.71 scale= 0.00 alpha= 4.33 freqs= 2.16 rel rates= 5.41 pinv= 1.43) 374s pass 4:+ 9.773 (branch= 0.00 scale= 0.00 alpha= 2.39 freqs= 0.80 rel rates= 5.48 pinv= 1.10) 374s pass 5:+ 6.269 (branch= 0.00 scale= 0.00 alpha= 1.38 freqs= 0.73 rel rates= 3.33 pinv= 0.84) 375s pass 6:+ 4.398 (branch= 0.00 scale= 0.00 alpha= 0.98 freqs= 0.20 rel rates= 2.61 pinv= 0.61) 376s pass 7:+ 3.776 (branch= 0.00 scale= 0.00 alpha= 0.60 freqs= 0.15 rel rates= 3.00 pinv= 0.03) 376s pass 8:+ 1.239 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.12 rel rates= 1.09 pinv= 0.03) 376s pass 9:+ 0.167 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.13 rel rates= 0.01 pinv= 0.02) 376s lnL after optimization: -22307.7309 376s gen current_lnL precision last_tree_imp 376s 0 -22307.7309 0.500 0 379s 100 -22158.8175 0.500 96 382s 200 -22111.6458 0.500 183 384s 300 -22027.8038 0.500 249 387s 400 -22003.2312 0.500 372 390s 500 -21984.1953 0.500 467 392s 600 -21969.2589 0.500 557 394s 700 -21924.5343 0.500 672 396s 800 -21899.3551 0.500 782 398s 900 -21894.2640 0.500 885 400s 1000 -21891.1125 0.500 979 402s 1100 -21887.6606 0.500 979 404s 1200 -21878.8844 0.500 1143 406s 1300 -21876.4736 0.500 1143 408s 1400 -21865.7272 0.500 1365 410s 1500 -21864.9978 0.500 1365 412s 1600 -21864.3710 0.500 1365 414s 1700 -21863.7698 0.500 1365 416s 1800 -21863.2315 0.500 1365 419s 1900 -21862.9026 0.500 1365 419s Optimization precision reduced 419s Optimizing parameters... improved 0.062 lnL 419s Optimizing branchlengths... improved 0.000 lnL 421s 2000 -21862.4153 0.451 1365 423s 2100 -21862.1706 0.451 1365 424s 2200 -21861.9399 0.451 1365 426s 2300 -21861.9170 0.451 1365 429s 2400 -21861.7947 0.451 1365 429s Optimization precision reduced 429s Optimizing parameters... improved 0.047 lnL 429s Optimizing branchlengths... improved 0.000 lnL 431s 2500 -21861.4457 0.402 1365 434s 2600 -21861.0274 0.402 1365 436s 2700 -21860.8127 0.402 1365 438s 2800 -21860.6529 0.402 1365 440s 2900 -21860.4212 0.402 1365 440s Optimization precision reduced 440s Optimizing parameters... improved 0.013 lnL 440s Optimizing branchlengths... improved 0.000 lnL 442s 3000 -21860.2060 0.353 1365 444s 3100 -21860.0935 0.353 1365 446s 3200 -21859.9596 0.353 1365 449s 3300 -21859.8921 0.353 1365 451s 3400 -21859.7868 0.353 1365 451s Optimization precision reduced 451s Optimizing parameters... improved 0.006 lnL 451s Optimizing branchlengths... improved 0.000 lnL 453s 3500 -21856.8746 0.304 3458 455s 3600 -21856.7916 0.304 3458 457s 3700 -21855.3935 0.304 3630 458s 3800 -21855.2922 0.304 3630 460s 3900 -21855.0193 0.304 3630 462s 4000 -21854.7632 0.304 3630 464s 4100 -21854.6721 0.304 3630 465s 4200 -21854.5691 0.304 3630 465s Optimization precision reduced 465s Optimizing parameters... improved 0.006 lnL 466s Optimizing branchlengths... improved 0.000 lnL 468s 4300 -21854.5156 0.255 3630 470s 4400 -21854.4647 0.255 3630 471s 4500 -21854.4130 0.255 3630 474s 4600 -21854.3817 0.255 3630 476s 4700 -21854.3474 0.255 3630 476s Optimization precision reduced 476s Optimizing parameters... improved 0.004 lnL 476s Optimizing branchlengths... improved 0.000 lnL 479s 4800 -21854.3237 0.206 3630 481s 4900 -21854.2471 0.206 3630 483s 5000 -21854.1819 0.206 3630 485s 5100 -21854.0797 0.206 3630 487s 5200 -21854.0003 0.206 3630 487s Optimization precision reduced 487s Optimizing parameters... improved 0.006 lnL 487s Optimizing branchlengths... improved 0.160 lnL 489s 5300 -21853.7731 0.157 3630 491s 5400 -21853.6687 0.157 3630 493s 5500 -21853.6600 0.157 3630 495s 5600 -21853.6467 0.157 3630 496s 5700 -21853.6230 0.157 3630 496s Optimization precision reduced 497s Optimizing parameters... improved 0.003 lnL 497s Optimizing branchlengths... improved 0.127 lnL 499s 5800 -21853.4225 0.108 3630 500s 5900 -21853.4200 0.108 3630 502s 6000 -21853.4109 0.108 3630 504s 6100 -21853.3454 0.108 3630 506s 6200 -21853.3066 0.108 3630 506s Optimization precision reduced 506s Optimizing