0s autopkgtest [02:19:02]: starting date and time: 2025-05-03 02:19:02+0000 0s autopkgtest [02:19:02]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [02:19:02]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jfng1zdd/out --timeout-copy=6000 --setup-commands '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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:mpich --apt-upgrade hyphy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=mpich/4.3.0-5 -- lxd -r lxd-armhf-10.145.243.197 lxd-armhf-10.145.243.197:autopkgtest/ubuntu/questing/armhf 19s autopkgtest [02:19:21]: testbed dpkg architecture: armhf 21s autopkgtest [02:19:23]: testbed apt version: 3.0.0 25s autopkgtest [02:19:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 26s autopkgtest [02:19:28]: testbed release detected to be: None 34s autopkgtest [02:19:36]: updating testbed package index (apt update) 36s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 36s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 36s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 36s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 36s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.4 kB] 36s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [169 kB] 36s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1934 kB] 36s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [204 kB] 36s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [1371 kB] 36s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [12.5 kB] 36s Get:11 http://ftpmaster.internal/ubuntu questing/main Sources [1390 kB] 36s Get:12 http://ftpmaster.internal/ubuntu questing/universe Sources [21.1 MB] 37s Get:13 http://ftpmaster.internal/ubuntu questing/multiverse Sources [299 kB] 37s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf Packages [1358 kB] 37s Get:15 http://ftpmaster.internal/ubuntu questing/universe armhf Packages [15.2 MB] 38s Get:16 http://ftpmaster.internal/ubuntu questing/multiverse armhf Packages [173 kB] 41s Fetched 43.7 MB in 5s (8253 kB/s) 42s Reading package lists... 47s autopkgtest [02:19:49]: upgrading testbed (apt dist-upgrade and autopurge) 49s Reading package lists... 49s Building dependency tree... 49s Reading state information... 50s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 50s Starting 2 pkgProblemResolver with broken count: 0 50s Done 51s Entering ResolveByKeep 51s 51s Calculating upgrade... 52s The following packages will be upgraded: 52s base-files distro-info-data dpkg dpkg-dev ed fwupd htop libdpkg-perl 52s libftdi1-2 libfwupd3 libnpth0t64 libnvme1t64 libsensors-config libsensors5 52s liburcu8t64 motd-news-config nano ubuntu-pro-client ubuntu-pro-client-l10n 52s usb.ids 52s 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Need to get 5431 kB of archives. 52s After this operation, 3722 kB disk space will be freed. 52s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf motd-news-config all 13.7ubuntu1 [5260 B] 52s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf base-files armhf 13.7ubuntu1 [75.4 kB] 52s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf dpkg armhf 1.22.18ubuntu3 [1254 kB] 52s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libnpth0t64 armhf 1.8-3 [7716 B] 52s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf distro-info-data all 0.64 [6664 B] 52s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client-l10n armhf 35.1ubuntu0 [19.7 kB] 52s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client armhf 35.1ubuntu0 [258 kB] 52s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf ed armhf 1.21.1-1 [53.0 kB] 52s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libsensors-config all 1:3.6.2-2 [6756 B] 52s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libsensors5 armhf 1:3.6.2-2 [26.8 kB] 52s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf liburcu8t64 armhf 0.15.2-2 [57.3 kB] 52s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf nano armhf 8.4-1 [278 kB] 52s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf usb.ids all 2025.04.01-1 [223 kB] 52s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf dpkg-dev all 1.22.18ubuntu3 [1089 kB] 52s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libdpkg-perl all 1.22.18ubuntu3 [281 kB] 52s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf fwupd armhf 2.0.8-3 [1414 kB] 53s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libfwupd3 armhf 2.0.8-3 [126 kB] 53s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf htop armhf 3.4.1-4 [147 kB] 53s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libftdi1-2 armhf 1.5-10 [27.8 kB] 53s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libnvme1t64 armhf 1.13-2 [74.3 kB] 53s Fetched 5431 kB in 1s (6003 kB/s) 53s (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 ... 63953 files and directories currently installed.) 53s Preparing to unpack .../motd-news-config_13.7ubuntu1_all.deb ... 53s Unpacking motd-news-config (13.7ubuntu1) over (13.6ubuntu2) ... 53s Preparing to unpack .../base-files_13.7ubuntu1_armhf.deb ... 53s Unpacking base-files (13.7ubuntu1) over (13.6ubuntu2) ... 53s Setting up base-files (13.7ubuntu1) ... 53s Installing new version of config file /etc/issue ... 53s Installing new version of config file /etc/issue.net ... 53s Installing new version of config file /etc/lsb-release ... 54s motd-news.service is a disabled or a static unit not running, not starting it. 54s (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 ... 63953 files and directories currently installed.) 54s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 54s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 54s Setting up dpkg (1.22.18ubuntu3) ... 55s (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 ... 63953 files and directories currently installed.) 55s Preparing to unpack .../libnpth0t64_1.8-3_armhf.deb ... 55s Unpacking libnpth0t64:armhf (1.8-3) over (1.8-2) ... 55s Setting up libnpth0t64:armhf (1.8-3) ... 55s (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 ... 63953 files and directories currently installed.) 55s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 55s Unpacking distro-info-data (0.64) over (0.63) ... 55s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 55s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 55s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 55s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 55s Preparing to unpack .../03-ed_1.21.1-1_armhf.deb ... 55s Unpacking ed (1.21.1-1) over (1.21-1) ... 55s Preparing to unpack .../04-libsensors-config_1%3a3.6.2-2_all.deb ... 55s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 55s Preparing to unpack .../05-libsensors5_1%3a3.6.2-2_armhf.deb ... 55s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 55s Preparing to unpack .../06-liburcu8t64_0.15.2-2_armhf.deb ... 55s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 55s Preparing to unpack .../07-nano_8.4-1_armhf.deb ... 55s Unpacking nano (8.4-1) over (8.3-1) ... 56s Preparing to unpack .../08-usb.ids_2025.04.01-1_all.deb ... 56s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 56s Preparing to unpack .../09-dpkg-dev_1.22.18ubuntu3_all.deb ... 56s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 56s Preparing to unpack .../10-libdpkg-perl_1.22.18ubuntu3_all.deb ... 56s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 56s Preparing to unpack .../11-fwupd_2.0.8-3_armhf.deb ... 56s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 56s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 56s Preparing to unpack .../12-libfwupd3_2.0.8-3_armhf.deb ... 56s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 56s Preparing to unpack .../13-htop_3.4.1-4_armhf.deb ... 56s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 56s Preparing to unpack .../14-libftdi1-2_1.5-10_armhf.deb ... 56s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 56s Preparing to unpack .../15-libnvme1t64_1.13-2_armhf.deb ... 56s Unpacking libnvme1t64 (1.13-2) over (1.11.1-2) ... 56s Setting up motd-news-config (13.7ubuntu1) ... 56s Setting up liburcu8t64:armhf (0.15.2-2) ... 56s Setting up distro-info-data (0.64) ... 56s Setting up htop (3.4.1-4) ... 56s Setting up libsensors-config (1:3.6.2-2) ... 56s Installing new version of config file /etc/sensors3.conf ... 56s Setting up libfwupd3:armhf (2.0.8-3) ... 56s Setting up libftdi1-2:armhf (1.5-10) ... 56s Setting up libnvme1t64 (1.13-2) ... 56s Setting up ed (1.21.1-1) ... 56s Setting up usb.ids (2025.04.01-1) ... 56s Setting up libsensors5:armhf (1:3.6.2-2) ... 56s Setting up libdpkg-perl (1.22.18ubuntu3) ... 56s Setting up nano (8.4-1) ... 56s Installing new version of config file /etc/nanorc ... 56s Setting up ubuntu-pro-client (35.1ubuntu0) ... 56s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 56s 56s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 56s 56s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 56s 58s Setting up fwupd (2.0.8-3) ... 