0s autopkgtest [18:24:32]: starting date and time: 2025-05-02 18:24:32+0000 0s autopkgtest [18:24:32]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [18:24:32]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9jgde_7e/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-1.secgroup --name adt-questing-s390x-hyphy-20250502-182432-juju-7f2275-prod-proposed-migration-environment-20-14a11ebf-3c2f-470b-aa69-c8165bbd726c --image adt/ubuntu-questing-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 112s autopkgtest [18:26:24]: testbed dpkg architecture: s390x 113s autopkgtest [18:26:25]: testbed apt version: 3.0.0 113s autopkgtest [18:26:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 113s autopkgtest [18:26:25]: testbed release detected to be: None 114s autopkgtest [18:26:26]: updating testbed package index (apt update) 114s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 114s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 114s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 114s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 115s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.1 kB] 115s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [170 kB] 115s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2005 kB] 115s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main s390x Packages [208 kB] 115s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x Packages [1295 kB] 115s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse s390x Packages [8572 B] 115s Fetched 3841 kB in 1s (3182 kB/s) 116s Reading package lists... 116s autopkgtest [18:26:28]: upgrading testbed (apt dist-upgrade and autopurge) 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 117s Entering ResolveByKeep 117s 117s Calculating upgrade... 118s The following packages will be upgraded: 118s fwupd htop libftdi1-2 libfwupd3 libnpth0t64 libsensors-config libsensors5 118s liburcu8t64 nano usb.ids 118s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 2536 kB of archives. 118s After this operation, 3749 kB disk space will be freed. 118s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x libnpth0t64 s390x 1.8-3 [8778 B] 118s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x libsensors-config all 1:3.6.2-2 [6756 B] 118s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x libsensors5 s390x 1:3.6.2-2 [29.2 kB] 118s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x liburcu8t64 s390x 0.15.2-2 [66.3 kB] 118s Get:5 http://ftpmaster.internal/ubuntu questing/main s390x nano s390x 8.4-1 [299 kB] 118s Get:6 http://ftpmaster.internal/ubuntu questing/main s390x usb.ids all 2025.04.01-1 [223 kB] 118s Get:7 http://ftpmaster.internal/ubuntu questing/main s390x fwupd s390x 2.0.8-3 [1548 kB] 118s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x libfwupd3 s390x 2.0.8-3 [135 kB] 118s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x htop s390x 3.4.1-4 [189 kB] 118s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x libftdi1-2 s390x 1.5-10 [31.4 kB] 119s Fetched 2536 kB in 1s (3703 kB/s) 119s (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 ... 81472 files and directories currently installed.) 119s Preparing to unpack .../libnpth0t64_1.8-3_s390x.deb ... 119s Unpacking libnpth0t64:s390x (1.8-3) over (1.8-2) ... 119s Setting up libnpth0t64:s390x (1.8-3) ... 119s (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 ... 81472 files and directories currently installed.) 119s Preparing to unpack .../0-libsensors-config_1%3a3.6.2-2_all.deb ... 119s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 119s Preparing to unpack .../1-libsensors5_1%3a3.6.2-2_s390x.deb ... 119s Unpacking libsensors5:s390x (1:3.6.2-2) over (1:3.6.0-10) ... 119s Preparing to unpack .../2-liburcu8t64_0.15.2-2_s390x.deb ... 119s Unpacking liburcu8t64:s390x (0.15.2-2) over (0.15.1-1) ... 119s Preparing to unpack .../3-nano_8.4-1_s390x.deb ... 119s Unpacking nano (8.4-1) over (8.3-1) ... 119s Preparing to unpack .../4-usb.ids_2025.04.01-1_all.deb ... 119s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 119s Preparing to unpack .../5-fwupd_2.0.8-3_s390x.deb ... 119s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 119s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 119s Preparing to unpack .../6-libfwupd3_2.0.8-3_s390x.deb ... 119s Unpacking libfwupd3:s390x (2.0.8-3) over (2.0.7-1) ... 119s Preparing to unpack .../7-htop_3.4.1-4_s390x.deb ... 119s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 119s Preparing to unpack .../8-libftdi1-2_1.5-10_s390x.deb ... 119s Unpacking libftdi1-2:s390x (1.5-10) over (1.5-8build1) ... 119s Setting up liburcu8t64:s390x (0.15.2-2) ... 119s Setting up htop (3.4.1-4) ... 119s Setting up libsensors-config (1:3.6.2-2) ... 119s Installing new version of config file /etc/sensors3.conf ... 119s Setting up libfwupd3:s390x (2.0.8-3) ... 119s Setting up libftdi1-2:s390x (1.5-10) ... 119s Setting up usb.ids (2025.04.01-1) ... 119s Setting up libsensors5:s390x (1:3.6.2-2) ... 119s Setting up nano (8.4-1) ... 119s Installing new version of config file /etc/nanorc ... 119s Setting up fwupd (2.0.8-3) ... 120s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 120s fwupd.service is a disabled or a static unit not running, not starting it. 120s Processing triggers for man-db (2.13.0-1) ... 121s Processing triggers for dbus (1.16.2-2ubuntu1) ... 121s Processing triggers for install-info (7.1.1-1) ... 121s Processing triggers for libc-bin (2.41-6ubuntu1) ... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 122s Solving dependencies... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s autopkgtest [18:26:34]: rebooting testbed after setup commands that affected boot 142s autopkgtest [18:26:54]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP Sun Apr 6 13:39:00 UTC 2025 145s autopkgtest [18:26:57]: @@@@@@@@@@@@@@@@@@@@ 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] 148s gpgv: Signature made Sat Feb 15 21:16:28 2025 UTC 148s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 148s gpgv: issuer "emollier@debian.org" 148s gpgv: Can't check signature: No public key 148s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.68+dfsg-1.dsc: no acceptable signature found 148s autopkgtest [18:27:00]: testing package hyphy version 2.5.68+dfsg-1 148s autopkgtest [18:27:00]: build not needed 150s autopkgtest [18:27:02]: test run-unit-tests: preparing testbed 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s Starting pkgProblemResolver with broken count: 0 150s Starting 2 pkgProblemResolver with broken count: 0 150s Done 151s The following NEW packages will be installed: 151s hyphy-common hyphy-mpi hyphy-pt libevent-pthreads-2.1-7t64 libfabric1 151s libgomp1 libhwloc-plugins libhwloc15 libmunge2 libopenmpi40 libpciaccess0 151s libpmix2t64 librdmacm1t64 libxnvctrl0 ocl-icd-libopencl1 151s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 151s Need to get 7237 kB of archives. 151s After this operation, 25.1 MB of additional disk space will be used. 151s Get:1 http://ftpmaster.internal/ubuntu questing/universe s390x hyphy-common all 2.5.68+dfsg-1 [633 kB] 151s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x libgomp1 s390x 15-20250404-0ubuntu1 [152 kB] 151s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10 [7870 B] 151s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x librdmacm1t64 s390x 56.0-4ubuntu1 [74.0 kB] 151s Get:5 http://ftpmaster.internal/ubuntu questing/universe s390x libfabric1 s390x 1.17.0-3.1 [558 kB] 151s Get:6 http://ftpmaster.internal/ubuntu questing/universe s390x libhwloc15 s390x 2.12.0-1 [176 kB] 151s Get:7 http://ftpmaster.internal/ubuntu questing/universe s390x libmunge2 s390x 0.5.16-1 [15.2 kB] 151s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x libpciaccess0 s390x 0.17-3build1 [19.0 kB] 151s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 151s Get:10 http://ftpmaster.internal/ubuntu questing/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1build1 [41.1 kB] 151s Get:11 http://ftpmaster.internal/ubuntu questing/universe s390x libhwloc-plugins s390x 2.12.0-1 [16.1 kB] 151s Get:12 http://ftpmaster.internal/ubuntu questing/universe s390x libpmix2t64 s390x 5.0.6-5 [715 kB] 151s Get:13 http://ftpmaster.internal/ubuntu questing/universe s390x libopenmpi40 s390x 5.0.7-1 [2196 kB] 151s Get:14 http://ftpmaster.internal/ubuntu questing/universe s390x hyphy-mpi s390x 2.5.68+dfsg-1 [1323 kB] 151s Get:15 http://ftpmaster.internal/ubuntu questing/universe s390x hyphy-pt s390x 2.5.68+dfsg-1 [1297 kB] 152s Fetched 7237 kB in 1s (8115 kB/s) 152s Selecting previously unselected package hyphy-common. 152s (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 ... 81470 files and directories currently installed.) 152s Preparing to unpack .../00-hyphy-common_2.5.68+dfsg-1_all.deb ... 152s Unpacking hyphy-common (2.5.68+dfsg-1) ... 