0s autopkgtest [00:28:45]: starting date: 2024-03-19 0s autopkgtest [00:28:45]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [00:28:45]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0eskhv69/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 phyml --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-10.44.124.165 lxd-armhf-10.44.124.165:autopkgtest/ubuntu/noble/armhf 50s autopkgtest [00:29:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 53s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3736 kB] 55s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 55s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 55s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 55s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [585 kB] 55s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 55s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 55s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 55s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3609 kB] 56s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 56s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [35.6 kB] 56s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 67s Fetched 8639 kB in 5s (1800 kB/s) 67s Reading package lists... 83s tee: /proc/self/fd/2: Permission denied 119s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 119s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 119s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 119s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease 119s Hit:5 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 119s Hit:6 http://ftpmaster.internal/ubuntu noble-security InRelease 119s Hit:7 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 119s Hit:8 http://ftpmaster.internal/ubuntu noble-proposed InRelease 125s Reading package lists... 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 128s Calculating upgrade... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s autopkgtest [00:30:59]: rebooting testbed after setup commands that affected boot 175s autopkgtest [00:31:40]: testbed running kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 180s autopkgtest [00:31:45]: testbed dpkg architecture: armhf 199s autopkgtest [00:32:04]: @@@@@@@@@@@@@@@@@@@@ apt-source phyml 208s Get:1 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (dsc) [2258 B] 208s Get:2 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (tar) [1804 kB] 208s Get:3 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (diff) [26.9 kB] 208s gpgv: Signature made Wed Oct 26 18:18:47 2022 UTC 208s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 208s gpgv: issuer "emollier@debian.org" 208s gpgv: Can't check signature: No public key 208s dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-3.dsc: no acceptable signature found 209s autopkgtest [00:32:14]: testing package phyml version 3:3.3.20220408-3 209s autopkgtest [00:32:14]: build not needed 216s autopkgtest [00:32:21]: test run-unit-test: preparing testbed 232s Reading package lists... 233s Building dependency tree... 233s Reading state information... 234s Correcting dependencies...Starting pkgProblemResolver with broken count: 1 234s Starting 2 pkgProblemResolver with broken count: 1 234s Investigating (0) phyml:armhf < none -> 3:3.3.20220408-3 @un uN Ib > 234s Broken phyml:armhf Depends on libopenmpi3:armhf < none | 4.1.6-5ubuntu1 @un uH > (>= 4.1.4) 234s Considering libopenmpi3:armhf 0 as a solution to phyml:armhf 0 234s Holding Back phyml:armhf rather than change libopenmpi3:armhf 234s Investigating (0) autopkgtest-satdep:armhf < 0 @iU K Nb Ib > 234s Broken autopkgtest-satdep:armhf Depends on phyml:armhf < none | 3:3.3.20220408-3 @un uH > 234s Considering phyml:armhf 0 as a solution to autopkgtest-satdep:armhf -2 234s Removing autopkgtest-satdep:armhf rather than change phyml:armhf 234s Done 235s Done 236s Starting pkgProblemResolver with broken count: 0 236s Starting 2 pkgProblemResolver with broken count: 0 236s Done 238s The following packages will be REMOVED: 238s autopkgtest-satdep 239s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 239s 1 not fully installed or removed. 239s After this operation, 0 B of additional disk space will be used. 239s (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.) 239s Removing autopkgtest-satdep (0) ... 