0s autopkgtest [11:59:29]: starting date and time: 2024-03-18 11:59:29+0000 0s autopkgtest [11:59:29]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [11:59:29]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ae4i205o/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade 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' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-15.secgroup --name adt-noble-arm64-phyml-20240318-115929-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 268s autopkgtest [12:03:57]: testbed dpkg architecture: arm64 269s autopkgtest [12:03:58]: testbed apt version: 2.7.12 269s autopkgtest [12:03:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 269s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 270s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 271s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 271s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 271s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3727 kB] 271s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 271s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 271s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 271s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 271s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4127 kB] 275s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 275s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 275s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 275s Fetched 9270 kB in 3s (3171 kB/s) 275s Reading package lists... 277s Reading package lists... 277s Building dependency tree... 277s Reading state information... 278s Calculating upgrade... 278s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 278s Reading package lists... 278s Building dependency tree... 278s Reading state information... 279s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 280s sh: Attempting to set up Debian/Ubuntu apt sources automatically 280s sh: Distribution appears to be Ubuntu 281s Reading package lists... 281s Building dependency tree... 281s Reading state information... 281s eatmydata is already the newest version (131-1). 281s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 281s Reading package lists... 281s Building dependency tree... 281s Reading state information... 282s dbus is already the newest version (1.14.10-4ubuntu1). 282s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 282s Reading package lists... 282s Building dependency tree... 282s Reading state information... 283s rng-tools-debian is already the newest version (2.4). 283s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 283s Reading package lists... 283s Building dependency tree... 283s Reading state information... 284s The following packages will be REMOVED: 284s cloud-init* python3-configobj* python3-debconf* 284s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 284s After this operation, 3252 kB disk space will be freed. 284s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75850 files and directories currently installed.) 284s Removing cloud-init (24.1.1-0ubuntu1) ... 284s Removing python3-configobj (5.0.8-3) ... 284s Removing python3-debconf (1.5.86) ... 285s Processing triggers for man-db (2.12.0-3) ... 285s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75461 files and directories currently installed.) 285s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 285s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 285s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 285s invoke-rc.d: policy-rc.d denied execution of try-restart. 285s Reading package lists... 286s Building dependency tree... 286s Reading state information... 286s linux-generic is already the newest version (6.8.0-11.11+1). 286s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 287s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 287s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 287s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 289s Reading package lists... 289s Reading package lists... 289s Building dependency tree... 289s Reading state information... 289s Calculating upgrade... 290s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 290s Reading package lists... 290s Building dependency tree... 290s Reading state information... 