58s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 58s fwupd.service is a disabled or a static unit not running, not starting it. 58s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 58s Setting up dpkg-dev (1.22.18ubuntu3) ... 58s Processing triggers for dbus (1.16.2-2ubuntu1) ... 58s Processing triggers for install-info (7.1.1-1) ... 58s Processing triggers for libc-bin (2.41-6ubuntu1) ... 59s Processing triggers for man-db (2.13.0-1) ... 60s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 60s Processing triggers for initramfs-tools (0.147ubuntu1) ... 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Starting pkgProblemResolver with broken count: 0 63s Starting 2 pkgProblemResolver with broken count: 0 63s Done 63s Solving dependencies... 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s autopkgtest [02:20:08]: rebooting testbed after setup commands that affected boot 106s autopkgtest [02:20:48]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 130s autopkgtest [02:21:12]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 147s Get:1 http://ftpmaster.internal/ubuntu questing/universe hyphy 2.5.68+dfsg-1 (dsc) [2420 B] 147s Get:2 http://ftpmaster.internal/ubuntu questing/universe hyphy 2.5.68+dfsg-1 (tar) [2633 kB] 147s Get:3 http://ftpmaster.internal/ubuntu questing/universe hyphy 2.5.68+dfsg-1 (diff) [17.3 kB] 147s gpgv: Signature made Sat Feb 15 21:16:28 2025 UTC 147s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 147s gpgv: issuer "emollier@debian.org" 147s gpgv: Can't check signature: No public key 147s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.68+dfsg-1.dsc: no acceptable signature found 147s autopkgtest [02:21:29]: testing package hyphy version 2.5.68+dfsg-1 149s autopkgtest [02:21:31]: build not needed 152s autopkgtest [02:21:34]: test run-unit-tests: preparing testbed 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 155s Starting pkgProblemResolver with broken count: 0 155s Starting 2 pkgProblemResolver with broken count: 0 155s Done 156s The following NEW packages will be installed: 156s hyphy-common hyphy-mpi hyphy-pt libgfortran5 libgomp1 libhwloc15 libmpich12 156s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 4664 kB of archives. 156s After this operation, 14.2 MB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu questing/universe armhf hyphy-common all 2.5.68+dfsg-1 [633 kB] 156s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15-20250404-0ubuntu1 [128 kB] 156s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15-20250404-0ubuntu1 [331 kB] 156s Get:4 http://ftpmaster.internal/ubuntu questing/universe armhf libhwloc15 armhf 2.12.0-1 [147 kB] 156s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf libmpich12 armhf 4.3.0-5 [1680 kB] 156s Get:6 http://ftpmaster.internal/ubuntu questing/universe armhf hyphy-mpi armhf 2.5.68+dfsg-1 [881 kB] 156s Get:7 http://ftpmaster.internal/ubuntu questing/universe armhf hyphy-pt armhf 2.5.68+dfsg-1 [862 kB] 157s Fetched 4664 kB in 1s (6315 kB/s) 157s Selecting previously unselected package hyphy-common. 157s (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 ... 63951 files and directories currently installed.) 157s Preparing to unpack .../0-hyphy-common_2.5.68+dfsg-1_all.deb ... 157s Unpacking hyphy-common (2.5.68+dfsg-1) ... 157s Selecting previously unselected package libgomp1:armhf. 157s Preparing to unpack .../1-libgomp1_15-20250404-0ubuntu1_armhf.deb ... 157s Unpacking libgomp1:armhf (15-20250404-0ubuntu1) ... 157s Selecting previously unselected package libgfortran5:armhf. 157s Preparing to unpack .../2-libgfortran5_15-20250404-0ubuntu1_armhf.deb ... 157s Unpacking libgfortran5:armhf (15-20250404-0ubuntu1) ... 157s Selecting previously unselected package libhwloc15:armhf. 157s Preparing to unpack .../3-libhwloc15_2.12.0-1_armhf.deb ... 157s Unpacking libhwloc15:armhf (2.12.0-1) ... 157s Selecting previously unselected package libmpich12:armhf. 157s Preparing to unpack .../4-libmpich12_4.3.0-5_armhf.deb ... 157s Unpacking libmpich12:armhf (4.3.0-5) ... 157s Selecting previously unselected package hyphy-mpi. 157s Preparing to unpack .../5-hyphy-mpi_2.5.68+dfsg-1_armhf.deb ... 157s Unpacking hyphy-mpi (2.5.68+dfsg-1) ... 157s Selecting previously unselected package hyphy-pt. 157s Preparing to unpack .../6-hyphy-pt_2.5.68+dfsg-1_armhf.deb ... 157s Unpacking hyphy-pt (2.5.68+dfsg-1) ... 157s Setting up hyphy-common (2.5.68+dfsg-1) ... 157s Setting up libgomp1:armhf (15-20250404-0ubuntu1) ... 157s Setting up libhwloc15:armhf (2.12.0-1) ... 157s Setting up libgfortran5:armhf (15-20250404-0ubuntu1) ... 157s Setting up libmpich12:armhf (4.3.0-5) ... 157s Setting up hyphy-mpi (2.5.68+dfsg-1) ... 157s Setting up hyphy-pt (2.5.68+dfsg-1) ... 157s Processing triggers for libc-bin (2.41-6ubuntu1) ... 157s Processing triggers for man-db (2.13.0-1) ... 169s autopkgtest [02:21:51]: test run-unit-tests: [----------------------- 171s + for i in *.bf 171s + '[' -f F81.bf ']' 171s + hyphy F81.bf 171s Log Likelihood = -1187.54703200744; 171s Tree givenTree=(256:0.01194157030973258,(822:0.02945351293498793,159:0.004470257085003581)Node2:0.003650055639925791,((113:0.02245388875674639,9939:0.07632630067786157)Node6:0.005078253846125897,(6760:0.06905819431706364,((317:0.03753836909488285,6767:0.07080218300676848)Node12:0.01229495366310879,((135:0.02047827059616498,(529:0.03338945307029744,105r:0.01321509390441439)Node18:0.02585927972142437)Node16:0.005410804961896208,(719:0.02967303110177573,136:0.008233024523449836)Node21:0.04884253286105816)Node15:0.01526772756426433)Node11:0.01379471897977262)Node9:0.02422003196170947)Node5:0.02149671369047894); 171s + for i in *.bf 171s + '[' -f F81relrate.bf ']' 171s + hyphy F81relrate.bf 171s 171s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.001004329241; 171s Tree threeTaxaTree=(a:0.08503862550048506,b:0.0733496659726116,c:0.16532297428869); 171s 171s 171s 1). With the outgroup at taxon #1, the P-value is:0.002155111413115529 171s Log Likelihood = -948.707254543075; 171s Tree threeTaxaTree=(a:0.08232758470178961,b:0.119434176151407,c:0.119434176151407); 171s 171s 171s 2). With the outgroup at taxon #2, the P-value is:0.008353507893323453 171s Log Likelihood = -947.479041953643; 171s Tree threeTaxaTree=(a:0.125176462807143,b:0.07126598668713274,c:0.125176462807143); 171s 171s 171s 3). With the outgroup at taxon #3, the P-value is:0.6669136542043973 171s Log Likelihood = -944.093621107705; 171s Tree threeTaxaTree=(a:0.07918239878311938,b:0.07918239878311938,c:0.1653649517185747); 171s + for i in *.bf 171s + '[' -f F81relratio.bf ']' 171s + hyphy F81relratio.bf 171s 171s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059588143; 171s Tree fourTaxaTree1=((1:0.1129136777212708,2:0.1073284341212764)Node1:0.09981582408869331,3:0.3469184571685557,4:0.3218847017632634); 171s Tree fourTaxaTree2=((1:0.08585401387286701,2:0.09337672071367417)Node1:0.07363354859520904,3:0.3933488462299679,4:0.3801939087080819); 171s + for i in *.bf 171s + '[' -f HKY85.bf ']' 171s + hyphy HKY85.bf 171s 171s 171s 1). Relative ratio constraint; the P-value is:0.6932596819954966 171s Log Likelihood = -2575.74636482119; 171s Global Parameters: 171s R=1.005331647214988; 171s 171s Tree fourTaxaTree1=((1:0.0995010752630784,2:0.09952542310992944)Node1:0.086894251296601,3:0.3693259760976677,4:0.3496333465726992); 171s Tree fourTaxaTree2=((1:0.099896588618542,2:0.09992103324724769)Node1:0.08723965295994933,3:0.3707940341631715,4:0.3510231271124503); 171s Log Likelihood = -1152.88077834189; 171s Tree givenTree=(256:0.01162422794812738,(822:0.02980649608213274,159:0.004016578035213079)Node2:0.003751040286659126,((113:0.02130156124261306,9939:0.07786164618036548)Node6:0.004320097443364392,(6760:0.07314674838520246,((317:0.03809749845596819,6767:0.071039342675423)Node12:0.006276019172971292,((135:0.01788765688763958,(529:0.03258473795076031,105r:0.01513842905906142)Node18:0.02833445647271447)Node16:0.00792200505967291,(719:0.02987921628181846,136:0.008041800656257675)Node21:0.04861605063139189)Node15:0.01598577054129312)Node11:0.01658540230178906)Node9:0.02665217595540978)Node5:0.02296628666558044); 171s + for i in *.bf 171s + '[' -f HKY852blocks.bf ']' 171s + hyphy HKY852blocks.bf 171s 171s ----- RESULTS ----- 171s Log Likelihood = -6801.91479154273; 171s Tree actinTree1=(ZMU60513:0,ZMU60514:0.01050229415739393,((((((ZMU60511:0.01039879500607869,ZMU60510:0.02379617015661894)Node8:0.08346711435353539,OSRAC2:0.1885132306476502)Node7:0.05842004544104068,(OSRAC1:0.01535844894021483,SVSOAC1:0.07342930727990576)Node12:0.07290684057231092)Node6:0,((OSRAC3:0.0732618293324602,ZMU60507:0.06502635733728304)Node16:0.07976126235850274,ZMU60509:0.1289303908762496)Node15:0.001266014976861183)Node5:0.08267782874448966,(MZEACT1G:0.1142644830015204,OSRAC7:0.03422182207338184)Node20:0)Node4:0.1059029507694401,ZMU60508:0.01700989113435951)Node3:0.05973115783001718); 