244s autopkgtest: WARNING: package phyml is not installed though it should be 246s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from noble-proposed 256s Reading package lists... 258s Building dependency tree... 258s Reading state information... 258s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 258s Starting 2 pkgProblemResolver with broken count: 0 258s Done 259s Done 259s Starting pkgProblemResolver with broken count: 0 260s Starting 2 pkgProblemResolver with broken count: 0 260s Done 261s The following additional packages will be installed: 261s libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libhwloc-plugins 261s libhwloc15 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 261s libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common phyml 261s Suggested packages: 261s opencl-icd gfortran | fortran-compiler 262s The following NEW packages will be installed: 262s libevent-pthreads-2.1-7 libfabric1 libhwloc-plugins libhwloc15 libmunge2 262s libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 libxnvctrl0 262s ocl-icd-libopencl1 openmpi-bin openmpi-common phyml 262s The following packages will be upgraded: 262s libevent-core-2.1-7 262s 1 upgraded, 14 newly installed, 0 to remove and 226 not upgraded. 262s 1 not fully installed or removed. 262s Need to get 4760 kB of archives. 262s After this operation, 12.2 MB of additional disk space will be used. 262s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 262s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-9build1 [7370 B] 262s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librdmacm1t64 armhf 50.0-2build1 [63.0 kB] 262s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libfabric1 armhf 1.17.0-3build1 [419 kB] 262s Get:5 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc15 armhf 2.10.0-1 [145 kB] 262s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmunge2 armhf 0.5.15-4 [17.1 kB] 262s Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libpciaccess0 armhf 0.17-3 [16.3 kB] 262s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libxnvctrl0 armhf 510.47.03-0ubuntu1 [10.4 kB] 262s Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf ocl-icd-libopencl1 armhf 2.3.2-1 [34.4 kB] 262s Get:10 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc-plugins armhf 2.10.0-1 [13.7 kB] 262s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpmix2t64 armhf 5.0.1-4.1 [616 kB] 263s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libopenmpi3t64 armhf 4.1.6-7ubuntu1 [2041 kB] 263s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-common all 4.1.6-7ubuntu1 [170 kB] 263s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-bin armhf 4.1.6-7ubuntu1 [83.2 kB] 263s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf phyml armhf 3:3.3.20220408-3build1 [1041 kB] 265s Fetched 4760 kB in 2s (2974 kB/s) 265s (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.) 265s Preparing to unpack .../00-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 265s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 265s Selecting previously unselected package libevent-pthreads-2.1-7:armhf. 265s Preparing to unpack .../01-libevent-pthreads-2.1-7_2.1.12-stable-9build1_armhf.deb ... 265s Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 265s Selecting previously unselected package librdmacm1t64:armhf. 265s Preparing to unpack .../02-librdmacm1t64_50.0-2build1_armhf.deb ... 265s Unpacking librdmacm1t64:armhf (50.0-2build1) ... 265s Selecting previously unselected package libfabric1:armhf. 265s Preparing to unpack .../03-libfabric1_1.17.0-3build1_armhf.deb ... 265s Unpacking libfabric1:armhf (1.17.0-3build1) ... 265s Selecting previously unselected package libhwloc15:armhf. 265s Preparing to unpack .../04-libhwloc15_2.10.0-1_armhf.deb ... 265s Unpacking libhwloc15:armhf (2.10.0-1) ... 265s Selecting previously unselected package libmunge2:armhf. 265s Preparing to unpack .../05-libmunge2_0.5.15-4_armhf.deb ... 265s Unpacking libmunge2:armhf (0.5.15-4) ... 265s Selecting previously unselected package libpciaccess0:armhf. 265s Preparing to unpack .../06-libpciaccess0_0.17-3_armhf.deb ... 265s Unpacking libpciaccess0:armhf (0.17-3) ... 265s Selecting previously unselected package libxnvctrl0:armhf. 265s Preparing to unpack .../07-libxnvctrl0_510.47.03-0ubuntu1_armhf.deb ... 