291s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 291s autopkgtest [12:04:20]: rebooting testbed after setup commands that affected boot 336s autopkgtest [12:05:05]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 338s autopkgtest [12:05:07]: @@@@@@@@@@@@@@@@@@@@ apt-source phyml 340s Get:1 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (dsc) [2258 B] 340s Get:2 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (tar) [1804 kB] 340s Get:3 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (diff) [26.9 kB] 340s gpgv: Signature made Wed Oct 26 18:18:47 2022 UTC 340s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 340s gpgv: issuer "emollier@debian.org" 340s gpgv: Can't check signature: No public key 340s dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-3.dsc: no acceptable signature found 340s autopkgtest [12:05:09]: testing package phyml version 3:3.3.20220408-3 341s autopkgtest [12:05:10]: build not needed 341s autopkgtest [12:05:10]: test run-unit-test: preparing testbed 353s Reading package lists... 353s Building dependency tree... 353s Reading state information... 354s Starting pkgProblemResolver with broken count: 0 354s Starting 2 pkgProblemResolver with broken count: 0 354s Done 354s The following additional packages will be installed: 354s libamd-comgr2 libamdhip64-5 libatomic1 libdrm-amdgpu1 354s libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 libhsakmt1 354s libhwloc-plugins libhwloc15 libllvm17 libmunge2 libopenmpi3 libpciaccess0 354s libpmix2 librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin 354s openmpi-common phyml 354s Suggested packages: 354s opencl-icd gfortran | fortran-compiler 354s The following NEW packages will be installed: 354s autopkgtest-satdep libamd-comgr2 libamdhip64-5 libatomic1 libdrm-amdgpu1 354s libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 libhsakmt1 354s libhwloc-plugins libhwloc15 libllvm17 libmunge2 libopenmpi3 libpciaccess0 354s libpmix2 librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin 354s openmpi-common phyml 354s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 354s Need to get 51.6 MB/51.6 MB of archives. 354s After this operation, 226 MB of additional disk space will be used. 354s Get:1 /tmp/autopkgtest.UyMVjD/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 355s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 356s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 356s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 356s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 356s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 356s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 356s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 356s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 356s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 356s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 356s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 356s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 356s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 356s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 356s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 356s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 356s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2 arm64 5.0.1-4 [659 kB] 356s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 357s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 357s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] 357s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-bin arm64 4.1.6-5ubuntu1 [123 kB] 357s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 phyml arm64 3:3.3.20220408-3 [975 kB] 357s Fetched 51.6 MB in 2s (22.9 MB/s) 357s Selecting previously unselected package libllvm17:arm64. 357s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75406 files and directories currently installed.) 357s Preparing to unpack .../00-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 357s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 358s Selecting previously unselected package libamd-comgr2:arm64. 358s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 358s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 358s Selecting previously unselected package libdrm-amdgpu1:arm64. 358s Preparing to unpack .../02-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 358s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 358s Selecting previously unselected package libhsakmt1:arm64. 358s Preparing to unpack .../03-libhsakmt1_5.7.0-1_arm64.deb ... 358s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 358s Selecting previously unselected package libhsa-runtime64-1. 358s Preparing to unpack .../04-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 358s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 358s Selecting previously unselected package libamdhip64-5. 358s Preparing to unpack .../05-libamdhip64-5_5.2.3-12_arm64.deb ... 358s Unpacking libamdhip64-5 (5.2.3-12) ... 358s Selecting previously unselected package libatomic1:arm64. 