0s autopkgtest [06:37:52]: starting date and time: 2024-03-24 06:37:52+0000 0s autopkgtest [06:37:52]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [06:37:52]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.i9ccn9cn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl,src:orthanc-python --apt-upgrade hyphy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2 orthanc-python/4.1+ds-2build3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-4.secgroup --name adt-noble-s390x-hyphy-20240324-063752-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 149s autopkgtest [06:40:21]: testbed dpkg architecture: s390x 149s autopkgtest [06:40:21]: testbed apt version: 2.7.12 149s autopkgtest [06:40:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 150s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 151s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 151s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 151s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 151s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4009 kB] 152s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [691 kB] 152s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 152s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 152s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 152s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4191 kB] 152s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 152s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.8 kB] 152s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 154s Fetched 9625 kB in 3s (3517 kB/s) 154s Reading package lists... 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Calculating upgrade... 157s The following packages will be REMOVED: 157s libssl3 157s The following NEW packages will be installed: 157s libssl3t64 157s The following packages have been kept back: 157s curl 157s The following packages will be upgraded: 157s openssl 158s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 158s Need to get 2685 kB of archives. 158s After this operation, 239 kB of additional disk space will be used. 158s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 158s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 159s Fetched 2685 kB in 1s (2055 kB/s) 159s (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 ... 52170 files and directories currently installed.) 159s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 159s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 159s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 159s wget depends on libssl3 (>= 3.0.0). 159s tnftp depends on libssl3 (>= 3.0.0). 159s tcpdump depends on libssl3 (>= 3.0.0). 159s systemd-resolved depends on libssl3 (>= 3.0.0). 159s systemd depends on libssl3 (>= 3.0.0). 159s sudo depends on libssl3 (>= 3.0.0). 159s s390-tools depends on libssl3 (>= 3.0.0). 159s rsync depends on libssl3 (>= 3.0.0). 159s python3-cryptography depends on libssl3 (>= 3.0.0). 159s openssh-server depends on libssl3 (>= 3.0.10). 159s openssh-client depends on libssl3 (>= 3.0.10). 159s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 159s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 159s libssh-4:s390x depends on libssl3 (>= 3.0.0). 159s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 159s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 159s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 159s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 159s libnvme1 depends on libssl3 (>= 3.0.0). 159s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 159s libkmod2:s390x depends on libssl3 (>= 3.0.0). 159s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 159s libcurl4:s390x depends on libssl3 (>= 3.0.0). 159s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 159s kmod depends on libssl3 (>= 3.0.0). 159s dhcpcd-base depends on libssl3 (>= 3.0.0). 159s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 159s 159s (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 ... 52170 files and directories currently installed.) 159s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 159s Selecting previously unselected package libssl3t64:s390x. 159s (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 ... 52159 files and directories currently installed.) 159s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 159s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 159s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 159s Setting up openssl (3.0.13-0ubuntu2) ... 159s Processing triggers for man-db (2.12.0-3) ... 160s Processing triggers for libc-bin (2.39-0ubuntu6) ... 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 161s Unknown architecture, assuming PC-style ttyS0 161s sh: Attempting to set up Debian/Ubuntu apt sources automatically 161s sh: Distribution appears to be Ubuntu 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s eatmydata is already the newest version (131-1). 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s dbus is already the newest version (1.14.10-4ubuntu1). 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 163s rng-tools-debian is already the newest version (2.4). 