parameters... improved 0.002 lnL 506s Optimizing branchlengths... improved 0.177 lnL 509s 6300 -21853.1105 0.059 3630 511s 6400 -21853.0919 0.059 3630 513s 6500 -21853.0657 0.059 3630 515s 6600 -21853.0604 0.059 3630 517s 6700 -21853.0545 0.059 3630 517s Optimization precision reduced 517s Optimizing parameters... improved 0.001 lnL 517s Optimizing branchlengths... improved 0.389 lnL 520s 6800 -21852.6613 0.010 3630 522s 6900 -21852.6481 0.010 3630 525s 7000 -21852.6475 0.010 3630 527s 7100 -21852.6435 0.010 3630 529s 7200 -21852.6362 0.010 3630 532s 7300 -21852.6318 0.010 3630 534s 7400 -21852.6242 0.010 3630 536s 7500 -21852.6148 0.010 3630 539s 7600 -21852.6053 0.010 3630 541s 7700 -21852.6026 0.010 3630 544s 7800 -21852.6017 0.010 3630 546s 7900 -21852.5797 0.010 3630 548s 8000 -21852.5690 0.010 3630 551s 8100 -21813.3771 0.010 8003 553s 8200 -21813.3740 0.010 8003 555s 8300 -21813.3186 0.010 8003 557s 8400 -21813.3087 0.010 8003 560s 8500 -21813.3000 0.010 8003 562s 8600 -21813.2588 0.010 8003 565s 8700 -21813.2299 0.010 8003 567s 8800 -21813.1998 0.010 8003 570s 8900 -21812.9933 0.010 8003 572s 9000 -21812.9799 0.010 8003 575s 9100 -21812.9652 0.010 8003 579s 9200 -21812.9524 0.010 8003 582s 9300 -21812.9400 0.010 8003 584s 9400 -21812.9328 0.010 8003 587s 9500 -21812.9327 0.010 8003 589s 9600 -21812.9290 0.010 8003 592s 9700 -21812.9220 0.010 8003 594s 9800 -21812.9094 0.010 8003 597s 9900 -21812.9094 0.010 8003 599s 10000 -21812.8894 0.010 8003 602s 10100 -21812.8894 0.010 8003 605s 10200 -21812.8880 0.010 8003 609s 10300 -21812.8880 0.010 8003 611s 10400 -21812.8863 0.010 8003 614s 10500 -21812.8671 0.010 8003 617s 10600 -21812.8669 0.010 8003 620s 10700 -21812.8669 0.010 8003 622s 10800 -21812.8660 0.010 8003 625s 10900 -21812.8607 0.010 8003 627s 11000 -21812.8607 0.010 8003 630s 11100 -21812.8436 0.010 8003 633s 11200 -21812.8432 0.010 8003 636s 11300 -21812.8432 0.010 8003 639s 11400 -21812.8426 0.010 8003 642s 11500 -21812.8426 0.010 8003 646s 11600 -21812.8404 0.010 8003 649s 11700 -21812.8395 0.010 8003 652s 11800 -21812.8375 0.010 8003 654s 11900 -21812.8332 0.010 8003 656s 12000 -21812.8123 0.010 8003 659s 12100 -21812.8112 0.010 8003 662s 12200 -21812.7945 0.010 8003 664s 12300 -21812.7945 0.010 8003 667s 12400 -21812.7886 0.010 8003 669s 12500 -21812.7851 0.010 8003 672s 12600 -21812.7837 0.010 8003 675s 12700 -21812.7808 0.010 8003 679s 12800 -21812.7742 0.010 8003 682s 12900 -21812.7741 0.010 8003 684s 13000 -21812.7737 0.010 8003 687s 13100 -21812.7717 0.010 8003 689s 13200 -21812.7618 0.010 8003 692s 13300 -21812.7573 0.010 8003 694s 13400 -21812.7573 0.010 8003 697s 13500 -21812.7549 0.010 8003 701s 13600 -21812.7547 0.010 8003 704s 13700 -21812.7540 0.010 8003 707s 13800 -21812.7540 0.010 8003 709s 13900 -21812.7540 0.010 8003 712s 14000 -21812.7540 0.010 8003 715s 14100 -21812.7533 0.010 8003 718s 14200 -21812.7533 0.010 8003 721s 14300 -21812.7533 0.010 8003 723s 14400 -21812.7486 0.010 8003 726s 14500 -21812.7482 0.010 8003 728s 14600 -21812.7418 0.010 8003 731s 14700 -21812.7389 0.010 8003 733s 14800 -21812.7389 0.010 8003 735s 14900 -21812.7387 0.010 8003 738s 15000 -21812.7374 0.010 8003 738s Optimizing parameters... improved 0.000 lnL 739s Optimizing branchlengths... improved 0.000 lnL 742s 15100 -21812.7369 0.010 8003 745s 15200 -21812.7369 0.010 8003 747s 15300 -21812.7369 0.010 8003 750s 15400 -21812.7320 0.010 8003 752s 15500 -21812.7302 0.010 8003 756s 15600 -21812.7302 0.010 8003 758s 15700 -21812.7299 0.010 8003 761s 15800 -21812.7299 0.010 8003 764s 15900 -21812.7299 0.010 8003 767s 16000 -21812.7299 0.010 8003 769s 16100 -21812.7297 0.010 8003 772s 16200 -21812.7274 0.010 8003 775s 16300 -21812.7269 0.010 8003 777s 16400 -21812.7257 0.010 8003 780s 16500 -21812.7243 0.010 8003 782s 16600 -21812.7236 0.010 8003 785s 16700 -21812.7236 0.010 8003 788s 16800 -21812.7236 0.010 8003 790s 16900 -21812.7236 0.010 8003 793s 17000 -21812.7234 0.010 8003 