171s Tree actinTree2=(ZMU60513:0.0101376220916668,ZMU60514:0.02362644627364487,((((((ZMU60511:0.03959555549781372,ZMU60510:0.02871061861643855)Node8:0.04600206724090228,OSRAC2:0.1281449899325073)Node7:0.02274125343580089,(OSRAC1:0.04040030135918662,SVSOAC1:0.05533587372230117)Node12:0.09056069178613274)Node6:0.02100608120850053,((OSRAC3:0.1082347706566669,ZMU60507:0.07346477215920497)Node16:0.05601727007819227,ZMU60509:0.1117727358925015)Node15:0.02915964108320797)Node5:0.04982863351139238,(MZEACT1G:0.10700588888039,OSRAC7:0.09561860582893986)Node20:0.02268275928477683)Node4:0.04830935838566316,ZMU60508:0.02346427961492001)Node3:0.05653279275237424); 171s + for i in *.bf 171s + '[' -f HKY852blocks2models.bf ']' 171s + hyphy HKY852blocks2models.bf 171s 171s ----- RESULTS ----- 171s Log Likelihood = -6049.33430813722; 171s Tree actinTree1=(ZMU60513:0.01367587046401638,ZMU60514:0.06665919602367845,((((((ZMU60511:0.1014641120057534,ZMU60510:0.08944656167127725)Node8:0.2110889304494738,OSRAC2:0.3685048915584501)Node7:0.06394907439697269,(OSRAC1:0.04344901787701395,SVSOAC1:0.2449014602439141)Node12:0.4077786194656216)Node6:0.1003519980953618,((OSRAC3:0.1861497830789513,ZMU60507:0.3290589884871684)Node16:0.1591658660544015,ZMU60509:0.4443739094270882)Node15:0.04672955703297877)Node5:0.1894652269297158,(MZEACT1G:0.324401554937936,OSRAC7:0.2477178040371583)Node20:0.009397308095440945)Node4:0.2662699745548637,ZMU60508:0.01033505016421862)Node3:0.2231171586782356); 171s Tree actinTree2=(ZMU60513:0.004498121404587605,ZMU60514:0.004483616666909012,((((((ZMU60511:0.004482582772357495,ZMU60510:0.005994558217343693)Node8:0.004874237261577059,OSRAC2:0.04746946578565068)Node7:0.003177874243367597,(OSRAC1:0.0120980013668255,SVSOAC1:0.007445359073743159)Node12:0.02730480421638957)Node6:0,((OSRAC3:0.04645235422282178,ZMU60507:0.009176463656911703)Node16:0.01045617117876243,ZMU60509:0.02448213421741781)Node15:0)Node5:0.01928018765745655,(MZEACT1G:0.03381565105374171,OSRAC7:0.03063271781779903)Node20:0.006213232319562574)Node4:0.007802704749005802,ZMU60508:0.004488393430311206)Node3:0.01512041297808624); 171s + for i in *.bf 171s + '[' -f HKY85relrate.bf ']' 171s + hyphy HKY85relrate.bf 171s 171s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371749483469; 171s Tree threeTaxaTree=(a:0.08472934037412166,b:0.07472890301156931,c:0.1740758557938472); 171s 171s 171s 1). Outgroup at taxon #1 171s a). Transition rate test. P-Value = 0.02098223879416872 171s Log Likelihood = -924.03588296772; 171s Tree threeTaxaTree=(a:0.08098747818602924,b:0.1064791178043113,c:0.1431094353098808); 171s 171s b). Transversion rate test. P-Value = 0.0365515192997512 171s Log Likelihood = -923.557343045343; 171s Tree threeTaxaTree=(a:0.08440222755317374,b:0.09108469954762791,c:0.1578859961612521); 171s 171s c). Both rates test. P-Value = 0.00632398552629243 171s Log Likelihood = -926.435155131853; 171s Tree threeTaxaTree=(a:0.08053673434172445,b:0.1248013497423081,c:0.1248013497423081); 171s 171s 171s 2). Outgroup at taxon #2 171s a). Transition rate test. P-Value = 0.02758027431692289 171s Log Likelihood = -923.79880651843; 171s Tree threeTaxaTree=(a:0.1158226503452241,b:0.07099209475456536,c:0.1443144822134573); 171s 171s b). Transversion rate test. P-Value = 0.1106459022619167 171s Log Likelihood = -922.644235271293; 171s Tree threeTaxaTree=(a:0.0976153101669943,b:0.07460629728292201,c:0.1609740140133684); 171s 171s c). Both rates test. P-Value = 0.02199510305616492 171s Log Likelihood = -925.188684922277; 171s Tree threeTaxaTree=(a:0.1299155543925802,b:0.07082227017415657,c:0.1299155543925802); 171s 171s 171s 3). Outgroup at taxon #3 171s a). Transition rate test. P-Value = 0.9291412412288365 171s Log Likelihood = -921.375703341929; 171s Tree threeTaxaTree=(a:0.08355046078962203,b:0.07588581166233505,c:0.1740233674116673); 171s + for i in *.bf 171s + '[' -f HKY85relratio.bf ']' 171s + hyphy HKY85relratio.bf 171s 171s b). Transversion rate test. P-Value = 0.5919912459797227 171s Log Likelihood = -921.515372127889; 171s Tree threeTaxaTree=(a:0.0811326387622152,b:0.0783668315308306,c:0.1741501081641941); 171s 171s c). Both rates test. P-Value = 0.8615417730841952 171s Log Likelihood = -921.52078121887; 171s Tree threeTaxaTree=(a:0.07975961308128718,b:0.07975961308128718,c:0.1741085573971581); 171s 171s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78448438335; 171s Tree fourTaxaTree1=((1:0.1137471201914315,2:0.1109458272579071)Node1:0.104085903996076,3:0.3524244630311429,4:0.3313458923456108); 171s Tree fourTaxaTree2=((1:0.08600483538490704,2:0.09359049281728829)Node1:0.08009543843528558,3:0.3858472498524633,4:0.3893810644686984); 171s 171s 171s 1). Relative ratio constraint on transitions; the P-value is:0.5738793625599388 171s Log Likelihood = -2541.23688980573; 171s Global Parameters: 171s R=0.8580636671704757; 171s 171s Tree fourTaxaTree1=((1:0.1087236125089041,2:0.09418261845403175)Node1:0.1115257358230563,3:0.3554308425770284,4:0.3552321117930402); 171s Tree fourTaxaTree2=((1:0.09042940333946518,2:0.1091728089031291)Node1:0.0729729386632967,3:0.3839422985363452,4:0.3657415465238657); 171s 171s 171s 2). Relative ratio constraint on transversions; the P-value is:0.5738082348535249 171s Log Likelihood = -2541.23709909009; 171s Global Parameters: 171s R=0.8594124128179874; 171s 171s Tree fourTaxaTree1=((1:0.1087000695612794,2:0.09418985341049585)Node1:0.1117932130274484,3:0.3553746232633633,4:0.3547712810100632); 171s Tree fourTaxaTree2=((1:0.0904580189608461,2:0.1092779814581864)Node1:0.07330035460711425,3:0.3842167406458111,4:0.3653957458529756); 171s 171s 171s 3). Relative ratio constraint on both rates; the P-value is:0.6565949282532821 171s Log Likelihood = -2543.19092026187; 171s Global Parameters: 171s R=0.9972176930513583; 171s 171s Tree fourTaxaTree1=((1:0.1004640214518551,2:0.100633019747797)Node1:0.0926095042244001,3:0.3712411460659182,4:0.3579566356877179); 171s Tree fourTaxaTree2=((1:0.1003679651208429,2:0.1006957777203389)Node1:0.09296733953971999,3:0.3699429784941881,4:0.3576743841411751); 171s + for i in *.bf 171s + '[' -f HKY85shared.bf ']' 171s + hyphy HKY85shared.bf 171s Log Likelihood = -1165.70259289855; 171s Global Parameters: 171s R=2.983249716375927; 171s 171s Tree givenTree=(256:0.01208930729064659,(822:0.02962743515800232,159:0.004651573327149412)Node2:0.003521288155942285,((113:0.02179792197615657,9939:0.07949641559104134)Node6:0.004907267345275718,(6760:0.07153257279430071,((317:0.03799895961843024,6767:0.07150722881827375)Node12:0.0117825689280443,((135:0.02022635217921053,(529:0.03405627454241462,105r:0.01305204309132222)Node18:0.02630344610507363)Node16:0.005818724756702952,(719:0.02974569203312183,136:0.008127663635706371)Node21:0.04880739487348786)Node15:0.01555349987978124)Node11:0.01396522599883533)Node9:0.02326256342167057)Node5:0.02146894156099761); 171s + for i in *.bf 171s + '[' -f JC69.bf ']' 171s + hyphy JC69.bf 171s Log Likelihood = -1227.45123365337; 171s Tree givenTree=(256:0.01208696694622769,(822:0.02897007115394309,159:0.004657405748661584)Node2:0.003647035496148864,((113:0.02417514449593859,9939:0.07266454126906927)Node6:0.005833877677539591,(6760:0.06389376388650213,((317:0.04027897712404133,6767:0.06820678814636526)Node12:0.01442297706077574,((135:0.02428976142188981,(529:0.03327882469866548,105r:0.0129676868309153)Node18:0.01987279268300712)Node16:0.003610886828061261,(719:0.02785585502509027,136:0.009989733850845532)Node21:0.05116660222311881)Node15:0.01669646444507292)Node11:0.008467916257329662)Node9:0.02635252646799721)Node5:0.02073905490525314); 171s + for i in *.bf 171s + '[' -f K2P.bf ']' 171s + hyphy K2P.bf 171s Log Likelihood = -1198.26195968369; 171s Tree givenTree=(256:0.01176775194683404,(822:0.02927198627708622,159:0.004289897859893596)Node2:0.003666798879418677,((113:0.02364929729973395,9939:0.07263496232589006)Node6:0.003385248075545885,(6760:0.06222507608795405,((317:0.04073403730255466,6767:0.06828641340159616)Node12:0.01246127310672501,((135:0.02262882060361016,(529:0.03393140558225619,105r:0.01240146696395444)Node18:0.02140651781233233)Node16:0.004487018388095514,(719:0.02880164746319956,136:0.008846375735041113)Node21:0.05081174043745197)Node15:0.01733237258834894)Node11:0.01105913820432522)Node9:0.02821203014947354)Node5:0.02370773184815646); 171s + for i in *.bf 171s + '[' -f K2Pshared.bf ']' 171s + hyphy K2Pshared.bf 171s Log Likelihood = -1210.49410568145; 171s Global Parameters: 171s R=2.61937089213609; 171s 171s Tree givenTree=(256:0.01221904543037774,(822:0.02897582226012976,159:0.004777340905979604)Node2:0.00354595736116002,((113:0.02375587644562367,9939:0.07495471211859238)Node6:0.005887352788767785,(6760:0.06492979268811275,((317:0.03970085569254105,6767:0.0694885884181338)Node12:0.01422960280589588,((135:0.02389542023749466,(529:0.03395941027442104,105r:0.01262809332180525)Node18:0.02072005270779515)Node16:0.003966885569619262,(719:0.02813866981825091,136:0.009501541498622829)Node21:0.0508033199750137)Node15:0.01659015735684541)Node11:0.008799343425496082)Node9:0.02626539731143737)Node5:0.02011348707091349); 171s + for i in *.bf 171s + '[' -f MatrixIndexing.bf ']' 171s + hyphy MatrixIndexing.bf 171s 171s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 171s { 171s {0.3911537154091415, 0.7619994263541884, 0.4373520834924076, 0.2366535834122108, 0.1943206508165041, 0.5925034597964267} 171s {0.1751866545936062, 0.498078879783414, 0.4832250383876323, 0.1319029685416964, 0.8278252295748855, 0.6906594910404318} 171s {0.7557494593215522, 0.1953065207217137, 0.6065837006565611, 0.870146549975068, 0.1181139988168408, 0.01610751520286023} 171s {0.7747665435948331, 0.009809303099710797, 0.5309334587144976, 0.02224074514169263, 0.9254504928657437, 0.7124948060867597} 171s {0.0701682467642632, 0.2739254753743125, 0.08948210908320782, 0.09427375162352662, 0.6933642639064612, 0.6870654636731058} 171s } 171s 171s 2). Accessing a second-row third-column element and a random element. 