265s Unpacking libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 265s Selecting previously unselected package ocl-icd-libopencl1:armhf. 265s Preparing to unpack .../08-ocl-icd-libopencl1_2.3.2-1_armhf.deb ... 265s Unpacking ocl-icd-libopencl1:armhf (2.3.2-1) ... 265s Selecting previously unselected package libhwloc-plugins:armhf. 265s Preparing to unpack .../09-libhwloc-plugins_2.10.0-1_armhf.deb ... 265s Unpacking libhwloc-plugins:armhf (2.10.0-1) ... 266s Selecting previously unselected package libpmix2t64:armhf. 266s Preparing to unpack .../10-libpmix2t64_5.0.1-4.1_armhf.deb ... 266s Unpacking libpmix2t64:armhf (5.0.1-4.1) ... 266s Selecting previously unselected package libopenmpi3t64:armhf. 266s Preparing to unpack .../11-libopenmpi3t64_4.1.6-7ubuntu1_armhf.deb ... 266s Unpacking libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 266s Selecting previously unselected package openmpi-common. 266s Preparing to unpack .../12-openmpi-common_4.1.6-7ubuntu1_all.deb ... 266s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 266s Selecting previously unselected package openmpi-bin. 266s Preparing to unpack .../13-openmpi-bin_4.1.6-7ubuntu1_armhf.deb ... 266s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 266s Selecting previously unselected package phyml. 266s Preparing to unpack .../14-phyml_3%3a3.3.20220408-3build1_armhf.deb ... 266s Unpacking phyml (3:3.3.20220408-3build1) ... 266s Setting up libpciaccess0:armhf (0.17-3) ... 266s Setting up libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 266s Setting up libmunge2:armhf (0.5.15-4) ... 266s Setting up libhwloc15:armhf (2.10.0-1) ... 266s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 266s Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ... 266s Setting up openmpi-common (4.1.6-7ubuntu1) ... 266s Setting up librdmacm1t64:armhf (50.0-2build1) ... 266s Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 266s Setting up libfabric1:armhf (1.17.0-3build1) ... 266s Setting up libhwloc-plugins:armhf (2.10.0-1) ... 266s Setting up libpmix2t64:armhf (5.0.1-4.1) ... 266s Setting up libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 266s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 266s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 266s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 266s Setting up phyml (3:3.3.20220408-3build1) ... 266s Setting up autopkgtest-satdep (0) ... 266s Processing triggers for man-db (2.12.0-3) ... 268s Processing triggers for libc-bin (2.39-0ubuntu2) ... 286s (Reading database ... 59089 files and directories currently installed.) 286s Removing autopkgtest-satdep (0) ... 297s autopkgtest [00:33:42]: test run-unit-test: [----------------------- 300s DNA interleaved sequence file, default parameters single processor: 300s + export PHYMLCPUS=1 300s + PHYMLCPUS=1 300s + echo 'DNA interleaved sequence file, default parameters single processor:' 300s + /usr/bin/phyml -i nucleic 300s 300s 300s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 300s 300s 300s 300s 300s 300s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 300s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 300s 300s . Sequence filename: nucleic 300s . Data type: dna 300s . Alphabet size: 4 300s . Sequence format: interleaved 300s . Number of data sets: 1 300s . Nb of bootstrapped data sets: 0 300s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 300s . Model name: HKY85 300s . Ts/tv ratio: estimated 300s . Proportion of invariable sites: 0.000000 300s . RAS model: discrete Gamma 300s . Number of subst. rate catgs: 4 300s . Gamma distribution parameter: estimated 300s . 'Middle' of each rate class: mean 300s . Nucleotide equilibrium frequencies: empirical 300s . Optimise tree topology: yes 300s . Starting tree: BioNJ 300s . Add random input tree: no 300s . Optimise branch lengths: yes 300s . Minimum length of an edge: 1e-08 300s . Optimise substitution model parameters: yes 300s . Run ID: none 300s . Random seed: 1710808425 300s . Subtree patterns aliasing: no 300s . Version: 3.3.3:3.3.20220408-3build1 300s . Byte alignment: 1 300s . AVX enabled: no 300s . SSE enabled: no 300s 300s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 300s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 300s 300s 300s 300s . 382 patterns found (out of a total of 886 sites). 