796s 17100 -21812.7215 0.010 8003 798s 17200 -21812.7189 0.010 8003 801s 17300 -21812.7183 0.010 8003 803s 17400 -21812.7165 0.010 8003 806s 17500 -21812.7164 0.010 8003 808s 17600 -21812.7129 0.010 8003 811s 17700 -21812.7129 0.010 8003 814s 17800 -21812.7129 0.010 8003 816s 17900 -21812.7117 0.010 8003 819s 18000 -21812.7117 0.010 8003 821s 18100 -21812.7100 0.010 8003 824s 18200 -21812.7094 0.010 8003 826s 18300 -21812.7063 0.010 8003 829s 18400 -21812.7063 0.010 8003 831s 18500 -21812.7055 0.010 8003 834s 18600 -21812.7055 0.010 8003 836s 18700 -21812.7053 0.010 8003 839s 18800 -21812.7052 0.010 8003 841s 18900 -21812.7052 0.010 8003 843s 19000 -21812.7045 0.010 8003 846s 19100 -21812.7036 0.010 8003 849s 19200 -21812.7036 0.010 8003 851s 19300 -21812.7034 0.010 8003 854s 19400 -21812.7034 0.010 8003 856s 19500 -21812.7034 0.010 8003 859s 19600 -21812.7010 0.010 8003 862s 19700 -21812.7010 0.010 8003 865s 19800 -21812.7010 0.010 8003 868s 19900 -21812.7010 0.010 8003 871s 20000 -21812.7010 0.010 8003 871s Optimizing parameters... improved 0.000 lnL 871s Optimizing branchlengths... improved 0.000 lnL 874s 20100 -21812.7006 0.010 8003 877s 20200 -21812.7001 0.010 8003 880s 20300 -21812.7001 0.010 8003 882s 20400 -21812.7001 0.010 8003 885s 20500 -21812.6978 0.010 8003 887s 20600 -21812.6958 0.010 8003 890s 20700 -21812.6945 0.010 8003 892s 20800 -21812.6945 0.010 8003 895s 20900 -21812.6923 0.010 8003 897s 21000 -21812.6923 0.010 8003 900s 21100 -21812.6912 0.010 8003 903s 21200 -21812.6912 0.010 8003 905s 21300 -21812.6912 0.010 8003 907s 21400 -21812.6912 0.010 8003 910s 21500 -21812.6906 0.010 8003 913s 21600 -21812.6906 0.010 8003 915s 21700 -21812.6906 0.010 8003 918s 21800 -21812.6906 0.010 8003 920s 21900 -21812.6906 0.010 8003 923s 22000 -21812.6905 0.010 8003 926s 22100 -21812.6905 0.010 8003 930s 22200 -21812.6905 0.010 8003 935s 22300 -21812.6901 0.010 8003 936s 22400 -21812.6900 0.010 8003 939s 22500 -21812.6900 0.010 8003 943s 22600 -21812.6900 0.010 8003 946s 22700 -21812.6890 0.010 8003 948s 22800 -21812.6890 0.010 8003 951s 22900 -21812.6889 0.010 8003 955s 23000 -21812.6889 0.010 8003 958s 23100 -21812.6881 0.010 8003 960s 23200 -21812.6872 0.010 8003 963s 23300 -21812.6856 0.010 8003 965s 23400 -21812.6856 0.010 8003 968s 23500 -21812.6856 0.010 8003 970s 23600 -21812.6855 0.010 8003 973s 23700 -21812.6855 0.010 8003 976s 23800 -21812.6848 0.010 8003 979s 23900 -21812.6844 0.010 8003 981s 24000 -21812.6844 0.010 8003 983s 24100 -21812.6844 0.010 8003 986s 24200 -21812.6844 0.010 8003 988s 24300 -21812.6844 0.010 8003 990s 24400 -21812.6844 0.010 8003 994s 24500 -21812.6844 0.010 8003 997s 24600 -21812.6834 0.010 8003 1000s 24700 -21812.6834 0.010 8003 1002s 24800 -21812.6832 0.010 8003 1005s 24900 -21812.6832 0.010 8003 1008s 25000 -21812.6832 0.010 8003 1008s Optimizing parameters... improved 0.000 lnL 1008s Optimizing branchlengths... improved 0.000 lnL 1011s 25100 -21812.6830 0.010 8003 1014s 25200 -21812.6830 0.010 8003 1016s 25300 -21812.6830 0.010 8003 1018s 25400 -21812.6830 0.010 8003 1022s 25500 -21812.6830 0.010 8003 1025s 25600 -21812.6824 0.010 8003 1028s 25700 -21812.6824 0.010 8003 1031s 25800 -21812.6824 0.010 8003 1034s 25900 -21812.6822 0.010 8003 1037s 26000 -21812.6822 0.010 8003 1040s 26100 -21812.6822 0.010 8003 1042s 26200 -21812.6822 0.010 8003 1045s 26300 -21812.6822 0.010 8003 1048s 26400 -21812.6822 0.010 8003 1051s 26500 -21812.6822 0.010 8003 1054s 26600 -21812.6821 0.010 8003 1056s 26700 -21812.6821 0.010 8003 1058s 26800 -21812.6817 0.010 8003 1061s 26900 -21812.6817 0.010 8003 1064s 27000 -21812.6812 0.010 8003 1066s 27100 -21812.6810 0.010 8003 1069s 27200 -21812.6800 0.010 8003 1071s 27300 -21812.6800 0.010 8003 1074s 27400 -21812.6800 0.010 8003 1077s 27500 -21812.6779 0.010 8003 1081s 27600 -21812.6775 0.010 8003 1084s 27700 -21812.6775 0.010 8003 1087s 27800 -21812.6761 0.010 8003 1090s 27900 -21812.6760 0.010 8003 1093s 28000 -21812.6760 0.010 8003 1096s 28100 -21812.6760 0.010 8003 1096s Reached termination condition! 