171s 171s matrix[1][2]=0.4832250383876323 171s matrix[0][4]=0.1943206508165041 171s 171s 3). Accessing the fourth row. 171s 171s matrix[3][-1]= 171s { 171s {0.7747665435948331, 0.009809303099710797, 0.5309334587144976, 0.02224074514169263, 0.9254504928657437, 0.7124948060867597} 171s } 171s 171s 4). Accessing the first column. 171s 171s matrix[-1][0]= 171s { 171s {0.3911537154091415} 171s {0.1751866545936062} 171s {0.7557494593215522} 171s {0.7747665435948331} 171s {0.0701682467642632} 171s } 171s 171s 5). Populating a matrix template (below the diagonal). 171s 171s { 171s {0, 0, 0, 0, 0, 0} 171s {1, 0, 0, 0, 0, 0} 171s {1, 1, 0, 0, 0, 0} 171s {1, 1, 1, 0, 0, 0} 171s {1, 1, 1, 1, 0, 0} 171s } 171s 171s 6). Extracting (by row) matrix elements using the template. 171s 171s { 171s {0.1751866545936062, 0.7557494593215522, 0.1953065207217137, 0.7747665435948331, 0.009809303099710797, 0.5309334587144976, 0.0701682467642632, 0.2739254753743125, 0.08948210908320782, 0.09427375162352662} 171s } 171s 171s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 171s 171s matrix[{{1,1}}][{{3,2}}]= 171s { 171s {0.498078879783414, 0.4832250383876323} 171s {0.1953065207217137, 0.6065837006565611} 171s {0.009809303099710797, 0.5309334587144976} 171s } 171s 171s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 171s 171s 171s { 171s {0.1530012290783756, 1.580643125764112, 1.19127684493515, 1.05600491854184, 1.03776051533375, 1.351060349870736} 171s {0.03069036394769947, 0.2480825704863006, 1.233506437724729, 1.017398393110112, 1.685294610720712, 1.477010532564228} 171s {0.5711572452648186, 0.03814463703642117, 0.3679437859022085, 1.757155018433513, 1.013950916716505, 1.00025945204601} 171s {0.6002631970738844, 9.622242730199584e-05, 0.2818903375825391, 0.0004946507444577244, 1.856458614745448, 1.507648848700609} 171s {0.004923582853970532, 0.07503516605904309, 0.008007047845979104, 0.008887540245174389, 0.4807540024625488, 1.47205895137234} 171s } 171s + for i in *.bf 171s + '[' -f MolecularClockF81.bf ']' 171s + hyphy MolecularClockF81.bf 171s 171s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124484594; 171s Tree theTree=(HVRNASS:0.02574919665281242,(RICRSS3:0.05627816196229702,((ZMSUCS1:0.07162024859194505,(OSRSS1A:0.06060618455867439,(TASUCSYN1:0.02788121661144526,HVSSYNMR:0.02036946313895453)Internal1:0.05183456911380498)Node9:0.02014947587484001)Node7:0.1581572896196412,(MZESUS1:0.07665747368573525,ORRSS2:0.05437772101387764)Internal2:0.02505248135203965)Node6:0.03255835250429668)Node4:0.0590061735353313,TAAJ153:0.01372210973358946); 171s 171s 171s 1). Global Molecular Clock; the P-value is:0 171s Log Likelihood = -11927.6152872493; 171s Tree theTree=(HVRNASS:0.02158166981772361,(RICRSS3:0.1233407360641715,((ZMSUCS1:0.05658071401187222,(OSRSS1A:0.04751121277440527,(TASUCSYN1:0.01824268045577751,HVSSYNMR:0.01824268045577751)Internal1:0.02926853231862776)Node9:0.009069501237466955)Node7:0.05763375047489699,(MZESUS1:0.07014762087326647,ORRSS2:0.07014762087326647)Internal2:0.04406684361350275)Node6:0.009126271577402338)Node4:0.0271485788059814,TAAJ153:0.150489314870153); 171s 171s 171s 2). Molecular Clock starting at Internal1; the P-value is:0.1603839549631757 171s Log Likelihood = -11476.6977495663; 171s Tree theTree=(HVRNASS:0.02574692039346265,(RICRSS3:0.05631337353711607,((ZMSUCS1:0.07169724453370424,(OSRSS1A:0.06052054583991417,(TASUCSYN1:0.02412439027280674,HVSSYNMR:0.02412439027280674)Internal1:0.05181073978783855)Node9:0.0201814863387963)Node7:0.1580576727021297,(MZESUS1:0.07661835911438251,ORRSS2:0.05441426276803153)Internal2:0.02508055017731211)Node6:0.03252717038463777)Node4:0.05897163549992854,TAAJ153:0.0137261481575488); 171s 171s 171s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610220638731263 171s Log Likelihood = -11479.8412474332; 171s Tree theTree=(HVRNASS:0.02577440784705996,(RICRSS3:0.05652985132445391,((ZMSUCS1:0.07147569373988488,(OSRSS1A:0.06061741340163201,(TASUCSYN1:0.02412260416960403,HVSSYNMR:0.02412260416960403)Internal1:0.05167997121679145)Node9:0.02036524986913387)Node7:0.1580488183337349,(MZESUS1:0.06553450350629444,ORRSS2:0.06553450350629444)Internal2:0.02502717219303627)Node6:0.03236307028387721)Node4:0.05874456286812835,TAAJ153:0.01369828181718582); 171s + for i in *.bf 171s + '[' -f MolecularClockHKY85.bf ']' 171s + hyphy MolecularClockHKY85.bf 172s 172s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013168618; 172s Tree theTree=(HVRNASS:0.02587788236959153,(RICRSS3:0.05729259205048916,((ZMSUCS1:0.07271757301267609,(OSRSS1A:0.06096030843672686,(TASUCSYN1:0.02742675661044371,HVSSYNMR:0.02082543096562779)Node11:0.05283733324177075)Node9:0.020513716019047)Node7:0.1590158518776523,(MZESUS1:0.07762572484315503,ORRSS2:0.05414486716163659)Node14:0.0260139228814737)Node6:0.03166984937717978)Node4:0.06041495005865165,TAAJ153:0.01384537531817507); 172s 172s 172s 1). Global Molecular Clock on transition rates; the P-value is:0 172s Log Likelihood = -11434.7016277338; 172s Tree theTree=(HVRNASS:0.02319852265708653,(RICRSS3:0.08333770336317255,((ZMSUCS1:0.06367115331692148,(OSRSS1A:0.05486245553911432,(TASUCSYN1:0.02325250855817955,HVSSYNMR:0.01890428723017799)Node11:0.04017750328458716)Node9:0.01327920055747998)Node7:0.1274462014524695,(MZESUS1:0.0723974068088815,ORRSS2:0.06226852818538089)Node14:0.03461587993567616)Node6:0.02067729181356993)Node4:0.03899761945067838,TAAJ153:0.08891418104794081); 172s 172s 172s 2). Global Molecular Clock on transversion rates; the P-value is:0 172s Log Likelihood = -11497.3782424408; 172s Tree theTree=(HVRNASS:0.02484414881184063,(RICRSS3:0.09398480687257285,((ZMSUCS1:0.06901395809945772,(OSRSS1A:0.05468852271507402,(TASUCSYN1:0.0227700412519488,HVSSYNMR:0.02034704245683567)Node11:0.04373152251687307)Node9:0.01673398114096065)Node7:0.09973502992339113,(MZESUS1:0.07447325568177149,ORRSS2:0.06134761653312838)Node14:0.03387134642434437)Node6:0.02079759829794434)Node4:0.05008306590661329,TAAJ153:0.07305937697091811); 172s 172s 172s 3). Global Molecular Clock on both rates; the P-value is:0 172s Log Likelihood = -11703.6262158785; 172s Tree theTree=(HVRNASS:0.02210035689983459,(RICRSS3:0.1239726111780801,((ZMSUCS1:0.05800841637026662,(OSRSS1A:0.04855580696226375,(TASUCSYN1:0.01834859617409475,HVSSYNMR:0.01834859617409475)Node11:0.030207210788169)Node9:0.009452609408002868)Node7:0.05730533449086256,(MZESUS1:0.07024259015881552,ORRSS2:0.07024259015881552)Node14:0.04507116070231365)Node6:0.008658860316950937)Node4:0.02800775049052099,TAAJ153:0.1519803616686011); 172s + for i in *.bf 172s + '[' -f Non-Rev.bf ']' 172s + hyphy Non-Rev.bf 172s + for i in *.bf 172s + '[' -f PBootstrapHetRates.bf ']' 172s + hyphy PBootstrapHetRates.bf 172s Log Likelihood = -1152.79448196346; 172s Global Parameters: 172s GC=0.263535162857407; 172s CG=0.1885075810361484; 172s GA=1.891157684016573; 172s CT=1.252838488250165; 172s GT=0.08574185427944443; 172s CA=0.9135943008346668; 172s AT=0.4263518112518535; 172s AG=1.563942170747208; 172s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2545757826591228; 172s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.027111686631889; 172s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.7914056218202234; 172s 172s Tree givenTree=(256:0.01344073842801947,(822:0.02842884385382469,159:0.006111495989743335)Node2:0.003451711393029723,((113:0.02187117637770682,9939:0.0793456551096081)Node6:0.004994565028460966,(6760:0.07326733500063939,((317:0.04009912767066131,6767:0.06981380532326563)Node12:0.01161315249224633,((135:0.02156415736325781,(529:0.03497027128736345,105r:0.01425491620796936)Node18:0.02379481304061909)Node16:0.005230087165647158,(719:0.02862945390643946,136:0.009575537402759279)Node21:0.04929461415423234)Node15:0.01636789094634425)Node11:0.01269357524311111)Node9:0.02193465992995534)Node5:0.02026691256394004); 