163s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s The following packages will be REMOVED: 163s cloud-init* python3-configobj* python3-debconf* 163s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 163s After this operation, 3256 kB disk space will be freed. 163s (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 ... 52172 files and directories currently installed.) 163s Removing cloud-init (24.1.2-0ubuntu1) ... 164s Removing python3-configobj (5.0.8-3) ... 164s Removing python3-debconf (1.5.86) ... 164s Processing triggers for man-db (2.12.0-3) ... 164s (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 ... 51783 files and directories currently installed.) 164s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 164s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 164s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 164s invoke-rc.d: policy-rc.d denied execution of try-restart. 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s linux-generic is already the newest version (6.8.0-11.11+1). 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 165s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 166s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 167s Reading package lists... 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s Calculating upgrade... 168s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 168s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 168s autopkgtest [06:40:40]: rebooting testbed after setup commands that affected boot 184s autopkgtest [06:40:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 187s autopkgtest [06:40:59]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 190s Get:1 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (dsc) [2423 B] 190s Get:2 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (tar) [2613 kB] 190s Get:3 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (diff) [17.0 kB] 190s gpgv: Signature made Sat Jan 13 16:06:18 2024 UTC 190s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 190s gpgv: issuer "emollier@debian.org" 190s gpgv: Can't check signature: No public key 190s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.59+dfsg-1.dsc: no acceptable signature found 190s autopkgtest [06:41:02]: testing package hyphy version 2.5.59+dfsg-1 191s autopkgtest [06:41:03]: build not needed 192s autopkgtest [06:41:04]: test run-unit-tests: preparing testbed 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 200s Starting pkgProblemResolver with broken count: 0 200s Starting 2 pkgProblemResolver with broken count: 0 200s Done 200s The following additional packages will be installed: 200s hyphy-common hyphy-mpi hyphy-pt libatomic1 libevent-pthreads-2.1-7 200s libfabric1 libgomp1 libhwloc-plugins libhwloc15 libmunge2 libopenmpi3 200s libpciaccess0 libpmix2 librdmacm1t64 libxnvctrl0 ocl-icd-libopencl1 200s Suggested packages: 200s opencl-icd 200s The following NEW packages will be installed: 200s autopkgtest-satdep hyphy-common hyphy-mpi hyphy-pt libatomic1 200s libevent-pthreads-2.1-7 libfabric1 libgomp1 libhwloc-plugins libhwloc15 200s libmunge2 libopenmpi3 libpciaccess0 libpmix2 librdmacm1t64 libxnvctrl0 200s ocl-icd-libopencl1 200s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 8348 kB/8349 kB of archives. 200s After this operation, 26.0 MB of additional disk space will be used. 200s Get:1 /tmp/autopkgtest.qA2hFY/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [716 B] 200s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x hyphy-common all 2.5.59+dfsg-1 [624 kB] 201s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 201s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libevent-pthreads-2.1-7 s390x 2.1.12-stable-9 [7692 B] 201s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240303-1ubuntu1 [9392 B] 201s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x librdmacm1t64 s390x 50.0-2 [74.1 kB] 201s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libfabric1 s390x 1.17.0-3build1 [566 kB] 201s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libhwloc15 s390x 2.10.0-1 [174 kB] 201s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x libmunge2 s390x 0.5.15-3ubuntu1 [17.3 kB] 201s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libpciaccess0 s390x 0.17-3 [18.5 kB] 201s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu1 [11.7 kB] 201s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1 [39.1 kB] 201s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x libhwloc-plugins s390x 2.10.0-1 [16.1 kB] 201s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x libpmix2 s390x 5.0.1-4 [722 kB] 201s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x libopenmpi3 s390x 4.1.6-5ubuntu1 [3024 kB] 202s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x hyphy-mpi s390x 2.5.59+dfsg-1 [1468 kB] 202s Get:17 http://ftpmaster.internal/ubuntu noble/universe s390x hyphy-pt s390x 2.5.59+dfsg-1 [1425 kB] 202s Fetched 8348 kB in 2s (4127 kB/s) 202s Selecting previously unselected package hyphy-common. 202s (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 ... 51728 files and directories currently installed.) 