1096s last topological improvement at gen 8003 1096s Improvement over last 500 gen = 0.00153 1096s Current score = -21812.6760 1096s Performing final optimizations... 1096s pass 1 : -21812.6757 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0001) 1097s pass 2 : -21812.6755 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0000) 1097s pass 3 : -21812.6701 (branch= 0.0053 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1098s pass 4 : -21812.6562 (branch= 0.0123 alpha= 0.0009 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0000) 1098s pass 5 : -21812.6505 (branch= 0.0046 alpha= 0.0006 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0000) 1099s pass 6 : -21812.6466 (branch= 0.0035 alpha= 0.0003 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0000) 1100s pass 7 : -21812.6431 (branch= 0.0032 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 1100s pass 8 : -21812.6424 (branch= 0.0005 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) 1101s pass 9 : -21812.6418 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1101s pass 10: -21812.6416 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1102s pass 11: -21812.6415 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1103s pass 12: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1103s pass 13: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1104s pass 14: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1105s pass 15: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1105s pass 16: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1106s Looking for minimum length branches... 1106s Final score = -21812.6414 1106s Time used so far = 0 hours, 12 minutes and 29 seconds 1106s 1106s MODEL REPORT - Parameter values are FINAL 1106s Model 1 1106s Number of states = 4 (nucleotide data) 1106s Nucleotide Relative Rate Matrix: 6 rates 1106s AC = 2.218, AG = 8.171, AT = 2.361, CG = 0.920, CT = 16.535, GT = 1.000 1106s Equilibrium State Frequencies: estimated 1106s (ACGT) 0.3476 0.2126 0.1499 0.2899 1106s Rate Heterogeneity Model: 1106s 4 discrete gamma distributed rate categories, alpha param estimated 1106s 0.5605 1106s with an invariant (invariable) site category, proportion estimated 1106s 0.3385 1106s Substitution rate categories under this model: 1106s rate proportion 1106s 0.0000 0.3385 1106s 0.0451 0.1654 1106s 0.2896 0.1654 1106s 0.8598 0.1654 1106s 2.8055 0.1654 1106s 1106s NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1106s No branches were short enough to be collapsed. 1106s 1106s >>>Completed Search rep 1 (of 2)<<< 1106s 1106s >>>Search rep 2 (of 2)<<< 1106s MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 1106s Model 1 1106s Number of states = 4 (nucleotide data) 1106s Nucleotide Relative Rate Matrix: 6 rates 1106s AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 1106s Equilibrium State Frequencies: estimated 1106s (ACGT) 0.3381 0.2238 0.1789 0.2592 1106s Rate Heterogeneity Model: 1106s 4 discrete gamma distributed rate categories, alpha param estimated 1106s 0.5000 1106s with an invariant (invariable) site category, proportion estimated 1106s 0.1344 1106s Substitution rate categories under this model: 1106s rate proportion 1106s 0.0000 0.1344 1106s 0.0334 0.2164 1106s 0.2519 0.2164 1106s 0.8203 0.2164 1106s 2.8944 0.2164 1106s 1106s Starting with seed=311831725 1106s 1106s creating likelihood stepwise addition starting tree... 1106s number of taxa added: 1110s 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 1110s Optimizing parameters... improved 77.457 lnL 1110s Optimizing branchlengths... improved 9.996 lnL 1120s 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 1120s Initial ln Likelihood: -22686.0099 1120s optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... 