172s 172s ----ORIGINAL DATA---- 172s Log Likelihood = -1127.31562027461; 172s Global Parameters: 172s alpha=0.3191246866615293; 172s kappa=0.3234741312041384; 172s 172s Tree givenTree=(256:0.01258867116303209,(822:0.0317550499305055,159:0.004693581052151676)Node2:0.003781846688879699,((113:0.02291510001727361,9939:0.09711825494153983)Node6:0.001984244781415576,(6760:0.08722285580406354,((317:0.04578654755052342,6767:0.08101533887466823)Node12:0.007439160796149111,((135:0.01866282137596953,(529:0.03695577395683033,105r:0.01500529527165549)Node18:0.0303654943365099)Node16:0.007148768572059639,(719:0.03339573808396597,136:0.007161550564659202)Node21:0.05754312789643579)Node15:0.01788266562995569)Node11:0.01883938461661665)Node9:0.02367336979972195)Node5:0.02501390479945613); 172s 172s Using the seed: 172s 1746239933 172s Category variable name: TRUE 172s Site Rate 172s 0 0.00000 172s 1 0.00000 172s 2 0.00000 172s 3 0.00000 172s 4 0.00000 172s 5 0.00000 172s 6 0.00000 172s 7 0.00000 172s 8 0.00004 172s 9 0.00006 172s 10 0.00006 172s 11 0.00007 172s 12 0.00007 172s 13 0.00010 172s 14 0.00015 172s 15 0.00015 172s 16 0.00021 172s 17 0.00024 172s 18 0.00043 172s 19 0.00079 172s 20 0.00083 172s 21 + for i in *.bf 172s + '[' -f REV.bf ']' 172s + hyphy REV.bf 172s 0.00088 172s 22 0.00101 172s 23 0.00121 172s 24 0.00124 172s 25 0.00139 172s 26 0.00175 172s 27 0.00187 172s 28 0.00238 172s 29 0.00298 172s 30 0.00302 172s 31 0.00312 172s 32 0.00321 172s 33 0.00338 172s 34 0.00342 172s 35 0.00375 172s 36 0.00402 172s 37 0.00418 172s 38 0.00426 172s 39 0.00447 172s 40 0.00548 172s 41 0.00627 172s 42 0.00629 172s 43 0.00637 172s 44 0.00717 172s 45 0.00823 172s 46 0.00856 172s 47 0.00858 172s 48 0.00858 172s 49 0.00865 172s 50 0.01035 172s 51 0.01072 172s 52 0.01187 172s 53 0.01189 172s 54 0.01278 172s 55 0.01412 172s 56 0.01744 172s 57 0.01889 172s 58 0.01969 172s 59 0.02033 172s 60 0.02122 172s 61 0.02172 172s 62 0.02235 172s 63 0.02281 172s 64 0.02443 172s 65 0.02602 172s 66 0.02914 172s 67 0.02999 172s 68 0.03035 172s 69 0.03193 172s 70 0.03198 172s 71 0.03264 172s 72 0.03360 172s 73 0.03484 172s 74 0.03609 172s 75 0.03695 172s 76 0.03908 172s 77 0.04208 172s 78 0.04221 172s 79 0.04294 172s 80 0.04475 172s 81 0.04485 172s 82 0.05028 172s 83 0.05031 172s 84 0.05145 172s 85 0.05272 172s 86 0.05500 172s 87 0.05636 172s 88 0.05675 172s 89 0.05705 172s 90 0.06024 172s 91 0.06384 172s 92 0.06401 172s 93 0.06407 172s 94 0.06668 172s 95 0.06689 172s 96 0.07373 172s 97 0.07715 172s 98 0.07846 172s 99 0.07875 172s 100 0.08133 172s 101 0.08292 172s 102 0.08390 172s 103 0.09434 172s 104 0.10107 172s 105 0.10145 172s 106 0.10472 172s 107 0.11693 172s 108 0.12813 172s 109 0.12817 172s 110 0.12854 172s 111 0.12886 172s 112 0.13777 172s 113 0.14037 172s 114 0.14049 172s 115 0.14087 172s 116 0.14144 172s 117 0.14239 172s 118 0.14768 172s 119 0.14792 172s 120 0.16061 172s 121 0.16181 172s 122 0.16567 172s 123 0.16621 172s 124 0.16693 172s 125 0.16873 172s 126 0.16986 172s 127 0.19413 172s 128 0.19694 172s 129 0.20046 172s 130 0.20458 172s 131 0.20586 172s 132 0.23264 172s 133 0.23414 172s 134 0.24137 172s 135 0.24841 172s 136 0.26890 172s 137 0.27702 172s 138 0.27837 172s 139 0.28252 172s 140 0.28636 172s 141 0.28923 172s 142 0.29368 172s 143 0.29805 172s 144 0.30541 172s 145 0.31866 172s 146 0.32087 172s 147 0.32787 172s 148 0.34798 172s 149 0.36918 172s 150 0.37641 172s 151 0.37998 172s 152 0.40629 172s 153 0.41092 172s 154 0.42095 172s 155 0.42790 172s 156 0.44117 172s 157 0.44389 172s 158 0.44552 172s 159 0.44908 172s 160 0.45980 172s 161 0.46726 172s 162 0.48166 172s 163 0.48265 172s 164 0.49247 172s 165 0.51100 172s 166 0.51744 172s 167 0.52332 172s 168 0.53398 172s 169 0.55287 172s 170 0.57095 172s 171 0.64791 172s 172 0.65151 172s 173 0.66997 172s 174 0.69493 172s 175 0.70613 172s 176 0.72210 172s 177 0.74343 172s 178 0.75020 172s 179 0.75646 172s 180 0.76582 172s 181 0.78771 172s 182 0.78941 172s 183 0.82235 172s 184 0.83073 172s 185 0.84128 172s 186 0.84662 172s 187 0.86209 172s 188 0.86648 172s 189 0.89196 172s 190 0.90600 172s 191 0.92577 172s 192 0.95599 172s 193 0.97126 172s 194 1.00613 172s 195 1.03510 172s 196 1.03957 172s 197 1.09669 172s 198 1.14842 172s 199 1.15106 172s 200 1.16547 172s 201 1.17297 172s 202 1.18067 172s 203 1.18209 172s 204 1.21522 172s 205 1.25747 172s 206 1.29753 172s 207 1.30455 172s 208 1.33728 172s 209 1.36187 172s 210 1.38020 172s 211 1.44559 172s 212 1.46180 172s 213 1.56984 172s 214 1.59284 172s 215 1.61981 172s 216 1.63538 172s 217 1.63674 172s 218 1.67631 172s 219 1.69127 172s 220 1.69506 172s 221 1.77214 172s 222 1.82851 172s 223 1.89938 172s 224 1.92752 172s 225 1.97228 172s 226 2.11808 172s 227 2.33881 172s 228 2.34604 172s 229 2.47701 172s 230 2.49689 172s 231 2.49901 172s 232 2.57373 172s 233 2.81015 172s 234 2.82529 172s 235 2.82874 172s 236 2.83208 172s 237 2.84840 172s 238 2.91009 172s 239 2.91679 172s 240 3.03332 172s 241 3.07229 172s 242 3.23117 172s 243 3.31948 172s 244 3.38722 172s 245 3.39941 172s 246 3.45936 172s 247 3.51829 172s 248 3.69329 172s 249 3.73898 172s 250 3.96215 172s 251 3.98402 172s 252 4.17947 172s 253 4.34825 172s 254 4.65664 172s 255 4.74265 172s 256 4.91060 172s 257 5.06845 172s 258 5.08961 172s 259 5.25067 172s 260 5.29401 172s 261 5.35044 172s 262 5.44802 172s 263 5.49589 172s 264 5.93731 172s 265 5.98131 172s 266 6.14448 172s 267 6.91145 172s 268 6.93055 172s 269 7.35347 172s 270 9.68466 172s 271 10.42562 172s 272 11.68656 172s 172s Mean = 1.08202580705841 172s Var = 3.35546650051419 (1/alpha) = 3.133571427711646 172s Log Likelihood = -1099.5665388497; 172s Tree givenTree=(256:0.01860402143877112,(822:0.02270203436361621,159:0.01094574789474005)Node2:0.003780101321669,((113:0.0182916674235868,9939:0.07804703030411331)Node6:0.007456943360603108,(6760:0.07116621521044149,((317:0.03718908565636331,6767:0.07207156868821403)Node12:0.01018712552554992,((135:0.02037136373409816,(529:0.03424156037408578,105r:0.01130306345437082)Node18:0.02851211743675544)Node16:0.006574155442802753,(719:0.02831061927772984,136:0.009598487153413772)Node21:0.04403970914688595)Node15:0.01655916794518934)Node11:0.01315254600351923)Node9:0.0291603444676124)Node5:0.01372288810163199); 172s + for i in *.bf 172s + '[' -f REVshared.bf ']' 172s + hyphy REVshared.bf 172s Log Likelihood = -1156.62566882287; 172s Global Parameters: 172s AT=0.3612557775631079; 172s GT=0.459329992460202; 172s CG=0.2458008734945079; 172s AG=1.841067910028053; 172s CT=1.198319611290255; 172s 172s Tree givenTree=(256:0.01207777082617417,(822:0.02972252764819471,159:0.004669830207978501)Node2:0.003489685077724224,((113:0.02209311572938878,9939:0.07980326209784899)Node6:0.004706754885626737,(6760:0.07207977755297752,((317:0.03906388596493073,6767:0.07101307566556925)Node12:0.01082398998554475,((135:0.02052071679331182,(529:0.03439888051353799,105r:0.01468353816218024)Node18:0.02466716008068647)Node16:0.005559323596174769,(719:0.02874522985064118,136:0.009475097396977484)Node21:0.04912069705550876)Node15:0.01582856772702502)Node11:0.01427609486628099)Node9:0.02298222966856438)Node5:0.02145840079658983); 172s + for i in *.bf 172s + '[' -f ReplicateConstraint1.bf ']' 172s + hyphy ReplicateConstraint1.bf 172s 1).Unconstrained HKY85 172s 172s Log Likelihood = -1152.88; 172s 172s Independent Parameters List 172s 172s Parameter 1 : hivTree.317.trvs 172s Parameter 2 : hivTree.317.trst 172s Parameter 3 : hivTree.6767.trvs 172s Parameter 4 : hivTree.6767.trst 172s Parameter 5 : hivTree.Node2.trvs 172s Parameter 6 : hivTree.Node2.trst 172s Parameter 7 : hivTree.135.trvs 172s Parameter 8 : hivTree.135.trst 172s Parameter 9 : hivTree.529.trvs 172s Parameter 10 : hivTree.529.trst 172s Parameter 11 : hivTree.105r.trvs 172s Parameter 12 : hivTree.105r.trst 172s Parameter 13 : hivTree.Node8.trvs 172s Parameter 14 : hivTree.Node8.trst 172s Parameter 15 : hivTree.iNode1.trvs 172s Parameter 16 : hivTree.iNode1.trst 172s Parameter 17 : hivTree.719.trvs 172s Parameter 18 : hivTree.719.trst 172s Parameter 19 : hivTree.136.trvs 172s Parameter 20 : hivTree.136.trst 172s Parameter 21 : hivTree.Node11.trvs 172s Parameter 22 : hivTree.Node11.trst 172s Parameter 23 : hivTree.Node5.trvs 172s Parameter 24 : hivTree.Node5.trst 172s Parameter 25 : hivTree.Node1.trvs 172s Parameter 26 : hivTree.Node1.trst 172s Parameter 27 : hivTree.6760.trvs 172s Parameter 28 : hivTree.6760.trst 172s Parameter 29 : hivTree.113.trvs 172s Parameter 30 : hivTree.113.trst 172s Parameter 31 : hivTree.9939.trvs 172s Parameter 32 : hivTree.9939.trst 172s Parameter 33 : hivTree.Node16.trvs 172s Parameter 34 : hivTree.Node16.trst 172s Parameter 35 : hivTree.256.trvs 172s Parameter 36 : hivTree.256.trst 