152s Selecting previously unselected package libgomp1:s390x. 152s Preparing to unpack .../01-libgomp1_15-20250404-0ubuntu1_s390x.deb ... 152s Unpacking libgomp1:s390x (15-20250404-0ubuntu1) ... 152s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 152s Preparing to unpack .../02-libevent-pthreads-2.1-7t64_2.1.12-stable-10_s390x.deb ... 152s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 152s Selecting previously unselected package librdmacm1t64:s390x. 152s Preparing to unpack .../03-librdmacm1t64_56.0-4ubuntu1_s390x.deb ... 152s Unpacking librdmacm1t64:s390x (56.0-4ubuntu1) ... 152s Selecting previously unselected package libfabric1:s390x. 152s Preparing to unpack .../04-libfabric1_1.17.0-3.1_s390x.deb ... 152s Unpacking libfabric1:s390x (1.17.0-3.1) ... 152s Selecting previously unselected package libhwloc15:s390x. 152s Preparing to unpack .../05-libhwloc15_2.12.0-1_s390x.deb ... 152s Unpacking libhwloc15:s390x (2.12.0-1) ... 152s Selecting previously unselected package libmunge2:s390x. 152s Preparing to unpack .../06-libmunge2_0.5.16-1_s390x.deb ... 152s Unpacking libmunge2:s390x (0.5.16-1) ... 152s Selecting previously unselected package libpciaccess0:s390x. 152s Preparing to unpack .../07-libpciaccess0_0.17-3build1_s390x.deb ... 152s Unpacking libpciaccess0:s390x (0.17-3build1) ... 152s Selecting previously unselected package libxnvctrl0:s390x. 152s Preparing to unpack .../08-libxnvctrl0_510.47.03-0ubuntu4_s390x.deb ... 152s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 152s Selecting previously unselected package ocl-icd-libopencl1:s390x. 152s Preparing to unpack .../09-ocl-icd-libopencl1_2.3.2-1build1_s390x.deb ... 152s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 152s Selecting previously unselected package libhwloc-plugins:s390x. 152s Preparing to unpack .../10-libhwloc-plugins_2.12.0-1_s390x.deb ... 152s Unpacking libhwloc-plugins:s390x (2.12.0-1) ... 152s Selecting previously unselected package libpmix2t64:s390x. 152s Preparing to unpack .../11-libpmix2t64_5.0.6-5_s390x.deb ... 152s Unpacking libpmix2t64:s390x (5.0.6-5) ... 152s Selecting previously unselected package libopenmpi40:s390x. 152s Preparing to unpack .../12-libopenmpi40_5.0.7-1_s390x.deb ... 152s Unpacking libopenmpi40:s390x (5.0.7-1) ... 152s Selecting previously unselected package hyphy-mpi. 152s Preparing to unpack .../13-hyphy-mpi_2.5.68+dfsg-1_s390x.deb ... 152s Unpacking hyphy-mpi (2.5.68+dfsg-1) ... 152s Selecting previously unselected package hyphy-pt. 152s Preparing to unpack .../14-hyphy-pt_2.5.68+dfsg-1_s390x.deb ... 152s Unpacking hyphy-pt (2.5.68+dfsg-1) ... 152s Setting up libpciaccess0:s390x (0.17-3build1) ... 152s Setting up libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 152s Setting up hyphy-common (2.5.68+dfsg-1) ... 152s Setting up libgomp1:s390x (15-20250404-0ubuntu1) ... 152s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 152s Setting up libmunge2:s390x (0.5.16-1) ... 152s Setting up libhwloc15:s390x (2.12.0-1) ... 152s Setting up ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 152s Setting up librdmacm1t64:s390x (56.0-4ubuntu1) ... 152s Setting up libfabric1:s390x (1.17.0-3.1) ... 152s Setting up hyphy-pt (2.5.68+dfsg-1) ... 152s Setting up libhwloc-plugins:s390x (2.12.0-1) ... 152s Setting up libpmix2t64:s390x (5.0.6-5) ... 152s Setting up libopenmpi40:s390x (5.0.7-1) ... 152s Setting up hyphy-mpi (2.5.68+dfsg-1) ... 152s Processing triggers for libc-bin (2.41-6ubuntu1) ... 152s Processing triggers for man-db (2.13.0-1) ... 154s autopkgtest [18:27:06]: test run-unit-tests: [----------------------- 154s + for i in *.bf 154s + '[' -f ExonIntron.bf ']' 154s + hyphy ExonIntron.bf 155s Log Likelihood = -1113.34521787156; 155s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04135183283037831,(ZMUBIS27F:0,(ZMU29160:0.05439916397994699,ZMU29161:0.03971477024179635)Node8:0.01201900651178909)Node6:0)Node4:0.02459453967369113,BLYMUB1:0.01186169400712634); 155s Tree exon2Tree=(BLYMUB2:0.03542650037446437,(RICRMA630:0.02936152844516879,(ZMUBIS27F:0.07548047664656496,(ZMU29160:0.0910675524555843,ZMU29161:0.02590433422145428)Node8:0.01160289579950156)Node6:0.04930238340870771)Node4:0.02931466895685761,BLYMUB1:0.02204839977342552); 155s Tree intronTree=(BLYMUB2:0.03120554830268615,(RICRMA630:0.04156299037892777,(ZMUBIS27F:0.02044281638474676,(ZMU29160:0.02068875146010898,ZMU29161:0.0101974096807372)Node8:0.02069020548829012)Node6:0)Node4:0,BLYMUB1:0.01036533056694192); 155s + for i in *.bf 155s + '[' -f F81.bf ']' 155s + hyphy F81.bf 155s Log Likelihood = -1187.54703200741; 155s Tree givenTree=(256:0.01194157029267311,(822:0.02945351296352873,159:0.004470256895920748)Node2:0.003650055612011835,((113:0.02245388925918836,9939:0.07632630069667352)Node6:0.00507825336743997,(6760:0.06905819377872334,((317:0.03753835955692442,6767:0.07080218299167945)Node12:0.01229495342004585,((135:0.02047826943376174,(529:0.03338945268929185,105r:0.0132150940440871)Node18:0.02585928015239317)Node16:0.005410805131527556,(719:0.02967303112999476,136:0.008233024513309602)Node21:0.0488425325075129)Node15:0.0152677277022724)Node11:0.01379471954396315)Node9:0.0242200377145979)Node5:0.02149671898415502); 155s + for i in *.bf 155s + '[' -f F81relrate.bf ']' 155s + hyphy F81relrate.bf 155s 155s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.00100432917; 155s Tree threeTaxaTree=(a:0.08503862542085412,b:0.07334966634443457,c:0.1653229746192066); 155s 155s 155s 1). With the outgroup at taxon #1, the P-value is:0.002155111412933564 155s Log Likelihood = -948.70725454308; 155s Tree threeTaxaTree=(a:0.08232758476832362,b:0.1194341761436603,c:0.1194341761436603); 155s 155s 155s 2). With the outgroup at taxon #2, the P-value is:0.00835350789267375 155s Log Likelihood = -947.479041953641; 155s Tree threeTaxaTree=(a:0.1251764627930641,b:0.07126598668948554,c:0.1251764627930641); 155s 155s 155s 3). With the outgroup at taxon #3, the P-value is:0.6669188835345545 155s Log Likelihood = -944.093618013177; 155s Tree threeTaxaTree=(a:0.07920469727888438,b:0.07920469727888438,c:0.1653351377508251); 155s + for i in *.bf 155s + '[' -f F81relratio.bf ']' 155s + hyphy F81relratio.bf 155s 155s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059588139; 155s Tree fourTaxaTree1=((1:0.1129136779920323,2:0.1073284320915713)Node1:0.09981582492782302,3:0.3469184588064214,4:0.3218847006333067); 155s Tree fourTaxaTree2=((1:0.08585401518196811,2:0.09337672236478001)Node1:0.07363355101677628,3:0.3933488423098771,4:0.3801939180704317); 155s 155s 155s 1). Relative ratio constraint; the P-value is:0.6932596818468655 155s Log Likelihood = -2575.74636482156; 155s Global Parameters: 155s R=1.0053316478899; 155s 155s Tree fourTaxaTree1=((1:0.09950107511308859,2:0.09952545031327653)Node1:0.08689424972645758,3:0.3693259755415116,4:0.3496333468044705); 155s Tree fourTaxaTree2=((1:0.0998965885350198,2:0.09992106062580745)Node1:0.08723965144213149,3:0.3707940338537308,4:0.3510231275807962); 155s + for i in *.bf 155s + '[' -f HKY85.bf ']' 155s + hyphy HKY85.bf 155s Log Likelihood = -1152.88077826404; 155s Tree givenTree=(256:0.01162422614266035,(822:0.02980653795675468,159:0.004016578412235303)Node2:0.003751036596743106,((113:0.02130155877818797,9939:0.07786162662077759)Node6:0.004320099446990751,(6760:0.07314669867708598,((317:0.03809748810194913,6767:0.07103933654839847)Node12:0.00627600221098434,((135:0.01788948939321033,(529:0.03258473043971895,105r:0.01513842538869179)Node18:0.02833445122159772)Node16:0.007922011835805555,(719:0.02987815396986863,136:0.008042480123180352)Node21:0.0486161522983343)Node15:0.01598575691616149)Node11:0.0165854144111049)Node9:0.02665217223515232)Node5:0.02296625603210102); 155s + for i in *.bf 155s + '[' -f HKY852blocks.bf ']' 155s + hyphy HKY852blocks.bf 155s 155s ----- RESULTS ----- 155s Log Likelihood = -6801.9148263338; 155s Tree actinTree1=(ZMU60513:0,ZMU60514:0.01050230977772896,((((((ZMU60511:0.01039475982171293,ZMU60510:0.02379127264315118)Node8:0.08350129234395702,OSRAC2:0.1885680398516594)Node7:0.05840772829839993,(OSRAC1:0.01535497545910735,SVSOAC1:0.07340925367204766)Node12:0.07288615912089128)Node6:0,((OSRAC3:0.07321433358020124,ZMU60507:0.06501195035382)Node16:0.07981173776168263,ZMU60509:0.1288626303387069)Node15:0.001271534262561479)Node5:0.08267450871932661,(MZEACT1G:0.1141432703132697,OSRAC7:0.03423928254531845)Node20:0)Node4:0.1059032247036438,ZMU60508:0.0170098247534731)Node3:0.05968931222048047); 155s Tree actinTree2=(ZMU60513:0.01014092292306223,ZMU60514:0.02362286884407728,((((((ZMU60511:0.03959829312920146,ZMU60510:0.02871380027563151)Node8:0.04599723493970469,OSRAC2:0.128154138284232)Node7:0.02273756978488254,(OSRAC1:0.04038033783895694,SVSOAC1:0.05534461112467003)Node12:0.09054855364537215)Node6:0.02101175042509908,((OSRAC3:0.1082179714927048,ZMU60507:0.07344552225415052)Node16:0.05600631064257176,ZMU60509:0.1117517114702624)Node15:0.02917056780618976)Node5:0.04979938417785699,(MZEACT1G:0.1069772100999577,OSRAC7:0.09558343724020676)Node20:0.02269280163348497)Node4:0.04830093381910772,ZMU60508:0.02347413788233664)Node3:0.0564962962635142); 