1121s pass 1:+ 335.662 (branch= 78.55 scale= 11.41 alpha= 0.01 freqs=126.41 rel rates=111.15 pinv= 8.14) 1121s pass 2:+ 46.292 (branch= 2.48 scale= 0.00 alpha= 4.51 freqs= 27.05 rel rates= 6.95 pinv= 5.30) 1121s pass 3:+ 15.858 (branch= 0.42 scale= 0.00 alpha= 6.33 freqs= 2.02 rel rates= 5.33 pinv= 1.75) 1122s pass 4:+ 7.739 (branch= 0.00 scale= 0.00 alpha= 3.11 freqs= 0.72 rel rates= 2.52 pinv= 1.38) 1122s pass 5:+ 6.052 (branch= 0.00 scale= 0.00 alpha= 1.76 freqs= 0.85 rel rates= 2.45 pinv= 0.99) 1123s pass 6:+ 6.465 (branch= 0.00 scale= 0.00 alpha= 1.16 freqs= 0.19 rel rates= 4.44 pinv= 0.67) 1123s pass 7:+ 3.826 (branch= 0.00 scale= 0.00 alpha= 0.66 freqs= 0.15 rel rates= 2.99 pinv= 0.03) 1123s pass 8:+ 0.933 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.15 rel rates= 0.75 pinv= 0.03) 1124s pass 9:+ 0.146 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.10 rel rates= 0.02 pinv= 0.03) 1124s lnL after optimization: -22263.0368 1124s gen current_lnL precision last_tree_imp 1124s 0 -22263.0368 0.500 0 1126s 100 -22185.5997 0.500 99 1128s 200 -22118.3558 0.500 193 1130s 300 -21994.9310 0.500 269 1132s 400 -21906.1877 0.500 387 1134s 500 -21891.4522 0.500 472 1136s 600 -21887.4013 0.500 596 1139s 700 -21884.4302 0.500 638 1141s 800 -21882.4301 0.500 638 1143s 900 -21881.0598 0.500 638 1145s 1000 -21879.1489 0.500 638 1147s 1100 -21871.8382 0.500 1076 1149s 1200 -21869.7278 0.500 1076 1150s 1300 -21831.6993 0.500 1233 1152s 1400 -21830.3589 0.500 1233 1154s 1500 -21829.4473 0.500 1233 1155s 1600 -21826.1978 0.500 1554 1157s 1700 -21825.1996 0.500 1554 1159s 1800 -21824.8756 0.500 1554 1160s 1900 -21823.7602 0.500 1554 1162s 2000 -21822.6044 0.500 1554 1164s 2100 -21821.2310 0.500 1554 1164s Optimization precision reduced 1164s Optimizing parameters... improved 0.075 lnL 1164s Optimizing branchlengths... improved 0.000 lnL 1166s 2200 -21820.8146 0.451 1554 1168s 2300 -21819.8286 0.451 1554 1169s 2400 -21819.2232 0.451 1554 1171s 2500 -21818.4568 0.451 2484 1173s 2600 -21818.0721 0.451 2484 1175s 2700 -21817.8194 0.451 2484 1177s 2800 -21817.5425 0.451 2484 1178s 2900 -21817.2992 0.451 2484 1180s 3000 -21817.0868 0.451 2484 1180s Optimization precision reduced 1180s Optimizing parameters... improved 0.028 lnL 1180s Optimizing branchlengths... improved 0.000 lnL 1182s 3100 -21817.0018 0.402 2484 1184s 3200 -21816.6923 0.402 2484 1186s 3300 -21816.3837 0.402 2484 1188s 3400 -21816.2517 0.402 2484 1190s 3500 -21816.0917 0.402 2484 1190s Optimization precision reduced 1190s Optimizing parameters... improved 0.015 lnL 1190s Optimizing branchlengths... improved 0.000 lnL 1192s 3600 -21815.9322 0.353 2484 1194s 3700 -21815.8305 0.353 2484 1196s 3800 -21815.6436 0.353 2484 1198s 3900 -21815.4903 0.353 2484 1200s 4000 -21815.3890 0.353 2484 1200s Optimization precision reduced 1200s Optimizing parameters... improved 0.013 lnL 1200s Optimizing branchlengths... improved 0.000 lnL 1202s 4100 -21815.3529 0.304 2484 1204s 4200 -21815.2894 0.304 2484 1206s 4300 -21815.2565 0.304 2484 1208s 4400 -21815.1557 0.304 2484 1210s 4500 -21815.1079 0.304 2484 1210s Optimization precision reduced 1210s Optimizing parameters... improved 0.006 lnL 1210s Optimizing branchlengths... improved 0.000 lnL 1213s 4600 -21815.0360 0.255 2484 1214s 4700 -21814.9941 0.255 2484 1216s 4800 -21814.9316 0.255 2484 1218s 4900 -21814.8456 0.255 2484 1220s 5000 -21814.7849 0.255 2484 1220s Optimization precision reduced 1220s Optimizing parameters... improved 0.006 lnL 1220s Optimizing branchlengths... improved 0.000 lnL 1222s 5100 -21814.6582 0.206 2484 1223s 5200 -21814.6542 0.206 2484 1225s 5300 -21814.6133 0.206 2484 1227s 5400 -21814.5713 0.206 2484 1228s 5500 -21814.5232 0.206 2484 1228s Optimization precision reduced 1229s Optimizing parameters... improved 0.006 lnL 1229s Optimizing branchlengths... improved 0.196 lnL 1230s 5600 -21814.2943 0.157 2484 1232s 5700 -21814.2155 0.157 2484 1234s 5800 -21814.1776 0.157 2484 1236s 5900 -21814.1170 0.157 2484 1237s 6000 -21814.0042 0.157 2484 1237s Optimization precision