300s 300s . 582 sites without polymorphism (65.69%). 300s 300s 300s . Computing pairwise distances... 300s 300s . Building BioNJ tree... 300s 300s . This analysis requires at least 11 MB of memory space. 300s 300s 302s . Score of initial tree: -5680.04 302s 302s . Starting first round of SPRs... 313s 313s 13s | 1 | lnL= -5453.4 | depth= 1/ 40 | improvements= 15 | delta_lnL= 0.0/ 1000.0 313s 313s . Second round of optimization... 320s 326s 20s | 2 | lnL= -5440.3 | depth= 4/ 36 | improvements= 22 | delta_lnL= 6.5/ 1000.0 333s 26s | 3 | lnL= -5433.9 | depth= 5/ 20 | improvements= 22 | delta_lnL= 53.5/ 1000.0 339s 33s | 4 | lnL= -5468.7 | depth= 6/ 16 | improvements= 23 | delta_lnL= 16.3/ 1000.0 343s 39s | 5 | lnL= -5437.9 | depth= 2/ 12 | improvements= 21 | delta_lnL= 5.8/ 1000.0 347s 43s | 6 | lnL= -5430.9 | depth= 1/ 9 | improvements= 21 | delta_lnL= 0.0/ 107.0 + 350s 47s | 7 | lnL= -5431.0 | depth= 5/ 7 | improvements= 20 | delta_lnL= 12.5/ 107.0 354s 50s | 8 | lnL= -5436.1 | depth= 1/ 9 | improvements= 13 | delta_lnL= 0.0/ 107.0 355s 53s | 9 | lnL= -5428.4 | depth= 1/ 7 | improvements= 21 | delta_lnL= 0.0/ 107.0 + 359s 55s | 10 | lnL= -5435.8 | depth= 3/ 5 | improvements= 14 | delta_lnL= 5.6/ 25.0 361s 59s | 11 | lnL= -5420.7 | depth= 1/ 7 | improvements= 13 | delta_lnL= 0.0/ 25.0 + 363s 61s | 12 | lnL= -5429.9 | depth= 1/ 5 | improvements= 11 | delta_lnL= 0.0/ 25.0 365s 63s | 13 | lnL= -5425.8 | depth= 2/ 5 | improvements= 13 | delta_lnL= 4.9/ 25.0 366s 65s | 14 | lnL= -5431.0 | depth= 5/ 6 | improvements= 16 | delta_lnL= 16.7/ 20.0 368s 66s | 15 | lnL= -5433.0 | depth= 1/ 9 | improvements= 11 | delta_lnL= 0.0/ 20.0 370s 68s | 16 | lnL= -5432.8 | depth= 2/ 7 | improvements= 14 | delta_lnL= 0.4/ 20.0 372s 70s | 17 | lnL= -5443.1 | depth= 1/ 6 | improvements= 21 | delta_lnL= 0.0/ 20.0 374s 72s | 18 | lnL= -5429.5 | depth= 1/ 5 | improvements= 20 | delta_lnL= 0.0/ 33.4 376s 74s | 19 | lnL= -5427.9 | depth= 2/ 5 | improvements= 16 | delta_lnL= 0.8/ 33.4 376s 76s | 20 | lnL= -5436.2 | depth= 1/ 6 | improvements= 16 | delta_lnL= 0.0/ 33.4 376s 376s . Third round of optimization... 388s 398s 88s | 21 | lnL= -5420.9 | depth= 1/ 10 | improvements= 10 | delta_lnL= 0.0/ 100.0 | triple moves= 5 412s 98s | 22 | lnL= -5420.3 | depth= 4/ 8 | improvements= 1 | delta_lnL= 5.9/ 100.0 | triple moves= 5 + 412s 112s | 23 | lnL= -5420.3 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 412s 412s . Final optimisation steps... 417s 417s 417s . Log likelihood of the current tree: -5420.25581993572723150. 417s 421s . Calculating fast branch supports (using 'aBayes'). 421s 421s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 421s 421s . Time used 0h2m1s 421s 421s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 421s + echo 'AA interleaved sequence file, default parameters single processor:' 421s + /usr/bin/phyml -i proteic -d aa 421s AA interleaved sequence file, default parameters single processor: 421s 421s 421s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 421s 421s 421s 421s 421s 421s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 421s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 421s 421s . Sequence filename: proteic 421s . Data type: aa 421s . Alphabet size: 20 421s . Sequence format: interleaved 421s . Number of data sets: 1 421s . Nb of bootstrapped data sets: 0 421s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 421s . Model name: LG 421s . Proportion of invariable sites: 0.000000 421s . RAS model: discrete Gamma 421s . Number of subst. rate catgs: 4 421s . Gamma distribution parameter: estimated 421s . 'Middle' of each rate class: mean 421s . Amino-acid equilibrium frequencies: empirical 421s . Optimise tree topology: yes 421s . Starting tree: BioNJ 421s . Add random input tree: no 421s . Optimise branch lengths: yes 421s . Minimum length of an edge: 1e-08 421s . Optimise substitution model parameters: yes 421s . Run ID: none 421s . Random seed: 1710808546 421s . Subtree patterns aliasing: no 421s . Version: 3.3.3:3.3.20220408-3build1 421s . Byte alignment: 1 421s . AVX enabled: no 421s . SSE enabled: no 421s 421s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 421s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 421s 421s 421s 421s . 429 patterns found (out of a total of 547 sites). 422s 422s . 