155s + for i in *.bf 155s + '[' -f HKY852blocks2models.bf ']' 155s + hyphy HKY852blocks2models.bf 155s 155s ----- RESULTS ----- 155s Log Likelihood = -6049.33430813159; 155s Tree actinTree1=(ZMU60513:0.01367586885977404,ZMU60514:0.06665919949232602,((((((ZMU60511:0.101464113604039,ZMU60510:0.08944655680437284)Node8:0.2110888705286092,OSRAC2:0.3685048365761481)Node7:0.06394907975146319,(OSRAC1:0.04344897065063234,SVSOAC1:0.2449015348765471)Node12:0.4077786203369075)Node6:0.1003520235213184,((OSRAC3:0.1861498082657218,ZMU60507:0.3290589916036422)Node16:0.1591658895868331,ZMU60509:0.4443739107228503)Node15:0.04672954921202992)Node5:0.1894652294663614,(MZEACT1G:0.3244015512459015,OSRAC7:0.2477178133859062)Node20:0.009397305907210237)Node4:0.2662699939967883,ZMU60508:0.01033505107257406)Node3:0.2231171697722504); 155s Tree actinTree2=(ZMU60513:0.004498121791825825,ZMU60514:0.004483616283842231,((((((ZMU60511:0.004482581800702767,ZMU60510:0.005994559205876783)Node8:0.004874237258533394,OSRAC2:0.04746946226901688)Node7:0.003177874176095716,(OSRAC1:0.01209799930457682,SVSOAC1:0.007445357730130606)Node12:0.02730479164877754)Node6:0,((OSRAC3:0.04645235421267548,ZMU60507:0.009176463820113128)Node16:0.01045616799504742,ZMU60509:0.02448213442572363)Node15:0)Node5:0.01928018290955173,(MZEACT1G:0.03381564509600732,OSRAC7:0.03063271553827078)Node20:0.006213231207485995)Node4:0.007802703908564781,ZMU60508:0.004488393571843782)Node3:0.01512041237488595); 155s + for i in *.bf 155s + '[' -f HKY85relrate.bf ']' 155s + hyphy HKY85relrate.bf 155s 155s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371749483469; 155s Tree threeTaxaTree=(a:0.08472934037640539,b:0.07472890301073792,c:0.1740758557939314); 155s 155s 155s 1). Outgroup at taxon #1 155s a). Transition rate test. P-Value = 0.02098223878915928 155s Log Likelihood = -924.035882967929; 155s Tree threeTaxaTree=(a:0.08098747102064291,b:0.1064791186012347,c:0.1431094352971405); 155s 155s b). Transversion rate test. P-Value = 0.03655151928353972 155s Log Likelihood = -923.557343045721; 155s Tree threeTaxaTree=(a:0.08440222750865296,b:0.09108469945663834,c:0.1578859989435999); 155s 155s c). Both rates test. P-Value = 0.006323985525620301 155s Log Likelihood = -926.43515513196; 155s Tree threeTaxaTree=(a:0.08053673509661195,b:0.1248013468409589,c:0.1248013468409589); 155s 155s 155s 2). Outgroup at taxon #2 155s a). Transition rate test. P-Value = 0.02758027431514154 155s Log Likelihood = -923.798806518486; 155s Tree threeTaxaTree=(a:0.1158226502981005,b:0.07099209997363684,c:0.1443144822148316); 155s 155s b). Transversion rate test. P-Value = 0.1106459022622994 155s Log Likelihood = -922.644235271291; 155s Tree threeTaxaTree=(a:0.09761531015244303,b:0.07460629728361079,c:0.1609740139995941); 155s 155s c). Both rates test. P-Value = 0.02199510305651253 155s Log Likelihood = -925.188684922261; 155s Tree threeTaxaTree=(a:0.1299155543951374,b:0.07082226999217919,c:0.1299155543951374); 155s 155s 155s 3). Outgroup at taxon #3 155s a). Transition rate test. P-Value = 0.9291412413426321 155s Log Likelihood = -921.375703341917; 155s Tree threeTaxaTree=(a:0.08355046076612951,b:0.07588581166881787,c:0.1740233675057789); 155s 155s b). Transversion rate test. P-Value = 0.5919912459813355 155s Log Likelihood = -921.515372127888; 155s Tree threeTaxaTree=(a:0.08113263880426226,b:0.07836683153103764,c:0.1741501081811796); 155s 155s c). Both rates test. P-Value = 0.8615417730777308 155s Log Likelihood = -921.520781218877; 155s Tree threeTaxaTree=(a:0.07975961326407401,b:0.07975961326407401,c:0.1741085573868653); 155s + for i in *.bf 155s + '[' -f HKY85relratio.bf ']' 155s + hyphy HKY85relratio.bf 155s 155s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78448439159; 155s Tree fourTaxaTree1=((1:0.1137470993258308,2:0.1109458369933073)Node1:0.1040859029600351,3:0.3524244696636145,4:0.3313458994519674); 155s Tree fourTaxaTree2=((1:0.08600482309908206,2:0.0935905016834595)Node1:0.08009543435709388,3:0.3858472298640774,4:0.3893810656064262); 155s 155s 155s 1). Relative ratio constraint on transitions; the P-value is:0.5738793652161414 155s Log Likelihood = -2541.23688980615; 155s Global Parameters: 155s R=0.8580637072944939; 155s 155s Tree fourTaxaTree1=((1:0.1087236154833182,2:0.09418261851726437)Node1:0.1115257358043487,3:0.3554308426851791,4:0.3552321157200707); 155s Tree fourTaxaTree2=((1:0.09042940662533522,2:0.1091728147734687)Node1:0.07297294246128291,3:0.3839423087109376,4:0.3657415600789745); 155s 155s 155s 2). Relative ratio constraint on transversions; the P-value is:0.5738082389395694 155s Log Likelihood = -2541.2370990863; 155s Global Parameters: 155s R=0.8594123631731592; 155s 155s Tree fourTaxaTree1=((1:0.1087000696562798,2:0.09418987354235921)Node1:0.1117932115740304,3:0.3553746239010244,4:0.3547712804136829); 155s Tree fourTaxaTree2=((1:0.09045802612707923,2:0.1092779911576534)Node1:0.07330034908319427,3:0.3842167366700268,4:0.3653957335472213); 155s 155s 155s 3). Relative ratio constraint on both rates; the P-value is:0.6565949322415472 155s Log Likelihood = -2543.19092025092; 155s Global Parameters: 155s R=0.9972175975860272; 155s 155s Tree fourTaxaTree1=((1:0.1004640276174484,2:0.1006330219351957)Node1:0.09260950533290647,3:0.3712411946372723,4:0.3579566461592324); 155s Tree fourTaxaTree2=((1:0.1003679616678768,2:0.1006957702760514)Node1:0.09296733182400158,3:0.3699429911655295,4:0.3576743603634694); 155s + for i in *.bf 155s + '[' -f HKY85shared.bf ']' 155s + hyphy HKY85shared.bf 155s Log Likelihood = -1165.70263637027; 155s Global Parameters: 155s R=2.979768010144316; 155s 155s Tree givenTree=(256:0.01208746838850984,(822:0.02961549880914984,159:0.004650946688192138)Node2:0.003522500918073305,((113:0.02179055794799955,9939:0.07946684135646476)Node6:0.004907388668402149,(6760:0.07150894983631456,((317:0.03799709424797661,6767:0.07150374320834688)Node12:0.01178540069744759,((135:0.02023004291579091,(529:0.03405634050743456,105r:0.01304907602704883)Node18:0.02630372245917584)Node16:0.005817631919489398,(719:0.02974526933137355,136:0.008127455790983453)Node21:0.04878635925643902)Node15:0.01555561563838646)Node11:0.01396339172956107)Node9:0.02325796517062001)Node5:0.02146718259151121); 155s + for i in *.bf 155s + '[' -f JC69.bf ']' 155s + hyphy JC69.bf 155s Log Likelihood = -1227.45123365421; 155s Tree givenTree=(256:0.01208696699028618,(822:0.02897006422106703,159:0.004657405983442174)Node2:0.003647035497490688,((113:0.02417515021679533,9939:0.07266454084713181)Node6:0.005833878643085603,(6760:0.06389376310860244,((317:0.04027897724540105,6767:0.06820677030772762)Node12:0.01442297767415096,((135:0.02428976190490537,(529:0.03327882401815401,105r:0.01296768690152428)Node18:0.01987279210343177)Node16:0.003610886822055106,(719:0.02785585477976698,136:0.009989733956154968)Node21:0.05116660029794081)Node15:0.01669646461465673)Node11:0.008467915759186385)Node9:0.02635251955795324)Node5:0.02073905542818759); 155s + for i in *.bf 155s + '[' -f K2P.bf ']' 155s + hyphy K2P.bf 155s Log Likelihood = -1198.26195968423; 155s Tree givenTree=(256:0.01176775031370344,(822:0.0292719860116029,159:0.004289897857996237)Node2:0.003666798874399228,((113:0.0236492972657858,9939:0.07263496220107925)Node6:0.003385248323383496,(6760:0.06222507572636254,((317:0.04073403747380949,6767:0.06828641380965536)Node12:0.01246127294706056,((135:0.02262882046804634,(529:0.03393140549990673,105r:0.01240146684363996)Node18:0.02140651771641591)Node16:0.004487018415306014,(719:0.02880164734805317,136:0.008846375607378306)Node21:0.05081174081401337)Node15:0.01733237284119596)Node11:0.01105913808965238)Node9:0.0282120300698555)Node5:0.0237077322531028); 155s + for i in *.bf 155s + '[' -f K2Pshared.bf ']' 155s + hyphy K2Pshared.bf 156s Log Likelihood = -1210.49410568317; 156s Global Parameters: 156s R=2.619370841864261; 156s 156s Tree givenTree=(256:0.01221904547039362,(822:0.02897582221482243,159:0.00477733888416755)Node2:0.003545957401861989,((113:0.0237558709136462,9939:0.07495471263771332)Node6:0.005887353049211616,(6760:0.06492979307279791,((317:0.03970085524740155,6767:0.06948858878320258)Node12:0.01422960268695541,((135:0.02389541996209878,(529:0.03395940228489892,105r:0.01262809344053399)Node18:0.02072005296824749)Node16:0.003966886470970252,(719:0.02813868298840856,136:0.009501536087332937)Node21:0.05080332046258954)Node15:0.01659015711587434)Node11:0.008799344415822127)Node9:0.02626539769522525)Node5:0.02011348739442558); 156s + for i in *.bf 156s + '[' -f MatrixIndexing.bf ']' 156s + hyphy MatrixIndexing.bf 156s + for i in *.bf 156s + '[' -f MolecularClockF81.bf ']' 156s + hyphy MolecularClockF81.bf 156s 156s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 156s { 156s {0.2183777180543117, 0.03669148730968393, 0.9302315786318461, 0.165391408178348, 0.01259535970459584, 0.9578645732155686} 156s {0.3790003220501822, 0.9131106878428512, 0.3821279458659999, 0.4887156133746532, 0.1919238833226086, 0.9797779773314897} 156s {0.3606448635367315, 0.5869224764376233, 0.003120268928613576, 0.06084196061381184, 0.4881261872332837, 0.436149634988082} 156s {0.7567334765933299, 0.9203143373411881, 0.7102219459391715, 0.2257305631008303, 0.7956887997676825, 0.4508078236716818} 156s {0.8006236073096803, 0.09082749977028638, 0.9020746948435145, 0.5669873786547658, 0.281288982667329, 0.07563486906598203} 156s } 156s 156s 2). Accessing a second-row third-column element and a random element. 