reduced 1237s Optimizing parameters... improved 0.003 lnL 1238s Optimizing branchlengths... improved 0.284 lnL 1239s 6100 -21813.7000 0.108 2484 1241s 6200 -21813.6607 0.108 2484 1243s 6300 -21813.6071 0.108 2484 1245s 6400 -21813.5699 0.108 2484 1247s 6500 -21813.5328 0.108 2484 1247s Optimization precision reduced 1248s Optimizing parameters... improved 0.002 lnL 1248s Optimizing branchlengths... improved 0.197 lnL 1250s 6600 -21813.3187 0.059 2484 1252s 6700 -21813.2935 0.059 2484 1253s 6800 -21813.2769 0.059 2484 1255s 6900 -21813.2532 0.059 2484 1258s 7000 -21813.2372 0.059 2484 1258s Optimization precision reduced 1258s Optimizing parameters... improved 0.038 lnL 1258s Optimizing branchlengths... improved 0.255 lnL 1260s 7100 -21812.9444 0.010 2484 1263s 7200 -21812.9444 0.010 2484 1266s 7300 -21812.9444 0.010 2484 1268s 7400 -21812.9422 0.010 2484 1271s 7500 -21812.9354 0.010 2484 1273s 7600 -21812.9217 0.010 2484 1276s 7700 -21812.9142 0.010 2484 1279s 7800 -21812.9084 0.010 2484 1281s 7900 -21812.9069 0.010 2484 1283s 8000 -21812.8959 0.010 2484 1285s 8100 -21812.8896 0.010 2484 1287s 8200 -21812.8771 0.010 2484 1290s 8300 -21812.8771 0.010 2484 1292s 8400 -21812.8607 0.010 2484 1295s 8500 -21812.8505 0.010 2484 1297s 8600 -21812.8486 0.010 2484 1299s 8700 -21812.8486 0.010 2484 1302s 8800 -21812.8486 0.010 2484 1304s 8900 -21812.8465 0.010 2484 1306s 9000 -21812.8427 0.010 2484 1309s 9100 -21812.8427 0.010 2484 1311s 9200 -21812.8395 0.010 2484 1314s 9300 -21812.8390 0.010 2484 1316s 9400 -21812.8332 0.010 2484 1318s 9500 -21812.8250 0.010 2484 1321s 9600 -21812.8248 0.010 2484 1323s 9700 -21812.8118 0.010 2484 1325s 9800 -21812.8027 0.010 2484 1327s 9900 -21812.8008 0.010 2484 1330s 10000 -21812.7985 0.010 2484 1332s 10100 -21812.7931 0.010 2484 1334s 10200 -21812.7928 0.010 2484 1337s 10300 -21812.7871 0.010 2484 1339s 10400 -21812.7864 0.010 2484 1341s 10500 -21812.7864 0.010 2484 1343s 10600 -21812.7767 0.010 2484 1346s 10700 -21812.7706 0.010 2484 1348s 10800 -21812.7705 0.010 2484 1351s 10900 -21812.7705 0.010 2484 1353s 11000 -21812.7705 0.010 2484 1356s 11100 -21812.7650 0.010 2484 1358s 11200 -21812.7612 0.010 2484 1360s 11300 -21812.7612 0.010 2484 1363s 11400 -21812.7590 0.010 2484 1365s 11500 -21812.7579 0.010 2484 1367s 11600 -21812.7579 0.010 2484 1370s 11700 -21812.7548 0.010 2484 1373s 11800 -21812.7545 0.010 2484 1375s 11900 -21812.7545 0.010 2484 1377s 12000 -21812.7527 0.010 2484 1380s 12100 -21812.7513 0.010 2484 1382s 12200 -21812.7497 0.010 2484 1385s 12300 -21812.7491 0.010 2484 1387s 12400 -21812.7471 0.010 2484 1390s 12500 -21812.7440 0.010 2484 1392s 12600 -21812.7440 0.010 2484 1395s 12700 -21812.7437 0.010 2484 1397s 12800 -21812.7409 0.010 2484 1400s 12900 -21812.7409 0.010 2484 1402s 13000 -21812.7408 0.010 2484 1404s 13100 -21812.7408 0.010 2484 1407s 13200 -21812.7408 0.010 2484 1409s 13300 -21812.7394 0.010 2484 1412s 13400 -21812.7363 0.010 2484 1414s 13500 -21812.7339 0.010 2484 1418s 13600 -21812.7339 0.010 2484 1420s 13700 -21812.7337 0.010 2484 1423s 13800 -21812.7233 0.010 2484 1425s 13900 -21812.7233 0.010 2484 1428s 14000 -21812.7233 0.010 2484 1430s 14100 -21812.7207 0.010 2484 1432s 14200 -21812.7206 0.010 2484 1434s 14300 -21812.7179 0.010 2484 1437s 14400 -21812.7179 0.010 2484 1439s 14500 -21812.7178 0.010 2484 1441s 14600 -21812.7160 0.010 2484 1444s 14700 -21812.7160 0.010 2484 1446s 14800 -21812.7159 0.010 2484 1449s 14900 -21812.7159 0.010 2484 1451s 15000 -21812.7157 0.010 2484 1452s Optimizing parameters... improved 0.000 lnL 1452s Optimizing branchlengths... improved 0.000 lnL 1454s 15100 -21812.7123 0.010 2484 1456s 15200 -21812.7123 0.010 2484 1459s 15300 -21812.7123 0.010 2484 1461s 15400 -21812.7123 0.010 2484 1464s 15500 -21812.7118 0.010 2484 1466s 15600 -21812.7118 0.010 2484 1469s 15700 -21812.7112 0.010 2484 1472s 15800 -21812.7076 0.010 2484 1475s 15900 -21812.7076 0.010 2484 1478s 16000 -21812.7076 0.010 2484 