136 sites without polymorphism (24.86%). 422s 422s 422s . Computing pairwise distances... 422s 422s . Building BioNJ tree... 422s 422s . This analysis requires at least 39 MB of memory space. 422s 422s 434s . Score of initial tree: -12569.85 434s 434s . Starting first round of SPRs... 481s 526s 59s | 1 | lnL= -12470.5 | depth= 1/ 40 | improvements= 17 | delta_lnL= 0.0/ 1000.0 571s 104s | 2 | lnL= -12495.5 | depth= 3/ 24 | improvements= 20 | delta_lnL= 20.7/ 1000.0 614s 148s | 3 | lnL= -12530.6 | depth= 4/ 14 | improvements= 25 | delta_lnL= 104.2/ 1000.0 658s 192s | 4 | lnL= -12565.1 | depth= 3/ 10 | improvements= 21 | delta_lnL= 59.3/ 1000.0 658s 236s | 5 | lnL= -12480.9 | depth= 2/ 9 | improvements= 15 | delta_lnL= 14.6/ 1000.0 658s 658s . Second round of optimization... 678s 697s 256s | 6 | lnL= -12464.4 | depth= 2/ 12 | improvements= 17 | delta_lnL= 24.9/ 208.5 717s 275s | 7 | lnL= -12472.1 | depth= 1/ 9 | improvements= 14 | delta_lnL= 0.0/ 208.5 737s 295s | 8 | lnL= -12462.6 | depth= 2/ 7 | improvements= 22 | delta_lnL= 41.2/ 208.5 750s 315s | 9 | lnL= -12481.5 | depth= 2/ 6 | improvements= 19 | delta_lnL= 1.9/ 208.5 774s 328s | 10 | lnL= -12468.0 | depth= 2/ 6 | improvements= 15 | delta_lnL= 69.3/ 82.3 788s 352s | 11 | lnL= -12456.9 | depth= 2/ 6 | improvements= 20 | delta_lnL= 15.1/ 82.3 801s 366s | 12 | lnL= -12473.1 | depth= 2/ 6 | improvements= 21 | delta_lnL= 13.0/ 82.3 817s 379s | 13 | lnL= -12462.3 | depth= 3/ 6 | improvements= 16 | delta_lnL= 16.5/ 82.3 833s 395s | 14 | lnL= -12452.8 | depth= 2/ 7 | improvements= 12 | delta_lnL= 5.1/ 138.5 833s 411s | 15 | lnL= -12482.7 | depth= 2/ 6 | improvements= 15 | delta_lnL= 24.2/ 138.5 833s 833s . Third round of optimization... 887s 963s 465s | 16 | lnL= -12443.5 | depth= 2/ 10 | improvements= 9 | delta_lnL= 10.0/ 138.5 | triple moves= 5 + 963s 541s | 17 | lnL= -12443.1 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 6 + 963s 963s . Final optimisation steps... 995s 995s 995s . Log likelihood of the current tree: -12443.04901404163319967. 995s 1017s . Calculating fast branch supports (using 'aBayes'). 1017s 1017s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 1017s 1017s . Time used 0h9m55s 1017s 1017s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1017s AA sequential sequence file, with customization single processor: 1017s + echo 'AA sequential sequence file, with customization single processor:' 1017s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 1017s 1017s 1017s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 1017s 1017s 1017s 1017s 1017s 1017s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1017s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1017s 1017s . Sequence filename: example.nex 1017s . Data type: dna 1017s . Alphabet size: 4 1017s . Sequence format: interleaved 1017s . Number of data sets: 1 1017s . Nb of bootstrapped data sets: 0 1017s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 1017s . Model name: HKY85 1017s . Ts/tv ratio: estimated 1017s . Proportion of invariable sites: 0.000000 1017s . RAS model: discrete Gamma 1017s . Number of subst. rate catgs: 4 1017s . Gamma distribution parameter: estimated 1017s . 'Middle' of each rate class: mean 1017s . Nucleotide equilibrium frequencies: empirical 1017s . Optimise tree topology: yes 1017s . Starting tree: BioNJ 1017s . Add random input tree: no 1017s . Optimise branch lengths: yes 1017s . Minimum length of an edge: 1e-08 1017s . Optimise substitution model parameters: yes 1017s . Run ID: none 1017s . Random seed: 1710809142 1017s . Subtree patterns aliasing: no 1017s . Version: 3.3.3:3.3.20220408-3build1 1017s . Byte alignment: 1 1017s . AVX enabled: no 1017s . SSE enabled: no 1017s 1017s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1017s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1017s 1017s 1017s 1017s . 1037 patterns found (out of a total of 2888 sites). 1017s 1017s . 1378 sites without polymorphism (47.71%). 1017s 1017s 1017s . Computing pairwise distances... 1017s 1017s . Building BioNJ tree... 1017s 1017s . This analysis requires at least 3 MB of memory space. 1017s 1017s 1018s . Score of initial tree: -12664.54 1018s 1018s . Starting first round of SPRs... 1018s 1018s 1s | 1 | lnL= -12578.9 | depth= 1/ 40 | improvements= 4 | delta_lnL= 0.0/ 1000.0 1018s 1018s . Second round of optimization... 