156s 156s matrix[1][2]=0.3821279458659999 156s matrix[1][3]=0.4887156133746532 156s 156s 3). Accessing the fourth row. 156s 156s matrix[3][-1]= 156s { 156s {0.7567334765933299, 0.9203143373411881, 0.7102219459391715, 0.2257305631008303, 0.7956887997676825, 0.4508078236716818} 156s } 156s 156s 4). Accessing the first column. 156s 156s matrix[-1][0]= 156s { 156s {0.2183777180543117} 156s {0.3790003220501822} 156s {0.3606448635367315} 156s {0.7567334765933299} 156s {0.8006236073096803} 156s } 156s 156s 5). Populating a matrix template (below the diagonal). 156s 156s { 156s {0, 0, 0, 0, 0, 0} 156s {1, 0, 0, 0, 0, 0} 156s {1, 1, 0, 0, 0, 0} 156s {1, 1, 1, 0, 0, 0} 156s {1, 1, 1, 1, 0, 0} 156s } 156s 156s 6). Extracting (by row) matrix elements using the template. 156s 156s { 156s {0.3790003220501822, 0.3606448635367315, 0.5869224764376233, 0.7567334765933299, 0.9203143373411881, 0.7102219459391715, 0.8006236073096803, 0.09082749977028638, 0.9020746948435145, 0.5669873786547658} 156s } 156s 156s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 156s 156s matrix[{{1,1}}][{{3,2}}]= 156s { 156s {0.9131106878428512, 0.3821279458659999} 156s {0.5869224764376233, 0.003120268928613576} 156s {0.9203143373411881, 0.7102219459391715} 156s } 156s 156s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 156s 156s 156s { 156s {0.04768882774260848, 1.001346265240997, 1.865330789883897, 1.027354317899217, 1.000158643086088, 1.917504540621443} 156s {0.1436412441141419, 0.8337711282528448, 1.146021767011768, 1.238842950756164, 1.03683477698963, 1.959964884863785} 156s {0.1300647175954277, 0.3444779933476725, 9.736078186871316e-06, 1.003701744171333, 1.238267174662903, 1.190226504100237} 156s {0.5726455545970278, 0.8469784795157501, 0.5044152124936235, 0.05095428711781794, 1.633120666075735, 1.203227693883598} 156s {0.6409981605815651, 0.008249634714521373, 0.8137387550770199, 0.3214746875538028, 0.07912349177002094, 1.005720633418628} 156s } 156s 156s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124410442; 156s Tree theTree=(HVRNASS:0.02574827003915251,(RICRSS3:0.05627401932555898,((ZMSUCS1:0.07161653296015821,(OSRSS1A:0.06059286854453253,(TASUCSYN1:0.02788131811908146,HVSSYNMR:0.02036889817886221)Internal1:0.05182591516663268)Node9:0.02015304387541888)Node7:0.1581472067904327,(MZESUS1:0.07665549800646637,ORRSS2:0.05437335699979026)Internal2:0.02505463207418868)Node6:0.03255395491215314)Node4:0.05900956877289115,TAAJ153:0.01372512585912899); 156s 156s 156s 1). Global Molecular Clock; the P-value is:0 156s Log Likelihood = -11927.6152872487; 156s Tree theTree=(HVRNASS:0.02158166980300945,(RICRSS3:0.1233407362186898,((ZMSUCS1:0.05658071396758304,(OSRSS1A:0.04751121276937992,(TASUCSYN1:0.01824268042586396,HVSSYNMR:0.01824268042586396)Internal1:0.02926853234351597)Node9:0.009069501198203109)Node7:0.05763375064978912,(MZESUS1:0.07014762057748961,ORRSS2:0.07014762057748961)Internal2:0.04406684403988256)Node6:0.00912627160131768)Node4:0.02714857889476727,TAAJ153:0.1504893151134571); 156s 156s 156s 2). Molecular Clock starting at Internal1; the P-value is:0.1603823818834074 156s Log Likelihood = -11476.6977495645; 156s Tree theTree=(HVRNASS:0.02574692014659945,(RICRSS3:0.05631337367960875,((ZMSUCS1:0.07169724692420028,(OSRSS1A:0.0605205457573009,(TASUCSYN1:0.02412439027870999,HVSSYNMR:0.02412439027870999)Internal1:0.05181073984300496)Node9:0.02018148577156538)Node7:0.1580576730838647,(MZESUS1:0.07661835897246028,ORRSS2:0.05441426218542413)Internal2:0.02508055232575791)Node6:0.03252716826799525)Node4:0.05897163515763024,TAAJ153:0.01372614848989393); 156s 156s 156s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610208699242444 156s Log Likelihood = -11479.8412474328; 156s Tree theTree=(HVRNASS:0.0257744078700305,(RICRSS3:0.05652985131039506,((ZMSUCS1:0.07147569478091721,(OSRSS1A:0.06061741363779699,(TASUCSYN1:0.02412260588056621,HVSSYNMR:0.02412260588056621)Internal1:0.05167997039837431)Node9:0.02036524950709426)Node7:0.1580488193248071,(MZESUS1:0.06553450344269375,ORRSS2:0.06553450344269375)Internal2:0.02502717229606453)Node6:0.0323630701594869)Node4:0.05874456232069336,TAAJ153:0.01369828187284068); 156s + for i in *.bf 156s + '[' -f MolecularClockHKY85.bf ']' 156s + hyphy MolecularClockHKY85.bf 156s 156s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013168621; 156s Tree theTree=(HVRNASS:0.02587788310816672,(RICRSS3:0.05729259341117145,((ZMSUCS1:0.07271757574108348,(OSRSS1A:0.06096030831220338,(TASUCSYN1:0.02742675775351242,HVSSYNMR:0.02082543201398321)Node11:0.05283733436172935)Node9:0.02051371675057346)Node7:0.1590158559334478,(MZESUS1:0.0776257291300682,ORRSS2:0.05414486810522159)Node14:0.02601392421900825)Node6:0.03166985124777269)Node4:0.06041495127620015,TAAJ153:0.0138453759867632); 156s 156s 156s 1). Global Molecular Clock on transition rates; the P-value is:0 156s Log Likelihood = -11434.7016277322; 156s Tree theTree=(HVRNASS:0.02319852161774676,(RICRSS3:0.0833377062327242,((ZMSUCS1:0.06367115499219736,(OSRSS1A:0.05486245496348469,(TASUCSYN1:0.02325250849621393,HVSSYNMR:0.01890428730583721)Node11:0.04017750364749997)Node9:0.01327920215296054)Node7:0.1274462001597074,(MZESUS1:0.07239740728544375,ORRSS2:0.06226852900448067)Node14:0.03461588001235261)Node6:0.02067729028909652)Node4:0.03899762259645041,TAAJ153:0.088914185312346); 156s 156s 156s 2). Global Molecular Clock on transversion rates; the P-value is:0 156s Log Likelihood = -11497.3782424389; 156s Tree theTree=(HVRNASS:0.0248441498546749,(RICRSS3:0.09398480771303848,((ZMSUCS1:0.06901395780743187,(OSRSS1A:0.05468852230548629,(TASUCSYN1:0.02277003768891075,HVSSYNMR:0.02034704267710716)Node11:0.04373152200210881)Node9:0.01673398162101423)Node7:0.09973503032687711,(MZESUS1:0.07447325594888533,ORRSS2:0.06134761685868839)Node14:0.03387134577765714)Node6:0.02079759852911136)Node4:0.05008306456465662,TAAJ153:0.0730593785718113); 156s 156s 156s 3). Global Molecular Clock on both rates; the P-value is:0 156s Log Likelihood = -11703.6262158648; 156s Tree theTree=(HVRNASS:0.02210035529736838,(RICRSS3:0.1239726115858658,((ZMSUCS1:0.05800841426031581,(OSRSS1A:0.04855580532654821,(TASUCSYN1:0.01834859419486989,HVSSYNMR:0.01834859419486989)Node11:0.03020721113167831)Node9:0.009452608933767606)Node7:0.0573053363370966,(MZESUS1:0.07024258960494426,ORRSS2:0.07024258960494426)Node14:0.04507116099246816)Node6:0.0086588609884534)Node4:0.02800775019951389,TAAJ153:0.1519803617853797); 156s + for i in *.bf 156s + '[' -f Non-Rev.bf ']' 156s + hyphy Non-Rev.bf 156s Log Likelihood = -1152.79165529732; 156s Global Parameters: 156s GC=0.26569102121304; 156s CG=0.188063031081954; 156s GA=1.896677029589602; 156s CT=1.254503284457873; 156s GT=0.08606525016539647; 156s CA=0.9136654100301735; 156s AT=0.4267966368232038; 156s AG=1.569770829524411; 156s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.255189752021803; 156s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.027114707793515; 156s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.7927720057903691; 156s 156s Tree givenTree=(256:0.01345285907058647,(822:0.0284363556041338,159:0.006118421573568233)Node2:0.003448883589852962,((113:0.02186063680238474,9939:0.07923550506207959)Node6:0.004994395188708147,(6760:0.07334418451663097,((317:0.04006118755995846,6767:0.06984633919051567)Node12:0.01162139767379974,((135:0.02155372644809483,(529:0.03498206319337741,105r:0.01423567247686968)Node18:0.02378928651748257)Node16:0.005231498957662635,(719:0.02861728362946316,136:0.009576398290235858)Node21:0.04935939152181669)Node15:0.01634483718004808)Node11:0.01269805725088614)Node9:0.02194243260992946)Node5:0.02025808245493778); 156s + for i in *.bf 156s + '[' -f PBootstrapHetRates.bf ']' 156s + hyphy PBootstrapHetRates.bf 156s 156s ----ORIGINAL DATA---- 156s Log Likelihood = -1127.31562028798; 156s Global Parameters: 156s alpha=0.3191273773124281; 156s kappa=0.3234743995494085; 156s 156s Tree