172s Parameter 37 : hivTree.822.trvs 172s Parameter 38 : hivTree.822.trst 172s Parameter 39 : hivTree.159.trvs 172s Parameter 40 : hivTree.159.trst 172s Parameter 41 : hivTree.Node21.trvs 172s Parameter 42 : hivTree.Node21.trst 172s Parameter 43 : hivTree.iNode2.trvs 172s Parameter 44 : hivTree.iNode2.trst 172s Parameter 45 : hivTree.Node15.trvs 172s Parameter 46 : hivTree.Node15.trst 172s 172s 2).HKY85 constrained to F81 172s 172s Log Likelihood = -1187.55; 172s 172s Independent Parameters List 172s 172s Parameter 1 : hivTree.317.trvs 172s Parameter 2 : hivTree.6767.trvs 172s Parameter 3 : hivTree.Node2.trvs 172s Parameter 4 : hivTree.135.trvs 172s Parameter 5 : hivTree.529.trvs 172s Parameter 6 : hivTree.105r.trvs 172s Parameter 7 : hivTree.Node8.trvs 172s Parameter 8 : hivTree.iNode1.trvs 172s Parameter 9 : hivTree.719.trvs 172s Parameter 10 : hivTree.136.trvs 172s Parameter 11 : hivTree.Node11.trvs 172s Parameter 12 : hivTree.Node5.trvs 172s Parameter 13 : hivTree.Node1.trvs 172s Parameter 14 : hivTree.6760.trvs 172s Parameter 15 : hivTree.113.trvs 172s Parameter 16 : hivTree.9939.trvs 172s Parameter 17 : hivTree.Node16.trvs 172s Parameter 18 : hivTree.256.trvs 172s Parameter 19 : hivTree.822.trvs 172s Parameter 20 : hivTree.159.trvs 172s Parameter 21 : hivTree.Node21.trvs 172s Parameter 22 : hivTree.iNode2.trvs 172s Parameter 23 : hivTree.Node15.trvs 172s 172s Constrained Parameters List 172s 172s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 172s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 172s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 172s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 172s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 172s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 172s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 172s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 172s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 172s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 172s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 172s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 172s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 172s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 172s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 172s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 172s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 172s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 172s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 172s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 172s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 172s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 172s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 172s 172s 3).HKY85 constrained to F81 on internal branches 172s 172s Log Likelihood = -1167.99; 172s 172s Independent Parameters List 172s 172s Parameter 1 : hivTree.Node2.trvs 172s Parameter 2 : hivTree.Node8.trvs 172s Parameter 3 : hivTree.iNode1.trvs 172s Parameter 4 : hivTree.Node11.trvs 172s Parameter 5 : hivTree.Node5.trvs 172s Parameter 6 : hivTree.Node1.trvs 172s Parameter 7 : hivTree.Node16.trvs 172s Parameter 8 : hivTree.Node21.trvs 172s Parameter 9 : hivTree.iNode2.trvs 172s Parameter 10 : hivTree.Node15.trvs 172s Parameter 11 : hivTree.317.trst 172s Parameter 12 : hivTree.317.trvs 172s Parameter 13 : hivTree.6767.trvs 172s Parameter 14 : hivTree.6767.trst 172s Parameter 15 : hivTree.135.trst 172s Parameter 16 : hivTree.135.trvs 172s Parameter 17 : hivTree.529.trvs 172s Parameter 18 : hivTree.529.trst 172s Parameter 19 : hivTree.105r.trst 172s Parameter 20 : hivTree.105r.trvs 172s Parameter 21 : hivTree.719.trvs 172s Parameter 22 : hivTree.719.trst 172s Parameter 23 : hivTree.136.trvs 172s Parameter 24 : hivTree.136.trst 172s Parameter 25 : hivTree.6760.trvs 172s Parameter 26 : hivTree.6760.trst 172s Parameter 27 : hivTree.113.trvs 172s Parameter 28 : hivTree.113.trst 172s Parameter 29 : hivTree.9939.trst 172s Parameter 30 : hivTree.9939.trvs 172s Parameter 31 : hivTree.256.trvs 172s Parameter 32 : hivTree.256.trst 172s Parameter 33 : hivTree.822.trvs 172s Parameter 34 : hivTree.822.trst 172s Parameter 35 : hivTree.159.trst 172s Parameter 36 : hivTree.159.trvs 172s 172s Constrained Parameters List 172s 172s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 172s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 172s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 172s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 172s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 172s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 172s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 172s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 172s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 172s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 172s 172s 4).HKY85 with shared ratio. 172s 172s Log Likelihood = -1165.7; 172s 172s Independent Parameters List 172s 172s Parameter 1 : R 172s Parameter 2 : hivTree.317.trst 172s Parameter 3 : hivTree.6767.trst 172s Parameter 4 : hivTree.Node2.trst 172s Parameter 5 : hivTree.135.trst 172s Parameter 6 : hivTree.529.trst 172s Parameter 7 : hivTree.105r.trst 172s Parameter 8 : hivTree.Node8.trst 172s Parameter 9 : hivTree.iNode1.trst 172s Parameter 10 : hivTree.719.trst 172s Parameter 11 : hivTree.136.trst 172s Parameter 12 : hivTree.Node11.trst 172s Parameter 13 : hivTree.Node5.trst 172s Parameter 14 : hivTree.Node1.trst 172s Parameter 15 : hivTree.6760.trst 172s Parameter 16 : hivTree.113.trst 172s Parameter 17 : hivTree.9939.trst 172s Parameter 18 : hivTree.Node16.trst 172s Parameter 19 : hivTree.256.trst 172s Parameter 20 : hivTree.822.trst 172s Parameter 21 : hivTree.159.trst 172s Parameter 22 : hivTree.Node21.trst 172s Parameter 23 : hivTree.iNode2.trst 172s Parameter 24 : hivTree.Node15.trst 172s 172s Constrained Parameters List 172s 172s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 172s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 172s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 172s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 172s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 172s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 172s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 172s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 172s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 172s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 172s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 172s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 172s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 172s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 172s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 172s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 172s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 172s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 172s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 172s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 172s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 172s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 172s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 172s + '[' -f ReplicateConstraint2.bf ']' 172s + hyphy ReplicateConstraint2.bf 172s 1).Unconstrained HKY85 172s 172s Log Likelihood = -1152.88; 172s 172s Independent Parameters List 172s 172s Parameter 1 : hivTree.317.trvs 172s Parameter 2 : hivTree.317.trst 172s Parameter 3 : hivTree.6767.trvs 172s Parameter 4 : hivTree.6767.trst 172s Parameter 5 : hivTree.Node2.trvs 172s Parameter 6 : hivTree.Node2.trst 172s Parameter 7 : hivTree.135.trvs 172s Parameter 8 : hivTree.135.trst 172s Parameter 9 : hivTree.529.trvs 172s Parameter 10 : hivTree.529.trst 172s Parameter 11 : hivTree.105r.trvs 172s Parameter 12 : hivTree.105r.trst 172s Parameter 13 : hivTree.Node8.trvs 172s Parameter 14 : hivTree.Node8.trst 172s Parameter 15 : hivTree.iNode1.trvs 172s Parameter 16 : hivTree.iNode1.trst 172s Parameter 17 : hivTree.719.trvs 172s Parameter 18 : hivTree.719.trst 172s Parameter 19 : hivTree.136.trvs 172s Parameter 20 : hivTree.136.trst 172s Parameter 21 : hivTree.Node11.trvs 172s Parameter 22 : hivTree.Node11.trst 172s Parameter 23 : hivTree.Node5.trvs 172s Parameter 24 : hivTree.Node5.trst 172s Parameter 25 : hivTree.Node1.trvs 172s Parameter 26 : hivTree.Node1.trst 172s Parameter 27 : hivTree.6760.trvs 172s Parameter 28 : hivTree.6760.trst 172s Parameter 29 : hivTree.113.trvs 172s Parameter 30 : hivTree.113.trst 172s Parameter 31 : hivTree.9939.trvs 172s Parameter 32 : hivTree.9939.trst 172s Parameter 33 : hivTree.Node16.trvs 172s Parameter 34 : hivTree.Node16.trst 172s Parameter 35 : hivTree.256.trvs 172s Parameter 36 : hivTree.256.trst 172s Parameter 37 : hivTree.822.trvs 172s Parameter 38 : hivTree.822.trst 