358s Preparing to unpack .../06-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 358s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 358s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 358s Preparing to unpack .../07-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 358s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 358s Selecting previously unselected package librdmacm1t64:arm64. 358s Preparing to unpack .../08-librdmacm1t64_50.0-2_arm64.deb ... 358s Unpacking librdmacm1t64:arm64 (50.0-2) ... 358s Selecting previously unselected package libfabric1:arm64. 358s Preparing to unpack .../09-libfabric1_1.17.0-3_arm64.deb ... 358s Unpacking libfabric1:arm64 (1.17.0-3) ... 358s Selecting previously unselected package libhwloc15:arm64. 358s Preparing to unpack .../10-libhwloc15_2.10.0-1_arm64.deb ... 358s Unpacking libhwloc15:arm64 (2.10.0-1) ... 359s Selecting previously unselected package libmunge2:arm64. 359s Preparing to unpack .../11-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 359s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 359s Selecting previously unselected package libpciaccess0:arm64. 359s Preparing to unpack .../12-libpciaccess0_0.17-3_arm64.deb ... 359s Unpacking libpciaccess0:arm64 (0.17-3) ... 359s Selecting previously unselected package libxnvctrl0:arm64. 359s Preparing to unpack .../13-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 359s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 359s Selecting previously unselected package ocl-icd-libopencl1:arm64. 359s Preparing to unpack .../14-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 359s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 359s Selecting previously unselected package libhwloc-plugins:arm64. 359s Preparing to unpack .../15-libhwloc-plugins_2.10.0-1_arm64.deb ... 359s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 359s Selecting previously unselected package libpmix2:arm64. 359s Preparing to unpack .../16-libpmix2_5.0.1-4_arm64.deb ... 359s Unpacking libpmix2:arm64 (5.0.1-4) ... 359s Selecting previously unselected package libucx0:arm64. 359s Preparing to unpack .../17-libucx0_1.16.0+ds-4_arm64.deb ... 359s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 359s Selecting previously unselected package libopenmpi3:arm64. 359s Preparing to unpack .../18-libopenmpi3_4.1.6-5ubuntu1_arm64.deb ... 359s Unpacking libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 359s Selecting previously unselected package openmpi-common. 359s Preparing to unpack .../19-openmpi-common_4.1.6-5ubuntu1_all.deb ... 359s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 359s Selecting previously unselected package openmpi-bin. 359s Preparing to unpack .../20-openmpi-bin_4.1.6-5ubuntu1_arm64.deb ... 359s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 359s Selecting previously unselected package phyml. 359s Preparing to unpack .../21-phyml_3%3a3.3.20220408-3_arm64.deb ... 359s Unpacking phyml (3:3.3.20220408-3) ... 359s Selecting previously unselected package autopkgtest-satdep. 359s Preparing to unpack .../22-1-autopkgtest-satdep.deb ... 359s Unpacking autopkgtest-satdep (0) ... 359s Setting up libpciaccess0:arm64 (0.17-3) ... 359s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 359s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 359s Setting up libhwloc15:arm64 (2.10.0-1) ... 359s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 359s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 359s Setting up openmpi-common (4.1.6-5ubuntu1) ... 359s Setting up librdmacm1t64:arm64 (50.0-2) ... 359s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 359s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 359s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 359s Setting up libfabric1:arm64 (1.17.0-3) ... 359s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 359s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 359s Setting up libhsakmt1:arm64 (5.7.0-1) ... 359s Setting up libpmix2:arm64 (5.0.1-4) ... 359s Setting up libhsa-runtime64-1 (5.7.1-1) ... 359s Setting up libamdhip64-5 (5.2.3-12) ... 359s Setting up libucx0:arm64 (1.16.0+ds-4) ... 359s Setting up libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 359s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 359s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 359s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 359s Setting up phyml (3:3.3.20220408-3) ... 359s Setting up autopkgtest-satdep (0) ... 359s Processing triggers for man-db (2.12.0-3) ... 359s Processing triggers for libc-bin (2.39-0ubuntu2) ... 363s (Reading database ... 75976 files and directories currently installed.) 363s Removing autopkgtest-satdep (0) ... 