1019s 1019s 1s | 2 | lnL= -12573.1 | depth= 1/ 36 | improvements= 3 | delta_lnL= 0.0/ 1000.0 1019s 1019s . Third round of optimization... 1021s 1023s 4s | 3 | lnL= -12563.5 | depth= 1/ 20 | improvements= 1 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 1023s 5s | 4 | lnL= -12563.5 | depth= 0/ 16 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 1023s 1023s . Final optimisation steps... 1025s 1025s 1025s . Log likelihood of the current tree: -12563.11885905565213761. 1025s 1026s . Calculating fast branch supports (using 'aBayes'). 1026s 1026s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 1026s 1026s . Time used 0h0m9s 1026s 1026s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1026s + export PHYMLCPUS=2 1026s + PHYMLCPUS=2 1026s + echo 'DNA interleaved sequence file, default parameters using 2 processors:' 1026s + /usr/bin/phyml -i nucleic 1026s DNA interleaved sequence file, default parameters using 2 processors: 1026s 1026s 1026s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 1026s 1026s 1026s 1026s 1026s 1026s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1026s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1026s 1026s . Sequence filename: nucleic 1026s . Data type: dna 1026s . Alphabet size: 4 1026s . Sequence format: interleaved 1026s . Number of data sets: 1 1026s . Nb of bootstrapped data sets: 0 1026s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 1026s . Model name: HKY85 1026s . Ts/tv ratio: estimated 1026s . Proportion of invariable sites: 0.000000 1026s . RAS model: discrete Gamma 1026s . Number of subst. rate catgs: 4 1026s . Gamma distribution parameter: estimated 1026s . 'Middle' of each rate class: mean 1026s . Nucleotide equilibrium frequencies: empirical 1026s . Optimise tree topology: yes 1026s . Starting tree: BioNJ 1026s . Add random input tree: no 1026s . Optimise branch lengths: yes 1026s . Minimum length of an edge: 1e-08 1026s . Optimise substitution model parameters: yes 1026s . Run ID: none 1026s . Random seed: 1710809151 1026s . Subtree patterns aliasing: no 1026s . Version: 3.3.3:3.3.20220408-3build1 1026s . Byte alignment: 1 1026s . AVX enabled: no 1026s . SSE enabled: no 1026s 1026s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1026s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1026s 1026s 1026s 1026s . 382 patterns found (out of a total of 886 sites). 1026s 1026s . 582 sites without polymorphism (65.69%). 1026s 1026s 1026s . Computing pairwise distances... 1026s 1026s . Building BioNJ tree... 1026s 1026s . This analysis requires at least 11 MB of memory space. 1026s 1026s 1029s . Score of initial tree: -5680.04 1029s 1029s . Starting first round of SPRs... 1039s 1049s 13s | 1 | lnL= -5484.2 | depth= 9/ 40 | improvements= 24 | delta_lnL= 64.6/ 1000.0 1059s 23s | 2 | lnL= -5446.1 | depth= 3/ 24 | improvements= 20 | delta_lnL= 9.7/ 1000.0 1067s 33s | 3 | lnL= -5440.3 | depth= 5/ 14 | improvements= 26 | delta_lnL= 7.6/ 1000.0 1074s 41s | 4 | lnL= -5435.4 | depth= 2/ 11 | improvements= 19 | delta_lnL= 4.8/ 1000.0 1078s 48s | 5 | lnL= -5439.3 | depth= 1/ 8 | improvements= 17 | delta_lnL= 0.0/ 1000.0 1085s 52s | 6 | lnL= -5475.7 | depth= 7/ 7 | improvements= 16 | delta_lnL= 18.1/ 129.2 1085s 59s | 7 | lnL= -5424.6 | depth= 2/ 13 | improvements= 9 | delta_lnL= 18.6/ 129.2 + 1085s 1085s . Second round of optimization... 1089s 1093s 63s | 8 | lnL= -5425.1 | depth= 5/ 12 | improvements= 15 | delta_lnL= 7.7/ 129.2 1095s 67s | 9 | lnL= -5424.7 | depth= 1/ 9 | improvements= 13 | delta_lnL= 0.0/ 129.2 1099s 69s | 10 | lnL= -5431.4 | depth= 1/ 7 | improvements= 15 | delta_lnL= 0.0/ 20.0 1100s 73s | 11 | lnL= -5434.9 | depth= 1/ 5 | improvements= 15 | delta_lnL= 0.0/ 20.0 1102s 74s | 12 | lnL= -5425.0 | depth= 1/ 5 | improvements= 15 | delta_lnL= 0.0/ 20.0 1103s 76s | 13 | lnL= -5421.5 | depth= 1/ 5 | improvements= 9 | delta_lnL= 0.0/ 20.0 + 1105s 77s | 14 | lnL= -5429.0 | depth= 1/ 5 | improvements= 7 | delta_lnL= 0.0/ 20.0 1107s 79s | 15 | lnL= -5440.7 | depth= 1/ 5 | improvements= 9 | delta_lnL= 0.0/ 20.0 1108s 81s | 16 | lnL= -5435.5 | depth= 2/ 5 | improvements= 22 | delta_lnL= 22.9/ 20.0 1110s 82s | 17 | lnL= -5429.1 | depth= 1/ 6 | improvements= 6 | delta_lnL= 0.0/ 20.0 1112s 84s | 18 | lnL= -5418.3 | depth= 1/ 5 | improvements= 6 | delta_lnL= 0.0/ 45.7 + 1114s 86s | 19 | lnL= -5446.2 | depth= 2/ 5 | improvements= 14 | delta_lnL= 10.8/ 45.7 1118s 88s | 20 | lnL= -5419.1 | depth= 2/ 6 | improvements= 9 | delta_lnL= 1.2/ 45.7 1119s 92s | 21 | lnL= -5423.7 | depth= 1/ 6 | improvements= 11 | delta_lnL= 0.0/ 45.7 1119s 93s | 22 | lnL= -5422.6 | depth= 1/ 5 | improvements= 5 | delta_lnL= 0.0/ 21.6 1119s 1119s . Third round of optimization... 