172s Parameter 39 : hivTree.159.trvs 172s Parameter 40 : hivTree.159.trst 172s Parameter 41 : hivTree.Node21.trvs 172s Parameter 42 : hivTree.Node21.trst 172s Parameter 43 : hivTree.iNode2.trvs 172s Parameter 44 : hivTree.iNode2.trst 172s Parameter 45 : hivTree.Node15.trvs 173s Parameter 46 : hivTree.Node15.trst 173s 173s 2).HKY85 constrained to F81 on the "iNode1" subtree 173s 173s Log Likelihood = -1157.82; 173s 173s Independent Parameters List 173s 173s Parameter 1 : hivTree.135.trvs 173s Parameter 2 : hivTree.529.trvs 173s Parameter 3 : hivTree.105r.trvs 173s Parameter 4 : hivTree.Node8.trvs 173s Parameter 5 : hivTree.317.trvs 173s Parameter 6 : hivTree.317.trst 173s Parameter 7 : hivTree.6767.trst 173s Parameter 8 : hivTree.6767.trvs 173s Parameter 9 : hivTree.Node2.trst 173s Parameter 10 : hivTree.Node2.trvs 173s Parameter 11 : hivTree.iNode1.trvs 173s Parameter 12 : hivTree.iNode1.trst 173s Parameter 13 : hivTree.719.trvs 173s Parameter 14 : hivTree.719.trst 173s Parameter 15 : hivTree.136.trvs 173s Parameter 16 : hivTree.136.trst 173s Parameter 17 : hivTree.Node11.trvs 173s Parameter 18 : hivTree.Node11.trst 173s Parameter 19 : hivTree.Node5.trvs 173s Parameter 20 : hivTree.Node5.trst 173s Parameter 21 : hivTree.Node1.trvs 173s Parameter 22 : hivTree.Node1.trst 173s Parameter 23 : hivTree.6760.trvs 173s Parameter 24 : hivTree.6760.trst 173s Parameter 25 : hivTree.113.trvs 173s Parameter 26 : hivTree.113.trst 173s Parameter 27 : hivTree.9939.trvs 173s Parameter 28 : hivTree.9939.trst 173s Parameter 29 : hivTree.Node16.trvs 173s Parameter 30 : hivTree.Node16.trst 173s Parameter 31 : hivTree.256.trvs 173s Parameter 32 : hivTree.256.trst 173s Parameter 33 : hivTree.822.trvs 173s Parameter 34 : hivTree.822.trst 173s Parameter 35 : hivTree.159.trvs 173s Parameter 36 : hivTree.159.trst 173s Parameter 37 : hivTree.Node21.trvs 173s Parameter 38 : hivTree.Node21.trst 173s Parameter 39 : hivTree.iNode2.trvs 173s Parameter 40 : hivTree.iNode2.trst 173s Parameter 41 : hivTree.Node15.trvs 173s Parameter 42 : hivTree.Node15.trst 173s 173s Constrained Parameters List 173s 173s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 173s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 173s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 173s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 173s 173s 3).HKY85 constrained to F81 on the "iNode1" branch 173s 173s Log Likelihood = -1152.88; 173s 173s Independent Parameters List 173s 173s Parameter 1 : hivTree.317.trvs 173s Parameter 2 : hivTree.317.trst 173s Parameter 3 : hivTree.6767.trvs 173s Parameter 4 : hivTree.6767.trst 173s Parameter 5 : hivTree.Node2.trvs 173s Parameter 6 : hivTree.Node2.trst 173s Parameter 7 : hivTree.135.trvs 173s Parameter 8 : hivTree.135.trst 173s Parameter 9 : hivTree.529.trvs 173s Parameter 10 : hivTree.529.trst 173s Parameter 11 : hivTree.105r.trvs 173s Parameter 12 : hivTree.105r.trst 173s Parameter 13 : hivTree.Node8.trvs 173s Parameter 14 : hivTree.Node8.trst 173s Parameter 15 : hivTree.iNode1.trvs 173s Parameter 16 : hivTree.iNode1.trst 173s Parameter 17 : hivTree.719.trvs 173s Parameter 18 : hivTree.719.trst 173s Parameter 19 : hivTree.136.trvs 173s Parameter 20 : hivTree.136.trst 173s Parameter 21 : hivTree.Node11.trvs 173s Parameter 22 : hivTree.Node11.trst 173s Parameter 23 : hivTree.Node5.trvs 173s Parameter 24 : hivTree.Node5.trst 173s Parameter 25 : hivTree.Node1.trvs 173s Parameter 26 : hivTree.Node1.trst 173s Parameter 27 : hivTree.6760.trvs 173s Parameter 28 : hivTree.6760.trst 173s Parameter 29 : hivTree.113.trvs 173s Parameter 30 : hivTree.113.trst 173s Parameter 31 : hivTree.9939.trvs 173s Parameter 32 : hivTree.9939.trst 173s Parameter 33 : hivTree.Node16.trvs 173s Parameter 34 : hivTree.Node16.trst 173s Parameter 35 : hivTree.256.trvs 173s Parameter 36 : hivTree.256.trst 173s Parameter 37 : hivTree.822.trvs 173s Parameter 38 : hivTree.822.trst 173s Parameter 39 : hivTree.159.trvs 173s Parameter 40 : hivTree.159.trst 173s Parameter 41 : hivTree.Node21.trvs 173s Parameter 42 : hivTree.Node21.trst 173s Parameter 43 : hivTree.iNode2.trvs 173s Parameter 44 : hivTree.iNode2.trst 173s Parameter 45 : hivTree.Node15.trvs 173s Parameter 46 : hivTree.Node15.trst 173s 173s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 173s 173s Log Likelihood = -1152.88; 173s 173s Independent Parameters List 173s 173s Parameter 1 : hivTree.317.trvs 173s Parameter 2 : hivTree.317.trst 173s Parameter 3 : hivTree.6767.trvs 173s Parameter 4 : hivTree.6767.trst 173s Parameter 5 : hivTree.Node2.trvs 173s Parameter 6 : hivTree.Node2.trst 173s Parameter 7 : hivTree.135.trvs 173s Parameter 8 : hivTree.135.trst 173s Parameter 9 : hivTree.529.trvs 173s Parameter 10 : hivTree.529.trst 173s Parameter 11 : hivTree.105r.trvs 173s Parameter 12 : hivTree.105r.trst 173s Parameter 13 : hivTree.Node8.trvs 173s Parameter 14 : hivTree.Node8.trst 173s Parameter 15 : hivTree.iNode1.trvs 173s Parameter 16 : hivTree.iNode1.trst 173s Parameter 17 : hivTree.719.trvs 173s Parameter 18 : hivTree.719.trst 173s Parameter 19 : hivTree.136.trvs 173s Parameter 20 : hivTree.136.trst 173s Parameter 21 : hivTree.Node11.trvs 173s Parameter 22 : hivTree.Node11.trst 173s Parameter 23 : hivTree.Node5.trvs 173s Parameter 24 : hivTree.Node5.trst 173s Parameter 25 : hivTree.Node1.trvs 173s Parameter 26 : hivTree.Node1.trst 173s Parameter 27 : hivTree.6760.trvs 173s Parameter 28 : hivTree.6760.trst 173s Parameter 29 : hivTree.113.trvs 173s Parameter 30 : hivTree.113.trst 173s Parameter 31 : hivTree.9939.trvs 173s Parameter 32 : hivTree.9939.trst 173s Parameter 33 : hivTree.Node16.trvs 173s Parameter 34 : hivTree.Node16.trst 173s Parameter 35 : hivTree.256.trvs 173s Parameter 36 : hivTree.256.trst 173s Parameter 37 : hivTree.822.trvs 173s Parameter 38 : hivTree.822.trst 173s Parameter 39 : hivTree.159.trvs 173s Parameter 40 : hivTree.159.trst 173s Parameter 41 : hivTree.Node21.trvs 173s Parameter 42 : hivTree.Node21.trst 173s Parameter 43 : hivTree.iNode2.trvs 173s Parameter 44 : hivTree.iNode2.trst 173s Parameter 45 : hivTree.Node15.trvs 173s Parameter 46 : hivTree.Node15.trst 173s 173s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 173s 173s Log Likelihood = -1152.88; 173s 173s Independent Parameters List 173s 173s Parameter 1 : hivTree.317.trvs 173s Parameter 2 : hivTree.317.trst 173s Parameter 3 : hivTree.6767.trvs 173s Parameter 4 : hivTree.6767.trst 173s Parameter 5 : hivTree.Node2.trvs 173s Parameter 6 : hivTree.Node2.trst 173s Parameter 7 : hivTree.135.trvs 173s Parameter 8 : hivTree.135.trst 173s Parameter 9 : hivTree.529.trvs 173s Parameter 10 : hivTree.529.trst 173s Parameter 11 : hivTree.105r.trvs 173s Parameter 12 : hivTree.105r.trst 173s Parameter 13 : hivTree.Node8.trvs 173s Parameter 14 : hivTree.Node8.trst 173s Parameter 15 : hivTree.iNode1.trvs 173s Parameter 16 : hivTree.iNode1.trst 173s Parameter 17 : hivTree.719.trvs 173s Parameter 18 : hivTree.719.trst 173s Parameter 19 : hivTree.136.trvs 173s Parameter 20 : hivTree.136.trst 173s Parameter 21 : hivTree.Node11.trvs 173s Parameter 22 : hivTree.Node11.trst 173s Parameter 23 : hivTree.Node5.trvs 173s Parameter 24 : hivTree.Node5.trst 173s Parameter 25 : hivTree.Node1.trvs 173s Parameter 26 : hivTree.Node1.trst 173s Parameter 27 : hivTree.6760.trvs 173s Parameter 28 : hivTree.6760.trst 173s Parameter 29 : hivTree.113.trvs 173s Parameter 30 : hivTree.113.trst 173s Parameter 31 : hivTree.9939.trvs 173s Parameter 32 : hivTree.9939.trst 173s Parameter 33 : hivTree.Node16.trvs 173s Parameter 34 : hivTree.Node16.trst 173s Parameter 35 : hivTree.256.trvs 173s Parameter 36 : hivTree.256.trst 173s Parameter 37 : hivTree.822.trvs 173s Parameter 38 : hivTree.822.trst 173s Parameter 39 : hivTree.159.trvs 173s Parameter 40 : hivTree.159.trst 173s Parameter 41 : hivTree.Node21.trvs 173s Parameter 42 : hivTree.Node21.trst 173s Parameter 43 : hivTree.iNode2.trvs 173s Parameter 44 : hivTree.iNode2.trst 173s Parameter 45 : hivTree.Node15.trvs 173s Parameter 46 : hivTree.Node15.trst 173s 173s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 173s 173s Log Likelihood = -1157.82; 173s 173s Independent Parameters List 173s 173s Parameter 1 : hivTree.135.trst 173s Parameter 2 : hivTree.529.trst 173s Parameter 3 : hivTree.105r.trst 173s Parameter 4 : hivTree.Node8.trst 173s Parameter 5 : hivTree.317.trvs 173s Parameter 6 : hivTree.317.trst 173s Parameter 7 : hivTree.6767.trst 173s Parameter 8 : hivTree.6767.trvs 173s Parameter 9 : hivTree.Node2.trst 173s Parameter 10 : hivTree.Node2.trvs 173s Parameter 11 : hivTree.iNode1.trvs 173s Parameter 12 : hivTree.iNode1.trst 173s Parameter 13 : hivTree.719.trvs 173s Parameter 14 : hivTree.719.trst 173s Parameter 15 : hivTree.136.trvs 173s Parameter 16 : hivTree.136.trst 173s Parameter 17 : hivTree.Node11.trvs 173s Parameter 18 : hivTree.Node11.trst 173s Parameter 19 : hivTree.Node5.trvs 173s