364s autopkgtest [12:05:33]: test run-unit-test: [----------------------- 364s + export PHYMLCPUS=1 364s + PHYMLCPUS=1 364s + echo 'DNA interleaved sequence file, default parameters single processor:' 364s + /usr/bin/phyml -i nucleic 364s DNA interleaved sequence file, default parameters single processor: 364s 364s 364s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 364s 364s 364s 364s 364s 364s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 364s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 364s 364s . Sequence filename: nucleic 364s . Data type: dna 364s . Alphabet size: 4 364s . Sequence format: interleaved 364s . Number of data sets: 1 364s . Nb of bootstrapped data sets: 0 364s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 364s . Model name: HKY85 364s . Ts/tv ratio: estimated 364s . Proportion of invariable sites: 0.000000 364s . RAS model: discrete Gamma 364s . Number of subst. rate catgs: 4 364s . Gamma distribution parameter: estimated 364s . 'Middle' of each rate class: mean 364s . Nucleotide equilibrium frequencies: empirical 364s . Optimise tree topology: yes 364s . Starting tree: BioNJ 364s . Add random input tree: no 364s . Optimise branch lengths: yes 364s . Minimum length of an edge: 1e-08 364s . Optimise substitution model parameters: yes 364s . Run ID: none 364s . Random seed: 1710763533 364s . Subtree patterns aliasing: no 364s . Version: 3.3.3:3.3.20220408-3 364s . Byte alignment: 1 364s . AVX enabled: no 364s . SSE enabled: no 364s 364s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 364s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 364s 364s 364s 364s . 382 patterns found (out of a total of 886 sites). 364s 364s . 582 sites without polymorphism (65.69%). 364s 364s 364s . Computing pairwise distances... 364s 364s . Building BioNJ tree... 364s 364s . This analysis requires at least 11 MB of memory space. 364s 364s 364s . Score of initial tree: -5680.04 364s 364s . Starting first round of SPRs... 367s 367s 2s | 1 | lnL= -5439.2 | depth= 1/ 40 | improvements= 10 | delta_lnL= 0.0/ 1000.0 367s 367s . Second round of optimization... 367s 369s 3s | 2 | lnL= -5442.4 | depth= 5/ 36 | improvements= 14 | delta_lnL= 5.5/ 1000.0 370s 5s | 3 | lnL= -5443.1 | depth= 2/ 20 | improvements= 15 | delta_lnL= 1.8/ 1000.0 371s 6s | 4 | lnL= -5436.0 | depth= 2/ 16 | improvements= 14 | delta_lnL= 0.3/ 1000.0 371s 7s | 5 | lnL= -5448.4 | depth= 3/ 12 | improvements= 23 | delta_lnL= 20.3/ 1000.0 371s 7s | 6 | lnL= -5428.8 | depth= 2/ 9 | improvements= 16 | delta_lnL= 4.0/ 20.0 + 372s 7s | 7 | lnL= -5438.2 | depth= 2/ 7 | improvements= 22 | delta_lnL= 8.3/ 20.0 372s 8s | 8 | lnL= -5429.0 | depth= 1/ 6 | improvements= 16 | delta_lnL= 0.0/ 20.0 373s 8s | 9 | lnL= -5433.1 | depth= 1/ 5 | improvements= 18 | delta_lnL= 0.0/ 20.0 373s 8s | 10 | lnL= -5441.6 | depth= 1/ 5 | improvements= 17 | delta_lnL= 0.0/ 20.0 373s 9s | 11 | lnL= -5442.0 | depth= 4/ 5 | improvements= 23 | delta_lnL= 25.4/ 20.0 374s 9s | 12 | lnL= -5445.7 | depth= 2/ 8 | improvements= 17 | delta_lnL= 2.0/ 20.0 374s 10s | 13 | lnL= -5429.6 | depth= 2/ 6 | improvements= 7 | delta_lnL= 10.3/ 20.0 374s 10s | 14 | lnL= -5432.8 | depth= 1/ 6 | improvements= 13 | delta_lnL= 0.0/ 50.9 375s 10s | 15 | lnL= -5424.9 | depth= 1/ 5 | improvements= 10 | delta_lnL= 0.0/ 50.9 + 375s 11s | 16 | lnL= -5430.0 | depth= 3/ 5 | improvements= 14 | delta_lnL= 14.2/ 50.9 376s 11s | 17 | lnL= -5426.5 | depth= 1/ 7 | improvements= 16 | delta_lnL= 0.0/ 50.9 376s 12s | 18 | lnL= -5442.5 | depth= 1/ 5 | improvements= 11 | delta_lnL= 0.0/ 28.5 376s 12s | 19 | lnL= -5437.8 | depth= 5/ 5 | improvements= 18 | delta_lnL= 18.5/ 28.5 377s 12s | 20 | lnL= -5433.0 | depth= 1/ 9 | improvements= 14 | delta_lnL= 0.0/ 28.5 377s 13s | 21 | lnL= -5423.1 | depth= 1/ 7 | improvements= 13 | delta_lnL= 0.0/ 28.5 + 378s 13s | 22 | lnL= -5430.1 | depth= 2/ 5 | improvements= 13 | delta_lnL= 0.6/ 37.0 378s 14s | 23 | lnL= -5425.7 | depth= 1/ 6 | improvements= 12 | delta_lnL= 0.0/ 37.0 378s 14s | 24 | lnL= -5430.3 | depth= 2/ 5 | improvements= 16 | delta_lnL= 0.7/ 37.0 379s 14s | 25 | lnL= -5429.6 | depth= 2/ 6 | improvements= 24 | delta_lnL= 23.2/ 37.0 379s 15s | 26 | lnL= -5426.6 | depth= 3/ 6 | improvements= 10 | delta_lnL= 5.1/ 20.0 379s 15s | 27 | lnL= -5442.0 | depth= 2/ 7 | improvements= 18 | delta_lnL= 31.4/ 20.0 380s 15s | 28 | lnL= -5423.3 | depth= 1/ 6 | improvements= 15 | delta_lnL= 0.0/ 20.0 380s 16s | 29 | lnL= -5425.0 | depth= 2/ 5 | improvements= 15 | delta_lnL= 1.6/ 20.0 380s 16s | 30 | lnL= -5426.1 | depth= 1/ 6 | improvements= 4 | delta_lnL= 0.0/ 62.8 380s 380s . Third round of optimization... 382s 384s 18s | 31 | lnL= -5420.7 | depth= 1/ 10 | improvements= 3 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 385s 20s | 32 | lnL= -5420.4 | depth= 3/ 8 | improvements= 1 | delta_lnL= 5.3/ 100.0 | triple moves= 5 + 388s 21s | 33 | lnL= -5420.3 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 388s 24s | 34 | lnL= -5420.3 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 388s 388s . Final optimisation steps... 