givenTree=(256:0.01258866603020129,(822:0.03175504988194595,159:0.004693590614879704)Node2:0.003781845685273023,((113:0.02291519184386138,9939:0.09711848163597341)Node6:0.001984266412507749,(6760:0.08722376564014625,((317:0.04578668088391827,6767:0.08101544475201138)Node12:0.007439113496466811,((135:0.01866285046261164,(529:0.03695581418343016,105r:0.01500530033310438)Node18:0.03036549920471035)Node16:0.007148804165673262,(719:0.03339574984926017,136:0.007161569050145382)Node21:0.05754322566158247)Node15:0.01788270410654002)Node11:0.01883940721880348)Node9:0.02367337483965643)Node5:0.02501393317797536); 156s 156s Using the seed: 156s 1746212109 156s Category variable name: TRUE 156s Site Rate 156s 0 0.00000 156s 1 0.00000 156s 2 0.00003 156s 3 0.00003 156s 4 0.00004 156s 5 0.00005 156s 6 0.00006 156s 7 0.00006 156s 8 0.00007 156s 9 0.00010 156s 10 0.00019 156s 11 0.00030 156s 12 0.00035 156s 13 0.00040 156s 14 0.00056 156s 15 0.00074 156s 16 0.00081 156s 17 0.00103 156s 18 0.00142 156s 19 0.00166 156s 20 0.00196 156s 21 0.00199 156s 22 0.00216 156s 23 0.00226 156s 24 0.00247 156s 25 0.00268 156s 26 0.00275 156s 27 0.00280 156s 28 0.00308 156s 29 0.00321 156s 30 0.00354 156s 31 0.00359 156s 32 0.00428 156s 33 0.00477 156s 34 0.00489 156s 35 0.00557 156s 36 0.00557 156s 37 0.00578 156s 38 0.00627 156s 39 0.00658 156s 40 0.00772 156s 41 0.00779 156s 42 0.01054 156s 43 0.01097 156s 44 0.01336 156s 45 0.01683 156s 46 0.01937 156s 47 0.01952 156s 48 0.02318 156s 49 0.02350 156s 50 0.02366 156s 51 0.02429 156s 52 0.02587 156s 53 0.02682 156s 54 0.02719 156s 55 0.02997 156s 56 0.03003 156s 57 0.03149 156s 58 0.03293 156s 59 0.03340 156s 60 0.03493 156s 61 0.03644 156s 62 0.04012 156s 63 0.04053 156s 64 0.04155 156s 65 0.04394 156s 66 0.04405 156s 67 0.04459 156s 68 0.05116 156s 69 0.05118 156s 70 0.06148 156s 71 0.06502 156s 72 0.06631 156s 73 0.06688 156s 74 0.06774 156s 75 0.06813 156s 76 0.06844 156s 77 0.07011 156s 78 0.07147 156s 79 0.07321 156s 80 0.07344 156s 81 0.07353 156s 82 0.07586 156s 83 0.07853 156s 84 0.08286 156s 85 0.08400 156s 86 0.08540 156s 87 0.08949 156s 88 0.09233 156s 89 0.09296 156s 90 0.09520 156s 91 0.09668 156s 92 0.10027 156s 93 0.10056 156s 94 0.10601 156s 95 0.11144 156s 96 0.11311 156s 97 0.11719 156s 98 0.12247 156s 99 0.12431 156s 100 0.12755 156s 101 0.12893 156s 102 0.13028 156s 103 0.13528 156s 104 0.13655 156s 105 0.13981 156s 106 0.14629 156s 107 0.15026 156s 108 0.15570 156s 109 0.15655 156s 110 0.15874 156s 111 0.15943 156s 112 0.16302 156s 113 0.16347 156s 114 0.16467 156s 115 0.16477 156s 116 0.16611 156s 117 0.17363 156s 118 0.17570 156s 119 0.18175 156s 120 0.19323 156s 121 0.20145 156s 122 0.20563 156s 123 0.20667 156s 124 0.21950 156s 125 0.22197 156s 126 0.22583 156s 127 0.23262 156s 128 0.24061 156s 129 0.24340 156s 130 0.25577 156s 131 0.26177 156s 132 0.27619 156s 133 0.27764 156s 134 0.28412 156s 135 0.31178 156s 136 0.32104 156s 137 0.32408 156s 138 0.33488 156s 139 0.33869 156s 140 0.34210 156s 141 0.34335 156s 142 0.34447 156s 143 0.35983 156s 144 0.36018 156s 145 0.36219 156s 146 0.36603 156s 147 0.39365 156s 148 0.40466 156s 149 0.41580 156s 150 0.41659 156s 151 0.42249 156s 152 0.45268 156s 153 0.45559 156s 154 0.47165 156s 155 0.47388 156s 156 0.48172 156s 157 0.48644 156s 158 0.50774 156s 159 0.50989 156s 160 0.53222 156s 161 0.54267 156s 162 0.56255 156s 163 0.58520 156s 164 0.58660 156s 165 0.58821 156s 166 0.60011 156s 167 0.60091 156s 168 0.64447 156s 169 0.67216 156s 170 0.70441 156s 171 0.75106 156s 172 0.76778 156s 173 0.77427 156s 174 0.78986 156s 175 0.80015 156s 176 0.81341 156s 177 0.83078 156s 178 0.90868 156s 179 0.93638 156s 180 0.95286 156s 181 1.01298 156s 182 1.02176 156s 183 1.05493 156s 184 1.05930 156s 185 1.08077 156s 186 1.08700 156s 187 1.09174 156s 188 1.10836 156s 189 1.16541 156s 190 1.18685 156s 191 1.22814 156s 192 1.26647 156s 193 1.30285 156s 194 1.31113 156s 195 1.31672 156s 196 1.34610 156s 197 1.34664 156s 198 1.35765 156s 199 1.36323 156s 200 1.37565 156s 201 1.38662 156s 202 1.40324 156s 203 1.41779 156s 204 1.42932 156s 205 1.43073 156s 206 1.45983 156s 207 1.46910 156s 208 1.47450 156s 209 1.47664 156s 210 1.51401 156s 211 1.58676 156s 212 1.59378 156s 213 1.61898 156s 214 1.63140 156s 215 1.66132 156s 216 1.78850 156s 217 1.79360 156s 218 1.82160 156s 219 1.84987 156s 220 1.85260 156s 221 1.90197 156s 222 1.96997 156s 223 2.00398 156s 224 2.06823 156s 225 2.12021 156s 226 2.17033 156s 227 2.22001 156s 228 2.24856 156s 229 2.32380 156s 230 2.34701 156s 231 2.34852 156s 232 2.45182 156s 233 2.46976 156s 234 2.47875 156s 235 2.49328 156s 236 2.52996 156s 237 2.53302 156s 238 2.55274 156s 239 2.62915 156s 240 2.74717 156s 241 2.80353 156s 242 2.81738 156s 243 2.92756 156s 244 3.03486 156s 245 3.05247 156s 246 3.10936 156s 247 3.28568 156s 248 3.43057 156s 249 3.46211 156s 250 3.52066 156s 251 3.72440 156s 252 3.90659 156s 253 4.08479 156s 254 4.41040 156s 255 4.53656 156s 256 4.56625 156s 257 4.83258 156s 258 4.95972 156s 259 5.07034 156s 260 5.09734 156s 261 5.10593 156s 262 5.38327 156s 263 5.53057 156s 264 5.57535 156s 265 5.60208 156s 266 5.65227 156s 267 6.42717 156s 268 7.88129 156s 269 8.37882 156s 270 8.61666 156s 271 9.20906 156s 272 10.77124 156s 156s Mean = 1.092437788252019 156s Var = 2.996693055123036 (1/alpha) = 3.13354500770704 156s + for i in *.bf 156s + '[' -f REV.bf ']' 156s + hyphy REV.bf 157s Log Likelihood = -1099.56653884966; 157s Tree givenTree=(256:0.01860402164875791,(822:0.02270203413475071,159:0.01094574759388466)Node2:0.003780101217329405,((113:0.01829166766947588,9939:0.07804702974436172)Node6:0.007456943521893166,(6760:0.07116621367863996,((317:0.03718908349440166,6767:0.07207156999164425)Node12:0.01018712208643521,((135:0.02037136378167769,(529:0.0342415611774925,105r:0.01130306249314219)Node18:0.02851211886320911)Node16:0.006574155883689221,(719:0.02831061972204768,136:0.009598486995267068)Node21:0.04403970934092158)Node15:0.01655916792217344)Node11:0.01315254971962312)Node9:0.02916035302493537)Node5:0.01372288724015338); 157s + for i in *.bf 157s + '[' -f REVshared.bf ']' 157s + hyphy REVshared.bf 157s Log Likelihood = -1156.62566882667; 157s Global Parameters: 157s AT=0.3612557707532429; 157s GT=0.4593298123086345; 157s CG=0.2458008710335668; 157s AG=1.841067871541799; 157s CT=1.19831959593928; 157s 157s Tree givenTree=(256:0.01207777370628983,(822:0.02972252729882586,159:0.004669830526470103)Node2:0.003489685051097042,((113:0.02209311599386244,9939:0.07980326206195534)Node6:0.0047067548617762,(6760:0.07207977771691124,((317:0.03906388616299454,6767:0.07101307557623723)Node12:0.01082398976997647,((135:0.0205207119103992,(529:0.03439888060799527,105r:0.01468354157322856)Node18:0.02466715900811692)Node16:0.005559323514115903,(719:0.02874522990173807,136:0.00947509956773661)Node21:0.04912069731888235)Node15:0.01582856751695401)Node11:0.01427609474551169)Node9:0.02298222954018246)Node5:0.02145840058461772); 157s + for i in *.bf 157s + '[' -f ReplicateConstraint1.bf ']' 157s + hyphy ReplicateConstraint1.bf 157s 1).Unconstrained HKY85 157s 157s Log Likelihood = -1152.88; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.317.trvs 157s Parameter 2 : hivTree.317.trst 157s Parameter 3 : hivTree.6767.trvs 157s Parameter 4 : hivTree.6767.trst 157s Parameter 5 : hivTree.Node2.trvs 157s Parameter 6 : hivTree.Node2.trst 157s Parameter 7 : hivTree.135.trvs 157s Parameter 8 : hivTree.135.trst 157s Parameter 9 : hivTree.529.trvs 157s Parameter 10 : hivTree.529.trst 157s Parameter 11 : hivTree.105r.trvs 157s Parameter 12 : hivTree.105r.trst 157s Parameter 13 : hivTree.Node8.trvs 157s Parameter 14 : hivTree.Node8.trst 157s Parameter 15 : hivTree.iNode1.trvs 157s Parameter 16 : hivTree.iNode1.trst 157s Parameter 17 : hivTree.719.trvs 157s Parameter 18 : hivTree.719.trst 157s Parameter 19 : hivTree.136.trvs 157s Parameter 20 : hivTree.136.trst 157s Parameter 21 : hivTree.Node11.trvs 157s Parameter 22 : hivTree.Node11.trst 157s Parameter 23 : hivTree.Node5.trvs 157s Parameter 24 : hivTree.Node5.trst 157s Parameter 25 : hivTree.Node1.trvs 157s Parameter 26 : hivTree.Node1.trst 157s Parameter 27 : hivTree.6760.trvs 157s Parameter 28 : hivTree.6760.trst 157s Parameter 29 : hivTree.113.trvs 157s Parameter 30 : hivTree.113.trst 157s Parameter 31 : hivTree.9939.trvs 157s Parameter 32 : hivTree.9939.trst 157s Parameter 33 : hivTree.Node16.trvs 157s Parameter 34 : hivTree.Node16.trst 157s Parameter 35 : hivTree.256.trvs 157s Parameter 36 : hivTree.256.trst 157s Parameter 37 : hivTree.822.trvs 157s Parameter 38 : hivTree.822.trst 157s Parameter 39 : hivTree.159.trvs 157s Parameter 40 : hivTree.159.trst 157s Parameter 41 : hivTree.Node21.trvs 157s Parameter 42 : hivTree.Node21.trst 157s Parameter 43 : hivTree.iNode2.trvs 157s Parameter 44 : hivTree.iNode2.trst 157s Parameter 45 : hivTree.Node15.trvs 157s Parameter 46 : hivTree.Node15.trst 157s 157s 2).HKY85 constrained