1129s 1139s 103s | 23 | lnL= -5416.1 | depth= 1/ 10 | improvements= 4 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 1152s 113s | 24 | lnL= -5415.8 | depth= 0/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 1152s 126s | 25 | lnL= -5415.8 | depth= 0/ 6 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 1152s 1152s . Final optimisation steps... 1157s 1157s 1157s . Log likelihood of the current tree: -5415.79612819373778621. 1157s 1161s . Calculating fast branch supports (using 'aBayes'). 1161s 1161s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 1161s 1161s . Time used 0h2m15s 1161s 1161s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1161s AA interleaved sequence file, default parameters using 2 processors: 1161s + echo 'AA interleaved sequence file, default parameters using 2 processors:' 1161s + /usr/bin/phyml -i proteic -d aa 1161s 1161s 1161s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 1161s 1161s 1161s 1161s 1161s 1161s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1161s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1161s 1161s . Sequence filename: proteic 1161s . Data type: aa 1161s . Alphabet size: 20 1161s . Sequence format: interleaved 1161s . Number of data sets: 1 1161s . Nb of bootstrapped data sets: 0 1161s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 1161s . Model name: LG 1161s . Proportion of invariable sites: 0.000000 1161s . RAS model: discrete Gamma 1161s . Number of subst. rate catgs: 4 1161s . Gamma distribution parameter: estimated 1161s . 'Middle' of each rate class: mean 1161s . Amino-acid equilibrium frequencies: empirical 1161s . Optimise tree topology: yes 1161s . Starting tree: BioNJ 1161s . Add random input tree: no 1161s . Optimise branch lengths: yes 1161s . Minimum length of an edge: 1e-08 1161s . Optimise substitution model parameters: yes 1161s . Run ID: none 1161s . Random seed: 1710809286 1161s . Subtree patterns aliasing: no 1161s . Version: 3.3.3:3.3.20220408-3build1 1161s . Byte alignment: 1 1161s . AVX enabled: no 1161s . SSE enabled: no 1161s 1161s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1161s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1161s 1161s 1161s 1161s . 429 patterns found (out of a total of 547 sites). 1161s 1161s . 136 sites without polymorphism (24.86%). 1161s 1161s 1162s . Computing pairwise distances... 1162s 1162s . Building BioNJ tree... 1162s 1162s . This analysis requires at least 39 MB of memory space. 1162s 1162s 1174s . Score of initial tree: -12569.85 1174s 1174s . Starting first round of SPRs... 1221s 1269s 59s | 1 | lnL= -12483.9 | depth= 2/ 40 | improvements= 18 | delta_lnL= 4.4/ 1000.0 1269s 107s | 2 | lnL= -12478.7 | depth= 1/ 24 | improvements= 15 | delta_lnL= 0.0/ 1000.0 1269s 1269s . Second round of optimization... 1311s 1355s 149s | 3 | lnL= -12514.0 | depth= 4/ 21 | improvements= 24 | delta_lnL= 52.2/ 1000.0 1398s 193s | 4 | lnL= -12463.0 | depth= 1/ 16 | improvements= 17 | delta_lnL= 0.0/ 1000.0 1413s 236s | 5 | lnL= -12470.2 | depth= 2/ 12 | improvements= 16 | delta_lnL= 5.1/ 1000.0 1428s 251s | 6 | lnL= -12540.2 | depth= 3/ 9 | improvements= 23 | delta_lnL= 46.5/ 104.4 1444s 266s | 7 | lnL= -12522.3 | depth= 5/ 7 | improvements= 25 | delta_lnL= 25.8/ 104.4 1460s 282s | 8 | lnL= -12490.5 | depth= 2/ 9 | improvements= 18 | delta_lnL= 47.7/ 104.4 1477s 298s | 9 | lnL= -12491.9 | depth= 2/ 7 | improvements= 25 | delta_lnL= 26.9/ 104.4 1500s 314s | 10 | lnL= -12567.0 | depth= 2/ 6 | improvements= 25 | delta_lnL= 53.9/ 95.4 1513s 338s | 11 | lnL= -12448.7 | depth= 2/ 6 | improvements= 13 | delta_lnL= 21.1/ 95.4 + 1527s 351s | 12 | lnL= -12493.4 | depth= 1/ 6 | improvements= 11 | delta_lnL= 0.0/ 95.4 1542s 365s | 13 | lnL= -12465.3 | depth= 2/ 5 | improvements= 15 | delta_lnL= 2.2/ 95.4 1558s 380s | 14 | lnL= -12467.3 | depth= 2/ 6 | improvements= 19 | delta_lnL= 16.3/ 107.8 1573s 396s | 15 | lnL= -12509.6 | depth= 3/ 6 | improvements= 18 | delta_lnL= 75.2/ 107.8 1588s 410s | 16 | lnL= -12487.3 | depth= 2/ 7 | improvements= 24 | delta_lnL= 13.5/ 107.8 1606s 426s | 17 | lnL= -12458.6 | depth= 1/ 6 | improvements= 19 | delta_lnL= 0.0/ 107.8 1623s 444s | 18 | lnL= -12468.5 | depth= 2/ 5 | improvements= 17 | delta_lnL= 8.9/ 150.4 1639s 461s | 19 | lnL= -12471.7 | depth= 2/ 6 | improvements= 16 | delta_lnL= 4.2/ 150.4 1639s 477s | 20 | lnL= -12482.8 | depth= 2/ 6 | improvements= 14 | delta_lnL= 13.4/ 150.4 1639s 1639s . Third round of optimization... 