Parameter 20 : hivTree.Node5.trst 173s Parameter 21 : hivTree.Node1.trvs 173s Parameter 22 : hivTree.Node1.trst 173s Parameter 23 : hivTree.6760.trvs 173s Parameter 24 : hivTree.6760.trst 173s Parameter 25 : hivTree.113.trvs 173s Parameter 26 : hivTree.113.trst 173s Parameter 27 : hivTree.9939.trvs 173s Parameter 28 : hivTree.9939.trst 173s Parameter 29 : hivTree.Node16.trvs 173s Parameter 30 : hivTree.Node16.trst 173s Parameter 31 : hivTree.256.trvs 173s Parameter 32 : hivTree.256.trst 173s Parameter 33 : hivTree.822.trvs 173s Parameter 34 : hivTree.822.trst 173s Parameter 35 : hivTree.159.trvs 173s Parameter 36 : hivTree.159.trst 173s Parameter 37 : hivTree.Node21.trvs 173s Parameter 38 : hivTree.Node21.trst 173s Parameter 39 : hivTree.iNode2.trvs 173s Parameter 40 : hivTree.iNode2.trst 173s Parameter 41 : hivTree.Node15.trvs 173s Parameter 42 : hivTree.Node15.trst 173s 173s Constrained Parameters List 173s 173s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 173s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 173s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 173s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 173s + '[' -f aa.bf ']' 173s + hyphy aa.bf 173s + for i in *.bf 173s + '[' -f definitions2.bf ']' 173s + hyphy definitions2.bf 173s Log Likelihood = -1134.73158058145; 173s Tree theTree=(((Langur:0.07430857509631776,Baboon:0.03833182825671787)Node2:0.02337959221916295,Human:0.05950610076736)Node1:0.02005975146239132,Rat:0.2458687003366046,(Cow:0.2551838845340924,Horse:0.5630260062235037)Node7:0.07055351859614073); 173s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 173s 173s Sample by MEAN: 173s 173s Sample mean = 0.5 (sample variance = 0.2450374540764348) 173s 173s Rate[0]= 0.06847689 (weight=0.2500000) 173s Rate[1]= 0.23837593 (weight=0.2500000) 173s Rate[2]= 0.50000000 (weight=0.2500000) 173s Rate[3]= 1.19314718 (weight=0.2500000) 173s ------------------------------------------------ 173s 173s Sample by MEDIAN: 173s 173s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 173s 173s Rate[0]= 0.06676570 (weight=0.2500000) 173s Rate[1]= 0.23500181 (weight=0.2500000) 173s Rate[2]= 0.49041463 (weight=0.2500000) 173s Rate[3]= 1.03972077 (weight=0.2500000) 173s ------------------------------------------------ 173s 173s Sample by SCALED_MEDIAN: 173s 173s Sample mean = 0.5 (sample variance = 0.2154404122636025) 173s 173s Rate[0]= 0.07289218 (weight=0.2500000) 173s Rate[1]= 0.25656580 (weight=0.2500000) 173s Rate[2]= 0.53541552 (weight=0.2500000) 173s Rate[3]= 1.13512650 (weight=0.2500000) 173s ------------------------------------------------ 173s 173s Sample by MEAN (numerical averaging): 173s 173s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 173s 173s Rate[0]= 0.06846096 (weight=0.2500000) 173s Rate[1]= 0.23834015 (weight=0.2500000) 173s Rate[2]= 0.49996411 (weight=0.2500000) 173s Rate[3]= 1.19314889 (weight=0.2500000) 173s ------------------------------------------------ 173s 173s Sample by MEAN (numerical CDF and averaging): 173s 173s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 173s 173s Rate[0]= 0.06849282 (weight=0.2500000) 173s Rate[1]= 0.23835613 (weight=0.2500000) 173s Rate[2]= 0.49994751 (weight=0.2500000) 173s Rate[3]= 1.19311765 (weight=0.2500000) 173s ------------------------------------------------ 173s 2). Equiprobable rates sampled from Exponential with lambda = 2 173s 173s Sample by MEDIAN (3 rate classes): 173s 173s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 173s 173s Rate[0]= 0.09116078 (weight=0.3333333) 173s Rate[1]= 0.34657359 (weight=0.3333333) 173s Rate[2]= 0.89587973 (weight=0.3333333) 173s ------------------------------------------------ 173s 173s Sample by MEDIAN (9 rate classes): 173s 173s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 173s 173s Rate[0]= 0.02857921 (weight=0.1111111) 173s Rate[1]= 0.09116078+ for i in *.bf 173s + '[' -f definitions3.bf ']' 173s + hyphy definitions3.bf 173s + for i in *.bf 173s + '[' -f displayFunction.bf ']' 173s + hyphy displayFunction.bf 173s + for i in *.bf 173s + '[' -f profile_test.bf ']' 173s + hyphy profile_test.bf 173s (weight=0.1111111) 173s Rate[2]= 0.16271120 (weight=0.1111111) 173s Rate[3]= 0.24623824 (weight=0.1111111) 173s Rate[4]= 0.34657359 (weight=0.1111111) 173s Rate[5]= 0.47223080 (weight=0.1111111) 173s Rate[6]= 0.64046692 (weight=0.1111111) 173s Rate[7]= 0.89587973 (weight=0.1111111) 173s Rate[8]= 1.44518588 (weight=0.1111111) 173s ------------------------------------------------ 173s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 173s 173s Sample by MEAN (10 rate classes): 173s 173s Sample mean = 1 (sample variance = 0.1057310289486724) 173s 173s Rate[0]= 0.52447499 (weight=0.1000000) 173s Rate[1]= 0.67866972 (weight=0.1000000) 173s Rate[2]= 0.77209919 (weight=0.1000000) 173s Rate[3]= 0.85214884 (weight=0.1000000) 173s Rate[4]= 0.92850815 (weight=0.1000000) 173s Rate[5]= 1.00664500 (weight=0.1000000) 173s Rate[6]= 1.09192933 (weight=0.1000000) 173s Rate[7]= 1.19267960 (weight=0.1000000) 173s Rate[8]= 1.32858029 (weight=0.1000000) 173s Rate[9]= 1.62426489 (weight=0.1000000) 173s ------------------------------------------------ 173s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 173s 173s Sample by MEAN (10 rate classes): 173s 173s Sample mean = 2 (sample variance = 0.04259071282256564) 173s 173s Rate[0]= 1.66431246 (weight=0.1000000) 173s Rate[1]= 1.79212822 (weight=0.1000000) 173s Rate[2]= 1.86123411 (weight=0.1000000) 173s Rate[3]= 1.91722052 (weight=0.1000000) 173s Rate[4]= 1.96832799 (weight=0.1000000) 173s Rate[5]= 2.01862937 (weight=0.1000000) 173s Rate[6]= 2.07152664 (weight=0.1000000) 173s Rate[7]= 2.13166629 (weight=0.1000000) 173s Rate[8]= 2.20930216 (weight=0.1000000) 173s Rate[9]= 2.36565224 (weight=0.1000000) 173s ------------------------------------------------ 173s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 173s 173s Sample by MEAN (8 rate classes): 173s 173s Sample mean = 0.5 (sample variance = 0.09375000225643569) 173s 173s Rate[0]= 0.06250000 (weight=0.1250000) 173s Rate[1]= 0.18750000 (weight=0.1250000) 173s Rate[2]= 0.31250001 (weight=0.1250000) 173s Rate[3]= 0.43750001 (weight=0.1250000) 173s Rate[4]= 0.56249993 (weight=0.1250000) 173s Rate[5]= 0.68750001 (weight=0.1250000) 173s Rate[6]= 0.81250002 (weight=0.1250000) 173s Rate[7]= 0.93750002 (weight=0.1250000) 173s ------------------------------------------------ 173s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 173s 173s Sample by MEAN (8 rate classes): 173s 173s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 173s 173s Rate[0]= 2.17658588 (weight=0.1250000) 173s Rate[1]= 2.55230783 (weight=0.1250000) 173s Rate[2]= 2.75432532 (weight=0.1250000) 173s Rate[3]= 2.92101185 (weight=0.1250000) 173s Rate[4]= 3.07898815 (weight=0.1250000) 173s Rate[5]= 3.24567468 (weight=0.1250000) 173s Rate[6]= 3.44769217 (weight=0.1250000) 173s Rate[7]= 3.82341415 (weight=0.1250000) 173s ------------------------------------------------ 173s 173s 173s Sample mean = 1 (sample variance = 0.9920002887656187) 173s 173s Rate[0]= 0.05175536 (weight=0.1000000) 173s Rate[1]= 0.16309623 (weight=0.1000000) 173s Rate[2]= 0.28842380 (weight=0.1000000) 173s Rate[3]= 0.43177086 (weight=0.1000000) 173s Rate[4]= 0.59921784 (weight=0.1000000) 173s Rate[5]= 0.80057298 (weight=0.1000000) 173s Rate[6]= 1.05324451 (weight=0.1000000) 173s Rate[7]= 1.39304259 (weight=0.1000000) 173s Rate[8]= 1.91629073 (weight=0.1000000) 173s Rate[9]= 3.30258509 (weight=0.1000000) 173s ------------------------------------------------ 174s 174s Total run time (seconds) : 0.000001 174s Total number of steps : 1500005 174s 174s 1 : s=0; 174s Call count: 1 174s Time (seconds): 1.8e-11 174s 2 : m={5,1}; 174s Call count: 1 174s Time (seconds): 3.1e-11 174s 3 : k=0; 174s Call count: 1 174s Time (seconds): 3e-12 174s 4 : Branch under condition 'k<250000' 174s to 174s s=s+k; 174s else 174s #profilePAUSE, ; 174s Call count: 250001 174s Time (seconds): 1.056070000000834e-07 174s 5 : s=s+k; 174s Call count: 250000 174s Time (seconds): 1.126440000000904e-07 174s 6 : t=Random(0,5); 174s Call count: 250000 174s Time (seconds): 9.65650000000742e-08 174s 7 : m[t]=m[t]+1; 174s Call count: 250000 174s Time (seconds): 1.928680000001694e-07 174s 8 : k=k+1; 174s Call count: 250000 174s Time (seconds): 1.073530000000851e-07 174s 9 : Go to step 4 174s Call count: 250000 174s Time (seconds): 5.794400000003643e-08 174s 10 : #profilePAUSE, ; 174s Call count: 1 174s Time (seconds): 2e-12 174s + for i in *.bf 174s + '[' -f shared.bf ']' 174s + hyphy shared.bf 174s + rm -f '*messages.log*' '*errors.log*' 174s autopkgtest [02:21:56]: test run-unit-tests: -----------------------] 178s autopkgtest [02:22:00]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 178s run-unit-tests PASS 182s autopkgtest [02:22:04]: @@@@@@@@@@@@@@@@@@@@ summary 182s run-unit-tests PASS