to F81 157s 157s Log Likelihood = -1187.55; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.317.trvs 157s Parameter 2 : hivTree.6767.trvs 157s Parameter 3 : hivTree.Node2.trvs 157s Parameter 4 : hivTree.135.trvs 157s Parameter 5 : hivTree.529.trvs 157s Parameter 6 : hivTree.105r.trvs 157s Parameter 7 : hivTree.Node8.trvs 157s Parameter 8 : hivTree.iNode1.trvs 157s Parameter 9 : hivTree.719.trvs 157s Parameter 10 : hivTree.136.trvs 157s Parameter 11 : hivTree.Node11.trvs 157s Parameter 12 : hivTree.Node5.trvs 157s Parameter 13 : hivTree.Node1.trvs 157s Parameter 14 : hivTree.6760.trvs 157s Parameter 15 : hivTree.113.trvs 157s Parameter 16 : hivTree.9939.trvs 157s Parameter 17 : hivTree.Node16.trvs 157s Parameter 18 : hivTree.256.trvs 157s Parameter 19 : hivTree.822.trvs 157s Parameter 20 : hivTree.159.trvs 157s Parameter 21 : hivTree.Node21.trvs 157s Parameter 22 : hivTree.iNode2.trvs 157s Parameter 23 : hivTree.Node15.trvs 157s 157s Constrained Parameters List 157s 157s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 157s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 157s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 157s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 157s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 157s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 157s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 157s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 157s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 157s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 157s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 157s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 157s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 157s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 157s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 157s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 157s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 157s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 157s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 157s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 157s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 157s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 157s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 157s 157s 3).HKY85 constrained to F81 on internal branches 157s 157s Log Likelihood = -1167.99; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.Node2.trvs 157s Parameter 2 : hivTree.Node8.trvs 157s Parameter 3 : hivTree.iNode1.trvs 157s Parameter 4 : hivTree.Node11.trvs 157s Parameter 5 : hivTree.Node5.trvs 157s Parameter 6 : hivTree.Node1.trvs 157s Parameter 7 : hivTree.Node16.trvs 157s Parameter 8 : hivTree.Node21.trvs 157s Parameter 9 : hivTree.iNode2.trvs 157s Parameter 10 : hivTree.Node15.trvs 157s Parameter 11 : hivTree.317.trst 157s Parameter 12 : hivTree.317.trvs 157s Parameter 13 : hivTree.6767.trvs 157s Parameter 14 : hivTree.6767.trst 157s Parameter 15 : hivTree.135.trst 157s Parameter 16 : hivTree.135.trvs 157s Parameter 17 : hivTree.529.trvs 157s Parameter 18 : hivTree.529.trst 157s Parameter 19 : hivTree.105r.trst 157s Parameter 20 : hivTree.105r.trvs 157s Parameter 21 : hivTree.719.trvs 157s Parameter 22 : hivTree.719.trst 157s Parameter 23 : hivTree.136.trvs 157s Parameter 24 : hivTree.136.trst 157s Parameter 25 : hivTree.6760.trvs 157s Parameter 26 : hivTree.6760.trst 157s Parameter 27 : hivTree.113.trvs 157s Parameter 28 : hivTree.113.trst 157s Parameter 29 : hivTree.9939.trst 157s Parameter 30 : hivTree.9939.trvs 157s Parameter 31 : hivTree.256.trvs 157s Parameter 32 : hivTree.256.trst 157s Parameter 33 : hivTree.822.trvs 157s Parameter 34 : hivTree.822.trst 157s Parameter 35 : hivTree.159.trst 157s Parameter 36 : hivTree.159.trvs 157s 157s Constrained Parameters List 157s 157s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 157s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 157s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 157s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 157s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 157s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 157s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 157s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 157s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 157s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 157s 157s 4).HKY85 with shared ratio. 157s 157s Log Likelihood = -1165.7; 157s 157s Independent Parameters List 157s 157s Parameter 1 : R 157s Parameter 2 : hivTree.317.trst 157s Parameter 3 : hivTree.6767.trst 157s Parameter 4 : hivTree.Node2.trst 157s Parameter 5 : hivTree.135.trst 157s Parameter 6 : hivTree.529.trst 157s Parameter 7 : hivTree.105r.trst 157s Parameter 8 : hivTree.Node8.trst 157s Parameter 9 : hivTree.iNode1.trst 157s Parameter 10 : hivTree.719.trst 157s Parameter 11 : hivTree.136.trst 157s Parameter 12 : hivTree.Node11.trst 157s Parameter 13 : hivTree.Node5.trst 157s Parameter 14 : hivTree.Node1.trst 157s Parameter 15 : hivTree.6760.trst 157s Parameter 16 : hivTree.113.trst 157s Parameter 17 : hivTree.9939.trst 157s Parameter 18 : hivTree.Node16.trst 157s Parameter 19 : hivTree.256.trst 157s Parameter 20 : hivTree.822.trst 157s Parameter 21 : hivTree.159.trst 157s Parameter 22 : hivTree.Node21.trst 157s Parameter 23 : hivTree.iNode2.trst 157s Parameter 24 : hivTree.Node15.trst 157s 157s Constrained Parameters List 157s 157s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 157s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 157s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 157s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 157s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 157s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 157s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 157s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 157s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 157s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 157s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 157s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 157s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 157s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 157s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 157s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 157s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 157s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 157s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 157s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 157s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 157s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 157s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 157s + '[' -f ReplicateConstraint2.bf ']' 157s + hyphy ReplicateConstraint2.bf 157s 1).Unconstrained HKY85 157s 157s Log Likelihood = -1152.88; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.317.trvs 157s Parameter 2 : hivTree.317.trst 157s Parameter 3 : hivTree.6767.trvs 157s Parameter 4 : hivTree.6767.trst 157s Parameter 5 : hivTree.Node2.trvs 157s Parameter 6 : hivTree.Node2.trst 157s Parameter 7 : hivTree.135.trvs 157s Parameter 8 : hivTree.135.trst 157s Parameter 9 : hivTree.529.trvs 157s Parameter 10 : hivTree.529.trst 157s Parameter 11 : hivTree.105r.trvs 157s Parameter 12 : hivTree.105r.trst 157s Parameter 13 : hivTree.Node8.trvs 157s Parameter 14 : hivTree.Node8.trst 157s Parameter 15 : hivTree.iNode1.trvs 157s Parameter 16 : hivTree.iNode1.trst 157s Parameter 17 : hivTree.719.trvs 157s Parameter 18 : hivTree.719.trst 157s Parameter 19 : hivTree.136.trvs 157s Parameter 20 : hivTree.136.trst 157s Parameter 21 : hivTree.Node11.trvs 157s Parameter 22 : hivTree.Node11.trst 157s Parameter 23 : hivTree.Node5.trvs 157s Parameter 24 : hivTree.Node5.trst 157s Parameter 25 : hivTree.Node1.trvs 157s Parameter 26 : hivTree.Node1.trst 157s Parameter 27 : hivTree.6760.trvs 157s Parameter 28 : hivTree.6760.trst 157s Parameter 29 : hivTree.113.trvs 157s Parameter 30 : hivTree.113.trst 157s Parameter 31 : hivTree.9939.trvs 157s Parameter 32 : hivTree.9939.trst 157s Parameter 33 : hivTree.Node16.trvs 157s Parameter 34 : hivTree.Node16.trst 157s Parameter 35 : hivTree.256.trvs 157s Parameter 36 : hivTree.256.trst 157s Parameter 37 : hivTree.822.trvs 157s Parameter 38 : hivTree.822.trst 157s Parameter 39 : hivTree.159.trvs 157s Parameter 40 : hivTree.159.trst 157s Parameter 41 : hivTree.Node21.trvs 157s Parameter 42 : hivTree.Node21.trst 157s Parameter 43 : hivTree.iNode2.trvs 157s Parameter 44 : hivTree.iNode2.trst 157s Parameter 45 : hivTree.Node15.trvs 157s Parameter 46 : hivTree.Node15.trst 157s 157s 2).HKY85 constrained to F81 on the "iNode1" subtree 157s 157s Log Likelihood = -1157.82; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.135.trvs 157s Parameter 2 : hivTree.529.trvs 157s Parameter 3 : hivTree.105r.trvs 157s Parameter 4 : hivTree.Node8.trvs 157s Parameter 5 : hivTree.317.trvs 157s Parameter 6 : hivTree.317.trst 157s Parameter 7 : hivTree.6767.trst 157s Parameter 8 : hivTree.6767.trvs 157s Parameter 9 : hivTree.Node2.trst 157s Parameter 10 : hivTree.Node2.trvs 157s Parameter 11 : hivTree.iNode1.trvs 157s Parameter 12 : hivTree.iNode1.trst 157s Parameter 13 : hivTree.719.trvs 157s Parameter 14 : hivTree.719.trst 157s Parameter 15 : hivTree.136.trvs 157s Parameter 16 : hivTree.136.trst 157s Parameter 17 : hivTree.Node11.trvs 157s Parameter 18 : hivTree.Node11.trst 157s Parameter 19 : hivTree.Node5.trvs 157s Parameter 20 : hivTree.Node5.trst 157s Parameter 21 : hivTree.Node1.trvs 157s Parameter 22 : hivTree.Node1.trst 157s Parameter 23 : hivTree.6760.trvs 157s Parameter 24 : hivTree.6760.trst 157s Parameter 25 : hivTree.113.trvs 157s Parameter 26 : hivTree.113.trst 157s Parameter 27 : hivTree.9939.trvs 157s Parameter 28 : hivTree.9939.trst 157s Parameter 29 : hivTree.Node16.trvs 157s Parameter 30 : hivTree.Node16.trst 157s Parameter 31 : hivTree.256.trvs 157s Parameter 32 : hivTree.256.trst 157s Parameter 33 : hivTree.822.trvs 157s Parameter 34 : hivTree.822.trst 157s Parameter 35 : hivTree.159.trvs 157s Parameter 36 : hivTree.159.trst 157s Parameter 37 : hivTree.Node21.trvs 157s Parameter 38 : hivTree.Node21.trst 157s Parameter 39 : hivTree.iNode2.trvs 157s Parameter 40 : hivTree.iNode2.trst 157s Parameter 41 : hivTree.Node15.trvs 157s Parameter 42 : hivTree.Node15.trst 157s 157s Constrained Parameters List 157s 157s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 157s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 157s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 157s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 157s 157s 3).HKY85 constrained to F81 on the "iNode1" branch 157s 157s Log Likelihood = -1152.88; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.317.trvs 157s Parameter 2 : hivTree.317.trst 157s Parameter 3 : hivTree.6767.trvs 157s Parameter 4 : hivTree.6767.trst 157s Parameter 5 : hivTree.Node2.trvs 157s Parameter 6 : hivTree.Node2.trst 157s Parameter 7 : hivTree.135.trvs 157s Parameter 8 : hivTree.135.trst 157s Parameter 9 : hivTree.529.trvs 157s Parameter 10 : hivTree.529.trst 157s Parameter 11 : hivTree.105r.trvs 157s Parameter 12 : hivTree.105r.trst 157s Parameter 13 : hivTree.Node8.trvs 157s Parameter 14 : hivTree.Node8.trst 157s Parameter 15 : hivTree.iNode1.trvs 157s Parameter 16 : hivTree.iNode1.trst 157s Parameter 17 : hivTree.719.trvs 157s Parameter 18 : hivTree.719.trst 157s Parameter 19 : hivTree.136.trvs 157s Parameter 20 : hivTree.136.trst 157s Parameter 21 : hivTree.Node11.trvs 157s Parameter 22 : hivTree.Node11.trst 157s Parameter 23 : hivTree.Node5.trvs 157s Parameter 24 : hivTree.Node5.trst 157s Parameter 25 : hivTree.Node1.trvs 157s Parameter 26 : hivTree.Node1.trst 157s Parameter 27 : hivTree.6760.trvs 157s Parameter 28 : hivTree.6760.trst 157s Parameter 29 : hivTree.113.trvs 157s Parameter 30 : hivTree.113.trst 157s Parameter 31 : hivTree.9939.trvs 157s Parameter 32 : hivTree.9939.trst 157s Parameter 33 : hivTree.Node16.trvs 157s Parameter 34 : hivTree.Node16.trst 157s Parameter 35 : hivTree.256.trvs 157s Parameter 36 : hivTree.256.trst 157s Parameter 37 : hivTree.822.trvs 157s Parameter 38 : hivTree.822.trst 157s Parameter 39 : hivTree.159.trvs 157s Parameter 40 : hivTree.159.trst 157s Parameter 41 : hivTree.Node21.trvs 157s Parameter 42 : hivTree.Node21.trst 157s Parameter 43 : hivTree.iNode2.trvs 157s Parameter 44 : hivTree.iNode2.trst 157s Parameter 45 : hivTree.Node15.trvs 157s Parameter 46 : hivTree.Node15.trst 157s 157s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 157s 157s Log Likelihood = -1152.88; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.317.trvs 157s Parameter 2 : hivTree.317.trst 157s Parameter 3 : hivTree.6767.trvs 157s Parameter 4 : hivTree.6767.trst 157s Parameter 5 : hivTree.Node2.trvs 157s Parameter 6 : hivTree.Node2.trst 157s Parameter 7 : hivTree.135.trvs 157s Parameter 8 : hivTree.135.trst 157s Parameter 9 : hivTree.529.trvs 157s Parameter 10 : hivTree.529.trst 157s Parameter 11 : hivTree.105r.trvs 157s Parameter 12 : hivTree.105r.trst 157s Parameter 13 : hivTree.Node8.trvs 157s Parameter 14 : hivTree.Node8.trst 157s Parameter 15 : hivTree.iNode1.trvs 157s Parameter 16 : hivTree.iNode1.trst 157s Parameter 17 : hivTree.719.trvs 157s Parameter 18 : hivTree.719.trst 157s Parameter 19 : hivTree.136.trvs 157s Parameter 20 : hivTree.136.trst 157s Parameter 21 : hivTree.Node11.trvs 157s Parameter 22 : hivTree.Node11.trst 157s Parameter 23 : hivTree.Node5.trvs 157s Parameter 24 : hivTree.Node5.trst 157s Parameter 25 : hivTree.Node1.trvs 157s Parameter 26 : hivTree.Node1.trst 157s Parameter 27 : hivTree.6760.trvs 157s Parameter 28 : hivTree.6760.trst 157s Parameter 29 : hivTree.113.trvs 157s Parameter 30 : hivTree.113.trst 157s Parameter 31 : hivTree.9939.trvs 157s Parameter 32 : hivTree.9939.trst 157s Parameter 33 : hivTree.Node16.trvs 157s Parameter 34 : hivTree.Node16.trst 157s Parameter 35 : hivTree.256.trvs 157s Parameter 36 : hivTree.256.trst 157s Parameter 37 : hivTree.822.trvs 157s Parameter 38 : hivTree.822.trst 157s Parameter 39 : hivTree.159.trvs 157s Parameter 40 : hivTree.159.trst 157s Parameter 41 : hivTree.Node21.trvs 157s Parameter 42 : hivTree.Node21.trst 157s Parameter 43 : hivTree.iNode2.trvs 157s Parameter 44 : hivTree.iNode2.trst 157s Parameter 45 : hivTree.Node15.trvs 157s Parameter 46 : hivTree.Node15.trst 157s 157s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 157s 157s Log Likelihood = -1152.88; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.317.trvs 157s Parameter 2 : hivTree.317.trst 157s Parameter 3 : hivTree.6767.trvs 157s Parameter 4 : hivTree.6767.trst 157s Parameter 5 : hivTree.Node2.trvs 157s Parameter 6 : hivTree.Node2.trst 157s Parameter 7 : hivTree.135.trvs 157s Parameter 8 : hivTree.135.trst 157s Parameter 9 : hivTree.529.trvs 157s Parameter 10 : hivTree.529.trst 157s Parameter 11 : hivTree.105r.trvs 157s Parameter 12 : hivTree.105r.trst 157s Parameter 13 : hivTree.Node8.trvs 157s Parameter 14 : hivTree.Node8.trst 157s Parameter 15 : hivTree.iNode1.trvs 157s Parameter 16 : hivTree.iNode1.trst 157s Parameter 17 : hivTree.719.trvs 157s Parameter 18 : hivTree.719.trst 157s Parameter 19 : hivTree.136.trvs 157s Parameter 20 : hivTree.136.trst 157s Parameter 21 : hivTree.Node11.trvs 157s Parameter 22 : hivTree.Node11.trst 157s Parameter 23 : hivTree.Node5.trvs 157s Parameter 24 : hivTree.Node5.trst 157s Parameter 25 : hivTree.Node1.trvs 157s Parameter 26 : hivTree.Node1.trst 157s Parameter 27 : hivTree.6760.trvs 157s Parameter 28 : hivTree.6760.trst 157s Parameter 29 : hivTree.113.trvs 157s Parameter 30 : hivTree.113.trst 157s Parameter 31 : hivTree.9939.trvs 157s Parameter 32 : hivTree.9939.trst 157s Parameter 33 : hivTree.Node16.trvs 157s Parameter 34 : hivTree.Node16.trst 157s Parameter 35 : hivTree.256.trvs 157s Parameter 36 : hivTree.256.trst 157s Parameter 37 : hivTree.822.trvs 157s Parameter 38 : hivTree.822.trst 157s Parameter 39 : hivTree.159.trvs 157s Parameter 40 : hivTree.159.trst 157s Parameter 41 : hivTree.Node21.trvs 157s Parameter 42 : hivTree.Node21.trst 157s Parameter 43 : hivTree.iNode2.trvs 157s Parameter 44 : hivTree.iNode2.trst 157s Parameter 45 : hivTree.Node15.trvs 157s Parameter 46 : hivTree.Node15.trst 157s 157s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 157s 157s Log Likelihood = -1157.82; 157s 157s Independent Parameters List 157s 157s Parameter 1 : hivTree.135.trst 157s Parameter 2 : hivTree.529.trst 157s Parameter 3 : hivTree.105r.trst 157s Parameter 4 : hivTree.Node8.trst 157s Parameter 5 : hivTree.317.trvs 157s Parameter 6 : hivTree.317.trst 157s Parameter 7 : hivTree.6767.trst 157s Parameter 8 : hivTree.6767.trvs 157s Parameter 9 : hivTree.Node2.trst 157s Parameter 10 : hivTree.Node2.trvs 157s Parameter 11 : hivTree.iNode1.trvs 157s Parameter 12 : hivTree.iNode1.trst 157s Parameter 13 : hivTree.719.trvs 157s Parameter 14 : hivTree.719.trst 157s Parameter 15 : hivTree.136.trvs 157s Parameter 16 : hivTree.136.trst 157s Parameter 17 : hivTree.Node11.trvs 157s Parameter 18 : hivTree.Node11.trst 157s Parameter 19 : hivTree.Node5.trvs 157s Parameter 20 : hivTree.Node5.trst 157s Parameter 21 : hivTree.Node1.trvs 157s Parameter 22 : hivTree.Node1.trst 157s Parameter 23 : hivTree.6760.trvs 157s Parameter 24 : hivTree.6760.trst 157s Parameter 25 : hivTree.113.trvs 157s Parameter 26 : hivTree.113.trst 157s Parameter 27 : hivTree.9939.trvs 157s Parameter 28 : hivTree.9939.trst 157s Parameter 29 : hivTree.Node16.trvs 157s Parameter 30 : hivTree.Node16.trst 157s Parameter 31 : hivTree.256.trvs 157s Parameter 32 : hivTree.256.trst 157s Parameter 33 : hivTree.822.trvs 157s Parameter 34 : hivTree.822.trst 157s Parameter 35 : hivTree.159.trvs 157s Parameter 36 : hivTree.159.trst 157s Parameter 37 : hivTree.Node21.trvs 157s Parameter 38 : hivTree.Node21.trst 157s Parameter 39 : hivTree.iNode2.trvs 157s Parameter 40 : hivTree.iNode2.trst 157s Parameter 41 : hivTree.Node15.trvs 157s Parameter 42 : hivTree.Node15.trst 157s 157s Constrained Parameters List 157s 157s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 157s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 157s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 157s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 157s + '[' -f aa.bf ']' 157s + hyphy aa.bf 157s Log Likelihood = -1134.73158058147; 157s Tree theTree=(((Langur:0.0743085762235474,Baboon:0.0383318287927434)Node2:0.02337958944178603,Human:0.05950609440553488)Node1:0.02005975178326679,Rat:0.2458687001652838,(Cow:0.2551838855176953,Horse:0.5630260104878223)Node7:0.07055352040119602); 157s + for i in *.bf 157s + '[' -f definitions2.bf ']' 157s + hyphy definitions2.bf 157s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 157s 157s Sample by MEAN: 157s 157s Sample mean = 0.5 (sample variance = 0.2450374540764348) 157s 157s Rate[0]= 0.06847689 (weight=0.2500000) 157s Rate[1]= 0.23837593 (weight=0.2500000) 157s Rate[2]= 0.50000000 (weight=0.2500000) 157s Rate[3]= 1.19314718 (weight=0.2500000) 157s ------------------------------------------------ 157s 157s Sample by MEDIAN: 157s 157s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 157s 157s Rate[0]= 0.06676570 (weight=0.2500000) 157s Rate[1]= 0.23500181 (weight=0.2500000) 157s Rate[2]= 0.49041463 (weight=0.2500000) 157s Rate[3]= 1.03972077 (weight=0.2500000) 157s ------------------------------------------------ 157s 157s Sample by SCALED_MEDIAN: 157s 157s Sample mean = 0.5 (sample variance = 0.2154404122636025) 157s 157s Rate[0]= 0.07289218 (weight=0.2500000) 157s Rate[1]= 0.25656580 (weight=0.2500000) 157s Rate[2]= 0.53541552 (weight=0.2500000) 157s Rate[3]= 1.13512650 (weight=0.2500000) 157s ------------------------------------------------ 157s 157s Sample by MEAN (numerical averaging): 157s 157s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 157s 157s Rate[0]= 0.06846096 (weight=0.2500000) 157s Rate[1]= 0.23834015 (weight=0.2500000) 157s Rate[2]= 0.49996411 (weight=0.2500000) 157s Rate[3]= 1.19314889 (weight=0.2500000) 157s ------------------------------------------------ 157s 157s Sample by MEAN (numerical CDF and averaging): 157s 157s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 157s 157s Rate[0]= 0.06849282 (weight=0.2500000) 157s Rate[1]= 0.23835613 (weight=0.2500000) 157s Rate[2]= 0.49994751 (weight=0.2500000) 157s Rate[3]= 1.19311765 (weight=0.2500000) 157s ------------------------------------------------ 157s 2). Equiprobable rates sampled from Exponential with lambda = 2 157s 157s Sample by MEDIAN (3 rate classes): 157s 157s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 157s 157s Rate[0]= 0.09116078 (weight=0.3333333) 157s Rate[1]= 0.34657359 (weight=0.3333333) 157s Rate[2]= 0.89587973 (weight=0.3333333) 157s ------------------------------------------------ 157s 157s Sample by MEDIAN (9 rate classes): 157s 157s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 157s 157s Rate[0]= 0.02857921 (weight=0.1111111) 157s Rate[1]= 0.09116078 (weight=0.1111111) 157s Rate[2]= 0.16271120 (weight=0.1111111) 157s Rate[3]= 0.24623824 (weight=0.1111111) 157s Rate[4]= 0.34657359 (weight=0.1111111) 157s Rate[5]= 0.47223080 (weight=0.1111111) 157s Rate[6]= 0.64046692 (weight=0.1111111) 157s Rate[7]= 0.89587973 (weight=0.1111111) 157s Rate[8]= 1.44518588 (weight=0.1111111) 157s ------------------------------------------------ 157s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 157s 157s Sample by MEAN (10 rate classes): 157s 157s Sample mean = 1 (sample variance = 0.1057310289486733) 157s 157s Rate[0]= 0.52447499 (weight=0.1000000) 157s Rate[1]= 0.67866972 (weight=0.1000000) 157s Rate[2]= 0.77209919 (weight=0.1000000) 157s Rate[3]= 0.85214884 (weight=0.1000000) 157s Rate[4]= 0.92850815 (weight=0.1000000) 157s Rate[5]= 1.00664500 (weight=0.1000000) 157s Rate[6]= 1.09192933 (weight=0.1000000) 157s Rate[7]= 1.19267960 (weight=0.1000000) 157s Rate[8]= 1.32858029 (weight=0.1000000) 157s Rate[9]= 1.62426489 (weight=0.1000000) 157s ------------------------------------------------ 157s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 157s 157s Sample by MEAN (10 rate classes): 157s 157s Sample mean = 2 (sample variance = 0.04259071282256012) 157s 157s Rate[0]= 1.66431246 (weight=0.1000000) 157s Rate[1]= 1.79212822 (weight=0.1000000) 157s Rate[2]= 1.86123411 (weight=0.1000000) 157s Rate[3]= 1.91722052 (weight=0.1000000) 157s Rate[4]= 1.96832799 (weight=0.1000000) 157s Rate[5]= 2.01862937 (weight=0.1000000) 157s Rate[6]= 2.07152664 (weight=0.1000000) 157s Rate[7]= 2.13166629 (weight=0.1000000) 157s Rate[8]= 2.20930216 (weight=0.1000000) 157s Rate[9]= 2.36565224 (weight=0.1000000) 157s ------------------------------------------------ 157s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 157s 157s Sample by MEAN (8 rate classes): 157s 157s Sample mean = 0.5 (sample variance = 0.09375000225643569) 157s 157s Rate[0]= 0.06250000 (weight=+ for i in *.bf 157s + '[' -f definitions3.bf ']' 157s + hyphy definitions3.bf 157s + for i in *.bf 157s + '[' -f displayFunction.bf ']' 157s + hyphy displayFunction.bf 157s + for i in *.bf 157s + '[' -f profile_test.bf ']' 157s + hyphy profile_test.bf 157s 0.1250000) 157s Rate[1]= 0.18750000 (weight=0.1250000) 157s Rate[2]= 0.31250001 (weight=0.1250000) 157s Rate[3]= 0.43750001 (weight=0.1250000) 157s Rate[4]= 0.56249993 (weight=0.1250000) 157s Rate[5]= 0.68750001 (weight=0.1250000) 157s Rate[6]= 0.81250002 (weight=0.1250000) 157s Rate[7]= 0.93750002 (weight=0.1250000) 157s ------------------------------------------------ 157s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 157s 157s Sample by MEAN (8 rate classes): 157s 157s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 157s 157s Rate[0]= 2.17658588 (weight=0.1250000) 157s Rate[1]= 2.55230783 (weight=0.1250000) 157s Rate[2]= 2.75432532 (weight=0.1250000) 157s Rate[3]= 2.92101185 (weight=0.1250000) 157s Rate[4]= 3.07898815 (weight=0.1250000) 157s Rate[5]= 3.24567468 (weight=0.1250000) 157s Rate[6]= 3.44769217 (weight=0.1250000) 157s Rate[7]= 3.82341415 (weight=0.1250000) 157s ------------------------------------------------ 157s 157s 157s Sample mean = 1 (sample variance = 0.9920002887656187) 157s 157s Rate[0]= 0.05175536 (weight=0.1000000) 157s Rate[1]= 0.16309623 (weight=0.1000000) 157s Rate[2]= 0.28842380 (weight=0.1000000) 157s Rate[3]= 0.43177086 (weight=0.1000000) 157s Rate[4]= 0.59921784 (weight=0.1000000) 157s Rate[5]= 0.80057298 (weight=0.1000000) 157s Rate[6]= 1.05324451 (weight=0.1000000) 157s Rate[7]= 1.39304259 (weight=0.1000000) 157s Rate[8]= 1.91629073 (weight=0.1000000) 157s Rate[9]= 3.30258509 (weight=0.1000000) 157s ------------------------------------------------ 157s 157s Total run time (seconds) : + for i in *.bf 157s + '[' -f shared.bf ']' 157s + hyphy shared.bf 157s 0.000000 157s Total number of steps : 1500005 157s 157s 1 : s=0; 157s Call count: 1 157s Time (seconds): 7e-12 157s 2 : m={5,1}; 157s Call count: 1 157s Time (seconds): 9e-12 157s 3 : k=0; 157s Call count: 1 157s Time (seconds): 2e-12 157s 4 : Branch under condition 'k<250000' 157s to 157s s=s+k; 157s else 157s #profilePAUSE, ; 157s Call count: 250001 157s Time (seconds): 2.471300000000472e-08 157s 5 : s=s+k; 157s Call count: 250000 157s Time (seconds): 3.114300000001041e-08 157s 6 : t=Random(0,5); 157s Call count: 250000 157s Time (seconds): 2.716100000000654e-08 157s 7 : m[t]=m[t]+1; 157s Call count: 250000 157s Time (seconds): 6.742100000004637e-08 157s 8 : k=k+1; 157s Call count: 250000 157s Time (seconds): 3.164500000001095e-08 157s 9 : Go to step 4 157s Call count: 250000 157s Time (seconds): 8.267000000000383e-09 157s 10 : #profilePAUSE, ; 157s Call count: 1 157s Time (seconds): 2e-12 157s + rm -f '*messages.log*' '*errors.log*' 158s autopkgtest [18:27:10]: test run-unit-tests: -----------------------] 158s run-unit-tests PASS 158s autopkgtest [18:27:10]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 158s autopkgtest [18:27:10]: @@@@@@@@@@@@@@@@@@@@ summary 158s run-unit-tests PASS 176s nova [W] Using flock in prodstack6-s390x 176s flock: timeout while waiting to get lock 176s Creating nova instance adt-questing-s390x-hyphy-20250502-182432-juju-7f2275-prod-proposed-migration-environment-20-14a11ebf-3c2f-470b-aa69-c8165bbd726c from image adt/ubuntu-questing-s390x-server-20250502.img (UUID 632ecfca-a19d-4f3a-af48-b7883fa0ccf2)... 176s nova [W] Timed out waiting for 28ee9ce7-8e0e-47a9-8836-bdb4aaa7ce2f to get deleted.