388s 388s 388s . Log likelihood of the current tree: -5420.255854787019416107796132564544677734. 388s 389s . Calculating fast branch supports (using 'aBayes'). 389s 389s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 389s 389s . Time used 0h0m25s 389s 389s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 389s AA interleaved sequence file, default parameters single processor: 389s + echo 'AA interleaved sequence file, default parameters single processor:' 389s + /usr/bin/phyml -i proteic -d aa 389s 389s 389s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 389s 389s 389s 389s 389s 389s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 389s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 389s 389s . Sequence filename: proteic 389s . Data type: aa 389s . Alphabet size: 20 389s . Sequence format: interleaved 389s . Number of data sets: 1 389s . Nb of bootstrapped data sets: 0 389s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 389s . Model name: LG 389s . Proportion of invariable sites: 0.000000 389s . RAS model: discrete Gamma 389s . Number of subst. rate catgs: 4 389s . Gamma distribution parameter: estimated 389s . 'Middle' of each rate class: mean 389s . Amino-acid equilibrium frequencies: empirical 389s . Optimise tree topology: yes 389s . Starting tree: BioNJ 389s . Add random input tree: no 389s . Optimise branch lengths: yes 389s . Minimum length of an edge: 1e-08 389s . Optimise substitution model parameters: yes 389s . Run ID: none 389s . Random seed: 1710763558 389s . Subtree patterns aliasing: no 389s . Version: 3.3.3:3.3.20220408-3 389s . Byte alignment: 1 389s . AVX enabled: no 389s . SSE enabled: no 389s 389s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 389s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 389s 389s 389s 389s . 429 patterns found (out of a total of 547 sites). 389s 389s . 136 sites without polymorphism (24.86%). 389s 389s 389s . Computing pairwise distances... 389s 389s . Building BioNJ tree... 389s 389s . This analysis requires at least 39 MB of memory space. 389s 389s 392s . Score of initial tree: -12569.85 392s 392s . Starting first round of SPRs... 403s 412s 14s | 1 | lnL= -12507.0 | depth= 1/ 40 | improvements= 20 | delta_lnL= 0.0/ 1000.0 422s 23s | 2 | lnL= -12473.6 | depth= 2/ 24 | improvements= 24 | delta_lnL= 10.1/ 1000.0 431s 33s | 3 | lnL= -12476.2 | depth= 2/ 14 | improvements= 23 | delta_lnL= 51.3/ 1000.0 440s 42s | 4 | lnL= -12488.1 | depth= 2/ 8 | improvements= 19 | delta_lnL= 24.5/ 1000.0 443s 51s | 5 | lnL= -12491.9 | depth= 2/ 8 | improvements= 17 | delta_lnL= 17.9/ 1000.0 443s 54s | 6 | lnL= -12482.6 | depth= 1/ 8 | improvements= 10 | delta_lnL= 0.0/ 102.5 443s 443s . Second round of optimization... 446s 449s 57s | 7 | lnL= -12481.9 | depth= 1/ 10 | improvements= 20 | delta_lnL= 0.0/ 102.5 452s 60s | 8 | lnL= -12484.2 | depth= 3/ 8 | improvements= 20 | delta_lnL= 18.0/ 102.5 455s 63s | 9 | lnL= -12485.1 | depth= 1/ 7 | improvements= 18 | delta_lnL= 0.0/ 102.5 460s 66s | 10 | lnL= -12475.9 | depth= 1/ 5 | improvements= 18 | delta_lnL= 0.0/ 36.0 463s 71s | 11 | lnL= -12456.5 | depth= 3/ 5 | improvements= 22 | delta_lnL= 15.4/ 36.0 465s 74s | 12 | lnL= -12453.6 | depth= 1/ 7 | improvements= 17 | delta_lnL= 0.0/ 36.0 467s 76s | 13 | lnL= -12453.8 | depth= 3/ 5 | improvements= 10 | delta_lnL= 9.2/ 36.0 469s 78s | 14 | lnL= -12464.7 | depth= 1/ 7 | improvements= 14 | delta_lnL= 0.0/ 30.9 472s 80s | 15 | lnL= -12454.6 | depth= 2/ 5 | improvements= 14 | delta_lnL= 7.3/ 30.9 472s 82s | 16 | lnL= -12462.0 | depth= 2/ 6 | improvements= 16 | delta_lnL= 2.7/ 30.9 472s 472s . Third round of optimization... 482s 496s 93s | 17 | lnL= -12445.6 | depth= 1/ 10 | improvements= 6 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 508s 107s | 18 | lnL= -12445.4 | depth= 0/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 8 + 519s 119s | 19 | lnL= -12444.7 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 535s 129s | 20 | lnL= -12443.1 | depth= 1/ 5 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 535s 146s | 21 | lnL= -12443.1 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 535s 535s . Final optimisation steps... 542s 542s 542s . Log likelihood of the current tree: -12443.048574183545497362501919269561767578. 542s 547s . Calculating fast branch supports (using 'aBayes'). 