1481s 16100 -21812.7050 0.010 2484 1484s 16200 -21812.7050 0.010 2484 1487s 16300 -21812.7046 0.010 2484 1490s 16400 -21812.7046 0.010 2484 1493s 16500 -21812.7040 0.010 2484 1496s 16600 -21812.7040 0.010 2484 1498s 16700 -21812.7037 0.010 2484 1501s 16800 -21812.7032 0.010 2484 1504s 16900 -21812.7032 0.010 2484 1507s 17000 -21812.7029 0.010 2484 1510s 17100 -21812.7026 0.010 2484 1513s 17200 -21812.7007 0.010 2484 1516s 17300 -21812.7005 0.010 2484 1519s 17400 -21812.7004 0.010 2484 1521s 17500 -21812.7002 0.010 2484 1525s 17600 -21812.7002 0.010 2484 1527s 17700 -21812.7000 0.010 2484 1529s 17800 -21812.7000 0.010 2484 1532s 17900 -21812.7000 0.010 2484 1535s 18000 -21812.6980 0.010 2484 1538s 18100 -21812.6979 0.010 2484 1540s 18200 -21812.6946 0.010 2484 1544s 18300 -21812.6938 0.010 2484 1546s 18400 -21812.6938 0.010 2484 1549s 18500 -21812.6938 0.010 2484 1553s 18600 -21812.6934 0.010 2484 1555s 18700 -21812.6934 0.010 2484 1559s 18800 -21812.6934 0.010 2484 1562s 18900 -21812.6934 0.010 2484 1565s 19000 -21812.6934 0.010 2484 1568s 19100 -21812.6934 0.010 2484 1571s 19200 -21812.6934 0.010 2484 1574s 19300 -21812.6933 0.010 2484 1577s 19400 -21812.6933 0.010 2484 1580s 19500 -21812.6924 0.010 2484 1583s 19600 -21812.6924 0.010 2484 1587s 19700 -21812.6924 0.010 2484 1590s 19800 -21812.6924 0.010 2484 1593s 19900 -21812.6921 0.010 2484 1597s 20000 -21812.6917 0.010 2484 1598s Optimizing parameters... improved 0.000 lnL 1598s Optimizing branchlengths... improved 0.000 lnL 1601s 20100 -21812.6913 0.010 2484 1603s 20200 -21812.6913 0.010 2484 1607s 20300 -21812.6913 0.010 2484 1611s 20400 -21812.6913 0.010 2484 1614s 20500 -21812.6913 0.010 2484 1617s 20600 -21812.6913 0.010 2484 1619s 20700 -21812.6913 0.010 2484 1622s 20800 -21812.6913 0.010 2484 1625s 20900 -21812.6909 0.010 2484 1628s 21000 -21812.6906 0.010 2484 1631s 21100 -21812.6906 0.010 2484 1634s 21200 -21812.6906 0.010 2484 1637s 21300 -21812.6906 0.010 2484 1639s 21400 -21812.6906 0.010 2484 1642s 21500 -21812.6906 0.010 2484 1644s 21600 -21812.6906 0.010 2484 1647s 21700 -21812.6900 0.010 2484 1650s 21800 -21812.6900 0.010 2484 1653s 21900 -21812.6877 0.010 2484 1656s 22000 -21812.6876 0.010 2484 1659s 22100 -21812.6876 0.010 2484 1662s 22200 -21812.6868 0.010 2484 1664s 22300 -21812.6868 0.010 2484 1666s 22400 -21812.6868 0.010 2484 1669s 22500 -21812.6860 0.010 2484 1672s 22600 -21812.6860 0.010 2484 1675s 22700 -21812.6860 0.010 2484 1677s 22800 -21812.6860 0.010 2484 1680s 22900 -21812.6860 0.010 2484 1682s 23000 -21812.6860 0.010 2484 1685s 23100 -21812.6860 0.010 2484 1687s 23200 -21812.6853 0.010 2484 1690s 23300 -21812.6852 0.010 2484 1692s 23400 -21812.6852 0.010 2484 1695s 23500 -21812.6841 0.010 2484 1698s 23600 -21812.6841 0.010 2484 1700s 23700 -21812.6841 0.010 2484 1703s 23800 -21812.6837 0.010 2484 1706s 23900 -21812.6837 0.010 2484 1708s 24000 -21812.6798 0.010 2484 1711s 24100 -21812.6798 0.010 2484 1713s 24200 -21812.6772 0.010 2484 1715s 24300 -21812.6772 0.010 2484 1718s 24400 -21812.6771 0.010 2484 1720s 24500 -21812.6771 0.010 2484 1723s 24600 -21812.6767 0.010 2484 1726s 24700 -21812.6764 0.010 2484 1728s 24800 -21812.6764 0.010 2484 1731s 24900 -21812.6758 0.010 2484 1734s 25000 -21812.6756 0.010 2484 1734s Optimizing parameters... improved 0.000 lnL 1734s Optimizing branchlengths... improved 0.000 lnL 1737s 25100 -21812.6753 0.010 2484 1740s 25200 -21812.6753 0.010 2484 1742s 25300 -21812.6750 0.010 2484 1745s 25400 -21812.6749 0.010 2484 1747s 25500 -21812.6749 0.010 2484 1749s 25600 -21812.6749 0.010 2484 1752s 25700 -21812.6749 0.010 2484 1754s 25800 -21812.6749 0.010 2484 1756s 25900 -21812.6747 0.010 2484 1759s 26000 -21812.6744 0.010 2484 1761s 26100 -21812.6744 0.010 2484 1763s 26200 -21812.6744 0.010 2484 1766s 26300 -21812.6744 0.010 2484 1768s 26400 -21812.6744 0.010 2484 1771s 26500 -21812.6744 0.010 2484 1773s 26600 -21812.6736 0.010 2484 1775s 26700 -21812.6735 0.010 2484 1778s 26800 -21812.6735 0.010 2484 1780s 26900 -21812.6733 0.010 2484 1783s 27000 -21812.6733 0.010 2484 1785s 27100 -21812.6727 0.010 2484 1785s Reached termination condition! 