1707s 1758s 545s | 21 | lnL= -12444.6 | depth= 2/ 10 | improvements= 7 | delta_lnL= 1.8/ 150.4 | triple moves= 5 + 1835s 596s | 22 | lnL= -12443.1 | depth= 2/ 8 | improvements= 1 | delta_lnL= 1.5/ 100.0 | triple moves= 5 + 1835s 673s | 23 | lnL= -12443.1 | depth= 0/ 6 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 6 + 1835s 1835s . Final optimisation steps... 1863s 1863s 1864s . Log likelihood of the current tree: -12443.04888160537302610. 1864s 1886s . Calculating fast branch supports (using 'aBayes'). 1886s 1886s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 1886s 1886s . Time used 0h12m4s 1886s 1886s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1886s AA sequential sequence file, with customization using 2 processors: 1886s + echo 'AA sequential sequence file, with customization using 2 processors:' 1886s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 1886s 1886s 1886s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 1886s 1886s 1886s 1886s 1886s 1886s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1886s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1886s 1886s . Sequence filename: example.nex 1886s . Data type: dna 1886s . Alphabet size: 4 1886s . Sequence format: interleaved 1886s . Number of data sets: 1 1886s . Nb of bootstrapped data sets: 0 1886s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 1886s . Model name: HKY85 1886s . Ts/tv ratio: estimated 1886s . Proportion of invariable sites: 0.000000 1886s . RAS model: discrete Gamma 1886s . Number of subst. rate catgs: 4 1886s . Gamma distribution parameter: estimated 1886s . 'Middle' of each rate class: mean 1886s . Nucleotide equilibrium frequencies: empirical 1886s . Optimise tree topology: yes 1886s . Starting tree: BioNJ 1886s . Add random input tree: no 1886s . Optimise branch lengths: yes 1886s . Minimum length of an edge: 1e-08 1886s . Optimise substitution model parameters: yes 1886s . Run ID: none 1886s . Random seed: 1710810011 1886s . Subtree patterns aliasing: no 1886s . Version: 3.3.3:3.3.20220408-3build1 1886s . Byte alignment: 1 1886s . AVX enabled: no 1886s . SSE enabled: no 1886s 1886s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1886s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1886s 1886s 1886s 1886s . 1037 patterns found (out of a total of 2888 sites). 1886s 1886s . 1378 sites without polymorphism (47.71%). 1886s 1886s 1886s . Computing pairwise distances... 1886s 1886s . Building BioNJ tree... 1886s 1886s . This analysis requires at least 3 MB of memory space. 1886s 1886s 1887s . Score of initial tree: -12664.54 1887s 1887s . Starting first round of SPRs... 1887s 1887s 1s | 1 | lnL= -12579.2 | depth= 1/ 40 | improvements= 4 | delta_lnL= 0.0/ 1000.0 1887s 1887s . Second round of optimization... 1888s 1888s 1s | 2 | lnL= -12631.2 | depth= 1/ 36 | improvements= 3 | delta_lnL= 0.0/ 1000.0 1888s 1888s . Third round of optimization... 1889s 1891s 3s | 3 | lnL= -12565.0 | depth= 1/ 20 | improvements= 3 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 1891s 5s | 4 | lnL= -12563.5 | depth= 0/ 16 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 1891s 1891s . Final optimisation steps... 1894s 1894s 1894s . Log likelihood of the current tree: -12563.11885905565213761. 1894s 1895s . Calculating fast branch supports (using 'aBayes'). 1895s 1895s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 1895s 1895s . Time used 0h0m9s 1895s 1895s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1895s PASS 1895s + echo PASS 1895s autopkgtest [01:00:20]: test run-unit-test: -----------------------] 1899s autopkgtest [01:00:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1899s run-unit-test PASS 1903s autopkgtest [01:00:28]: @@@@@@@@@@@@@@@@@@@@ summary 1903s run-unit-test PASS