547s 547s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 547s 547s . Time used 0h2m38s 547s 547s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 547s AA sequential sequence file, with customization single processor: 547s + echo 'AA sequential sequence file, with customization single processor:' 547s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 547s 547s 547s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 547s 547s 547s 547s 547s 547s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 547s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 547s 547s . Sequence filename: example.nex 547s . Data type: dna 547s . Alphabet size: 4 547s . Sequence format: interleaved 547s . Number of data sets: 1 547s . Nb of bootstrapped data sets: 0 547s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 547s . Model name: HKY85 547s . Ts/tv ratio: estimated 547s . Proportion of invariable sites: 0.000000 547s . RAS model: discrete Gamma 547s . Number of subst. rate catgs: 4 547s . Gamma distribution parameter: estimated 547s . 'Middle' of each rate class: mean 547s . Nucleotide equilibrium frequencies: empirical 547s . Optimise tree topology: yes 547s . Starting tree: BioNJ 547s . Add random input tree: no 547s . Optimise branch lengths: yes 547s . Minimum length of an edge: 1e-08 547s . Optimise substitution model parameters: yes 547s . Run ID: none 547s . Random seed: 1710763716 547s . Subtree patterns aliasing: no 547s . Version: 3.3.3:3.3.20220408-3 547s . Byte alignment: 1 547s . AVX enabled: no 547s . SSE enabled: no 547s 547s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 547s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 547s 547s 547s 547s . 1037 patterns found (out of a total of 2888 sites). 547s 547s . 1378 sites without polymorphism (47.71%). 547s 547s 547s . Computing pairwise distances... 547s 547s . Building BioNJ tree... 547s 547s . This analysis requires at least 3 MB of memory space. 547s 547s 547s . Score of initial tree: -12664.54 547s 547s . Starting first round of SPRs... 547s 547s 0s | 1 | lnL= -12638.5 | depth= 1/ 40 | improvements= 1 | delta_lnL= 0.0/ 1000.0 547s 547s . Second round of optimization... 547s 547s 0s | 2 | lnL= -12601.5 | depth= 1/ 36 | improvements= 4 | delta_lnL= 0.0/ 1000.0 547s 547s . Third round of optimization... 547s 547s 0s | 3 | lnL= -12575.9 | depth= 1/ 20 | improvements= 2 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 548s 0s | 4 | lnL= -12564.1 | depth= 1/ 16 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 548s 1s | 5 | lnL= -12563.5 | depth= 0/ 12 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 548s 548s . Final optimisation steps... 548s 548s 548s . Log likelihood of the current tree: -12563.118859055624852771870791912078857422. 548s 548s . Calculating fast branch supports (using 'aBayes'). 548s 548s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 548s 548s . Time used 0h0m1s 548s 548s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 548s + export PHYMLCPUS=2 548s + PHYMLCPUS=2 548s + echo 'DNA interleaved sequence file, default parameters using 2 processors:' 548s DNA interleaved sequence file, default parameters using 2 processors: 548s + /usr/bin/phyml -i nucleic 548s 548s 548s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 548s 548s 548s 548s 548s 548s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 548s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 548s 548s . Sequence filename: nucleic 548s . Data type: dna 548s . Alphabet size: 4 548s . Sequence format: interleaved 548s . Number of data sets: 1 548s . Nb of bootstrapped data sets: 0 548s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 548s . Model name: HKY85 548s . Ts/tv ratio: estimated 548s . Proportion of invariable sites: 0.000000 548s . RAS model: discrete Gamma 548s . Number of subst. rate catgs: 4 548s . Gamma distribution parameter: estimated 548s . 'Middle' of each rate class: mean 548s . Nucleotide equilibrium frequencies: empirical 548s . Optimise tree topology: yes 548s . Starting tree: BioNJ 548s . Add random input tree: no 548s . Optimise branch lengths: yes 548s . Minimum length of an edge: 1e-08 548s . Optimise substitution model parameters: yes 548s . Run ID: none 548s . Random seed: 1710763717 548s . Subtree patterns aliasing: no 548s . Version: 3.3.3:3.3.20220408-3 548s . Byte alignment: 1 548s . AVX enabled: no 548s . SSE enabled: no 548s 548s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 548s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 548s 548s 548s 548s . 382 patterns found (out of a total of 886 sites). 548s 548s . 582 sites without polymorphism (65.69%). 548s 548s 548s . Computing pairwise distances... 548s 548s . Building BioNJ tree... 548s 548s . This analysis requires at least 11 MB of memory space. 548s 548s 549s . Score of initial tree: -5680.04 549s 549s . Starting first round of SPRs... 551s 553s 3s | 1 | lnL= -5435.5 | depth= 5/ 40 | improvements= 17 | delta_lnL= 7.0/ 1000.0 553s 5s | 2 | lnL= -5430.1 | depth= 1/ 24 | improvements= 11 | delta_lnL= 0.0/ 1000.0 + 553s 553s . Second round of optimization... 