1785s last topological improvement at gen 2484 1785s Improvement over last 500 gen = 0.00092 1785s Current score = -21812.6727 1785s Performing final optimizations... 1786s pass 1 : -21812.6724 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0000) 1786s pass 2 : -21812.6670 (branch= 0.0052 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0000) 1787s pass 3 : -21812.6632 (branch= 0.0035 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0000) 1787s pass 4 : -21812.6567 (branch= 0.0064 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0000) 1788s pass 5 : -21812.6506 (branch= 0.0059 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0000) 1788s pass 6 : -21812.6451 (branch= 0.0052 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0001) 1789s pass 7 : -21812.6429 (branch= 0.0021 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) 1789s pass 8 : -21812.6421 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1790s pass 9 : -21812.6418 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1790s pass 10: -21812.6417 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1791s pass 11: -21812.6415 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1792s pass 12: -21812.6415 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1792s pass 13: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1793s pass 14: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1793s pass 15: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1794s pass 16: -21812.6414 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 1794s Looking for minimum length branches... 1794s Final score = -21812.6414 1794s Time used = 0 hours, 23 minutes and 58 seconds 1794s 1794s MODEL REPORT - Parameter values are FINAL 1794s Model 1 1794s Number of states = 4 (nucleotide data) 1794s Nucleotide Relative Rate Matrix: 6 rates 1794s AC = 2.214, AG = 8.155, AT = 2.357, CG = 0.918, CT = 16.505, GT = 1.000 1794s Equilibrium State Frequencies: estimated 1794s (ACGT) 0.3476 0.2126 0.1499 0.2899 1794s Rate Heterogeneity Model: 1794s 4 discrete gamma distributed rate categories, alpha param estimated 1794s 0.5606 1794s with an invariant (invariable) site category, proportion estimated 1794s 0.3385 1794s Substitution rate categories under this model: 1794s rate proportion 1794s 0.0000 0.3385 1794s 0.0451 0.1654 1794s 0.2897 0.1654 1794s 0.8598 0.1654 1794s 2.8054 0.1654 1794s 1794s NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1794s No branches were short enough to be collapsed. 1794s 1794s >>>Completed Search rep 2 (of 2)<<< 1794s 1794s ####################################################### 1794s 1794s Completed 2 replicate search(es) (of 2). 1794s 1794s NOTE: Unless the following output indicates that search replicates found the 1794s same topology, you should assume that they found different topologies. 1794s Results: 1794s Replicate 1 : -21812.6414 (best) 1794s Replicate 2 : -21812.6414 (same topology as 1) 1794s 1794s Parameter estimates across search replicates: 1794s r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv 1794s rep 1: 2.218 8.171 2.361 0.92 16.54 1 0.348 0.213 0.150 0.290 0.561 0.338 1794s rep 2: 2.214 8.155 2.357 0.9179 16.51 1 0.348 0.213 0.150 0.290 0.561 0.339 1794s 1794s Treelengths: 1794s TL 1794s rep 1: 2.941 1794s rep 2: 2.941 1794s 1794s Saving final trees from all search reps to rana.nuc.GTRIG.best.all.tre 1794s 1794s Saving final tree from best search rep (#1) to rana.nuc.GTRIG.best.tre 1794s ####################################################### 1794s autopkgtest [00:47:22]: test run-unit-test: -----------------------] 1800s autopkgtest [00:47:28]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1800s run-unit-test PASS 1805s autopkgtest [00:47:33]: @@@@@@@@@@@@@@@@@@@@ summary 1805s run-unit-test PASS