554s 555s 6s | 3 | lnL= -5449.0 | depth= 1/ 21 | improvements= 21 | delta_lnL= 0.0/ 1000.0 556s 7s | 4 | lnL= -5458.2 | depth= 3/ 16 | improvements= 13 | delta_lnL= 6.3/ 1000.0 556s 8s | 5 | lnL= -5458.3 | depth= 5/ 12 | improvements= 30 | delta_lnL= 16.1/ 1000.0 556s 8s | 6 | lnL= -5436.6 | depth= 1/ 9 | improvements= 14 | delta_lnL= 0.0/ 20.0 557s 8s | 7 | lnL= -5433.3 | depth= 5/ 7 | improvements= 23 | delta_lnL= 9.3/ 20.0 557s 9s | 8 | lnL= -5442.9 | depth= 2/ 9 | improvements= 24 | delta_lnL= 10.3/ 20.0 557s 9s | 9 | lnL= -5451.2 | depth= 2/ 7 | improvements= 24 | delta_lnL= 10.3/ 20.0 558s 9s | 10 | lnL= -5434.1 | depth= 1/ 6 | improvements= 15 | delta_lnL= 0.0/ 20.5 558s 10s | 11 | lnL= -5440.8 | depth= 1/ 5 | improvements= 13 | delta_lnL= 0.0/ 20.5 559s 10s | 12 | lnL= -5429.2 | depth= 1/ 5 | improvements= 9 | delta_lnL= 0.0/ 20.5 + 559s 11s | 13 | lnL= -5435.4 | depth= 3/ 5 | improvements= 12 | delta_lnL= 19.9/ 20.5 559s 11s | 14 | lnL= -5437.2 | depth= 3/ 7 | improvements= 14 | delta_lnL= 14.1/ 20.0 560s 11s | 15 | lnL= -5436.6 | depth= 2/ 7 | improvements= 14 | delta_lnL= 5.0/ 20.0 560s 11s | 16 | lnL= -5435.7 | depth= 1/ 6 | improvements= 17 | delta_lnL= 0.0/ 20.0 560s 12s | 17 | lnL= -5433.9 | depth= 1/ 5 | improvements= 10 | delta_lnL= 0.0/ 20.0 560s 12s | 18 | lnL= -5423.8 | depth= 2/ 5 | improvements= 17 | delta_lnL= 8.8/ 28.2 + 561s 12s | 19 | lnL= -5428.4 | depth= 1/ 6 | improvements= 14 | delta_lnL= 0.0/ 28.2 562s 13s | 20 | lnL= -5431.5 | depth= 2/ 5 | improvements= 20 | delta_lnL= 7.0/ 28.2 562s 14s | 21 | lnL= -5433.1 | depth= 1/ 6 | improvements= 16 | delta_lnL= 0.0/ 28.2 562s 14s | 22 | lnL= -5426.6 | depth= 1/ 5 | improvements= 11 | delta_lnL= 0.0/ 20.0 562s 14s | 23 | lnL= -5431.4 | depth= 3/ 5 | improvements= 6 | delta_lnL= 4.3/ 20.0 563s 14s | 24 | lnL= -5427.5 | depth= 5/ 7 | improvements= 9 | delta_lnL= 8.2/ 20.0 563s 15s | 25 | lnL= -5426.9 | depth= 2/ 9 | improvements= 14 | delta_lnL= 1.8/ 20.0 563s 15s | 26 | lnL= -5439.8 | depth= 2/ 7 | improvements= 9 | delta_lnL= 2.0/ 20.0 563s 15s | 27 | lnL= -5431.9 | depth= 6/ 6 | improvements= 9 | delta_lnL= 19.8/ 20.0 563s 563s . Third round of optimization... 565s 567s 17s | 28 | lnL= -5421.9 | depth= 6/ 10 | improvements= 6 | delta_lnL= 11.5/ 100.0 | triple moves= 5 + 569s 19s | 29 | lnL= -5420.5 | depth= 1/ 12 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 569s 21s | 30 | lnL= -5420.4 | depth= 0/ 9 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 569s 569s . Final optimisation steps... 570s 570s 570s . Log likelihood of the current tree: -5420.255981770986181800253689289093017578. 570s 571s . Calculating fast branch supports (using 'aBayes'). 571s 571s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 571s 571s . Time used 0h0m23s 571s 571s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 571s AA interleaved sequence file, default parameters using 2 processors: 571s + echo 'AA interleaved sequence file, default parameters using 2 processors:' 571s + /usr/bin/phyml -i proteic -d aa 571s 571s 571s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 571s 571s 571s 571s 571s 571s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 571s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 571s 571s . Sequence filename: proteic 571s . Data type: aa 571s . Alphabet size: 20 571s . Sequence format: interleaved 571s . Number of data sets: 1 571s . Nb of bootstrapped data sets: 0 571s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 571s . Model name: LG 571s . Proportion of invariable sites: 0.000000 571s . RAS model: discrete Gamma 571s . Number of subst. rate catgs: 4 571s . Gamma distribution parameter: estimated 571s . 'Middle' of each rate class: mean 571s . Amino-acid equilibrium frequencies: empirical 571s . Optimise tree topology: yes 571s . Starting tree: BioNJ 571s . Add random input tree: no 571s . Optimise branch lengths: yes 571s . Minimum length of an edge: 1e-08 571s . Optimise substitution model parameters: yes 571s . Run ID: none 571s . Random seed: 1710763740 571s . Subtree patterns aliasing: no 571s . Version: 3.3.3:3.3.20220408-3 571s . Byte alignment: 1 571s . AVX enabled: no 571s . SSE enabled: no 571s 571s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 571s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 571s 571s 571s 571s . 429 patterns found (out of a total of 547 sites). 571s 571s . 136 sites without polymorphism (24.86%). 571s 571s 571s . Computing pairwise distances... 571s 571s . Building BioNJ tree... 571s 571s . This analysis requires at least 39 MB of memory space. 571s 571s 574s . Score of initial tree: -12569.85 574s 574s . Starting first round of SPRs... 584s 584s 13s | 1 | lnL= -12481.2 | depth= 2/ 40 | improvements= 13 | delta_lnL= 6.4/ 1000.0 584s 584s . Second round of optimization... 594s 603s 23s | 2 | lnL= -12489.2 | depth= 1/ 36 | improvements= 19 | delta_lnL= 0.0/ 1000.0 613s 32s | 3 | lnL= -12489.6 | depth= 1/ 20 | improvements= 15 | delta_lnL= 0.0/ 1000.0 623s 42s | 4 | lnL= -12464.2 | depth= 2/ 16 | improvements= 13 | delta_lnL= 6.0/ 1000.0 625s 52s | 5 | lnL= -12525.3 | depth= 2/ 12 | improvements= 20 | delta_lnL= 3.2/ 1000.0 627s 54s | 6 | lnL= -12487.7 | depth= 2/ 9 | improvements= 18 | delta_lnL= 23.1/ 20.0 630s 56s | 7 | lnL= -12464.3 | depth= 3/ 7 | improvements= 17 | delta_lnL= 8.0/ 20.0 632s 59s | 8 | lnL= -12465.2 | depth= 2/ 7 | improvements= 16 | delta_lnL= 79.8/ 20.0 636s 61s | 9 | lnL= -12468.7 | depth= 2/ 6 | improvements= 18 | delta_lnL= 12.6/ 20.0 643s 65s | 10 | lnL= -12478.7 | depth= 4/ 6 | improvements= 26 | delta_lnL= 43.5/ 159.5 643s 72s | 11 | lnL= -12453.8 | depth= 1/ 8 | improvements= 15 | delta_lnL= 0.0/ 159.5 643s 643s . Third round of optimization... 655s 671s 84s | 12 | lnL= -12443.1 | depth= 1/ 10 | improvements= 4 | delta_lnL= 0.0/ 159.5 | triple moves= 5 + 671s 100s | 13 | lnL= -12443.1 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 671s 671s . Final optimisation steps... 677s 677s 677s . Log likelihood of the current tree: -12443.048713260022850590758025646209716797. 677s 682s . Calculating fast branch supports (using 'aBayes'). 682s 682s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 682s 682s . Time used 0h1m51s 682s 682s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 682s AA sequential sequence file, with customization using 2 processors: 682s + echo 'AA sequential sequence file, with customization using 2 processors:' 682s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 682s 682s 682s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 682s 682s 682s 682s 682s 682s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 682s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 682s 682s . Sequence filename: example.nex 682s . Data type: dna 682s . Alphabet size: 4 682s . Sequence format: interleaved 682s . Number of data sets: 1 682s . Nb of bootstrapped data sets: 0 682s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 682s . Model name: HKY85 682s . Ts/tv ratio: estimated 682s . Proportion of invariable sites: 0.000000 682s . RAS model: discrete Gamma 682s . Number of subst. rate catgs: 4 682s . Gamma distribution parameter: estimated 682s . 'Middle' of each rate class: mean 682s . Nucleotide equilibrium frequencies: empirical 682s . Optimise tree topology: yes 682s . Starting tree: BioNJ 682s . Add random input tree: no 682s . Optimise branch lengths: yes 682s . Minimum length of an edge: 1e-08 682s . Optimise substitution model parameters: yes 682s . Run ID: none 682s . Random seed: 1710763851 682s . Subtree patterns aliasing: no 682s . Version: 3.3.3:3.3.20220408-3 682s . Byte alignment: 1 682s . AVX enabled: no 682s . SSE enabled: no 682s 682s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 682s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 682s 682s 682s 682s . 1037 patterns found (out of a total of 2888 sites). 682s 682s . 1378 sites without polymorphism (47.71%). 682s 682s 682s . Computing pairwise distances... 682s 682s . Building BioNJ tree... 682s 682s . This analysis requires at least 3 MB of memory space. 682s 682s 682s . Score of initial tree: -12664.54 682s 682s . Starting first round of SPRs... 682s 682s 0s | 1 | lnL= -12637.7 | depth= 2/ 40 | improvements= 5 | delta_lnL= 60.8/ 1000.0 682s 682s . Second round of optimization... 682s 682s 0s | 2 | lnL= -12587.2 | depth= 2/ 36 | improvements= 6 | delta_lnL= 554.7/ 1000.0 682s 0s | 3 | lnL= -12576.8 | depth= 1/ 20 | improvements= 3 | delta_lnL= 0.0/ 1000.0 682s 682s . Third round of optimization... 682s 683s 0s | 4 | lnL= -12564.6 | depth= 1/ 16 | improvements= 1 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 683s 1s | 5 | lnL= -12563.5 | depth= 0/ 12 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 683s 683s . Final optimisation steps... 683s 683s 683s . Log likelihood of the current tree: -12563.118859055624852771870791912078857422. 683s 683s . Calculating fast branch supports (using 'aBayes'). 683s 683s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 683s 683s . Time used 0h0m1s 683s 683s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 683s + echo PASS 683s PASS 684s autopkgtest [12:10:53]: test run-unit-test: -----------------------] 684s run-unit-test PASSautopkgtest [12:10:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 684s 685s autopkgtest [12:10:54]: @@@@@@@@@@@@@@@@@@@@ summary 685s run-unit-test PASS 711s Creating nova instance adt-noble-arm64-phyml-20240318-115929-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240317.img (UUID 7a23b7f2-4731-4803-bcc6-08355044298e)...