202s Preparing to unpack .../00-hyphy-common_2.5.59+dfsg-1_all.deb ... 202s Unpacking hyphy-common (2.5.59+dfsg-1) ... 202s Selecting previously unselected package libgomp1:s390x. 202s Preparing to unpack .../01-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 202s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 202s Selecting previously unselected package libevent-pthreads-2.1-7:s390x. 202s Preparing to unpack .../02-libevent-pthreads-2.1-7_2.1.12-stable-9_s390x.deb ... 202s Unpacking libevent-pthreads-2.1-7:s390x (2.1.12-stable-9) ... 202s Selecting previously unselected package libatomic1:s390x. 202s Preparing to unpack .../03-libatomic1_14-20240303-1ubuntu1_s390x.deb ... 202s Unpacking libatomic1:s390x (14-20240303-1ubuntu1) ... 202s Selecting previously unselected package librdmacm1t64:s390x. 202s Preparing to unpack .../04-librdmacm1t64_50.0-2_s390x.deb ... 202s Unpacking librdmacm1t64:s390x (50.0-2) ... 202s Selecting previously unselected package libfabric1:s390x. 202s Preparing to unpack .../05-libfabric1_1.17.0-3build1_s390x.deb ... 202s Unpacking libfabric1:s390x (1.17.0-3build1) ... 202s Selecting previously unselected package libhwloc15:s390x. 202s Preparing to unpack .../06-libhwloc15_2.10.0-1_s390x.deb ... 202s Unpacking libhwloc15:s390x (2.10.0-1) ... 202s Selecting previously unselected package libmunge2:s390x. 202s Preparing to unpack .../07-libmunge2_0.5.15-3ubuntu1_s390x.deb ... 202s Unpacking libmunge2:s390x (0.5.15-3ubuntu1) ... 202s Selecting previously unselected package libpciaccess0:s390x. 202s Preparing to unpack .../08-libpciaccess0_0.17-3_s390x.deb ... 202s Unpacking libpciaccess0:s390x (0.17-3) ... 202s Selecting previously unselected package libxnvctrl0:s390x. 202s Preparing to unpack .../09-libxnvctrl0_510.47.03-0ubuntu1_s390x.deb ... 202s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu1) ... 202s Selecting previously unselected package ocl-icd-libopencl1:s390x. 202s Preparing to unpack .../10-ocl-icd-libopencl1_2.3.2-1_s390x.deb ... 202s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1) ... 202s Selecting previously unselected package libhwloc-plugins:s390x. 202s Preparing to unpack .../11-libhwloc-plugins_2.10.0-1_s390x.deb ... 202s Unpacking libhwloc-plugins:s390x (2.10.0-1) ... 202s Selecting previously unselected package libpmix2:s390x. 202s Preparing to unpack .../12-libpmix2_5.0.1-4_s390x.deb ... 202s Unpacking libpmix2:s390x (5.0.1-4) ... 203s Selecting previously unselected package libopenmpi3:s390x. 203s Preparing to unpack .../13-libopenmpi3_4.1.6-5ubuntu1_s390x.deb ... 203s Unpacking libopenmpi3:s390x (4.1.6-5ubuntu1) ... 203s Selecting previously unselected package hyphy-mpi. 203s Preparing to unpack .../14-hyphy-mpi_2.5.59+dfsg-1_s390x.deb ... 203s Unpacking hyphy-mpi (2.5.59+dfsg-1) ... 203s Selecting previously unselected package hyphy-pt. 203s Preparing to unpack .../15-hyphy-pt_2.5.59+dfsg-1_s390x.deb ... 203s Unpacking hyphy-pt (2.5.59+dfsg-1) ... 203s Selecting previously unselected package autopkgtest-satdep. 203s Preparing to unpack .../16-1-autopkgtest-satdep.deb ... 203s Unpacking autopkgtest-satdep (0) ... 203s Setting up libpciaccess0:s390x (0.17-3) ... 203s Setting up hyphy-common (2.5.59+dfsg-1) ... 203s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 203s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu1) ... 203s Setting up libmunge2:s390x (0.5.15-3ubuntu1) ... 203s Setting up libhwloc15:s390x (2.10.0-1) ... 203s Setting up libatomic1:s390x (14-20240303-1ubuntu1) ... 203s Setting up ocl-icd-libopencl1:s390x (2.3.2-1) ... 203s Setting up librdmacm1t64:s390x (50.0-2) ... 203s Setting up libevent-pthreads-2.1-7:s390x (2.1.12-stable-9) ... 203s Setting up libfabric1:s390x (1.17.0-3build1) ... 203s Setting up hyphy-pt (2.5.59+dfsg-1) ... 203s Setting up libhwloc-plugins:s390x (2.10.0-1) ... 203s Setting up libpmix2:s390x (5.0.1-4) ... 203s Setting up libopenmpi3:s390x (4.1.6-5ubuntu1) ... 203s Setting up hyphy-mpi (2.5.59+dfsg-1) ... 203s Setting up autopkgtest-satdep (0) ... 203s Processing triggers for man-db (2.12.0-3) ... 203s Processing triggers for libc-bin (2.39-0ubuntu6) ... 206s (Reading database ... 52560 files and directories currently installed.) 206s Removing autopkgtest-satdep (0) ... 206s autopkgtest [06:41:18]: test run-unit-tests: [----------------------- 206s + for i in *.bf 206s + '[' -f ExonIntron.bf ']' 206s + hyphy ExonIntron.bf 207s Log Likelihood = -1113.34523097096; 207s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04134922360054386,(ZMUBIS27F:0,(ZMU29160:0.05439434932282533,ZMU29161:0.03970999166190733)Node8:0.01201941509476627)Node6:0)Node4:0.02459325579552285,BLYMUB1:0.01185776317071451); 207s Tree exon2Tree=(BLYMUB2:0.03542712686531091,(RICRMA630:0.02935212677492443,(ZMUBIS27F:0.07545618687547105,(ZMU29160:0.09103008402713363,ZMU29161:0.02595058167991688)Node8:0.01157418952698801)Node6:0.04928334034159242)Node4:0.02930702521183928,BLYMUB1:0.02204339627174455); 207s Tree intronTree=(BLYMUB2:0.03120148612094109,(RICRMA630:0.04155588332931375,(ZMUBIS27F:0.0204450048634299,(ZMU29160:0.02069042064766667,ZMU29161:0.01019777223217759)Node8:0.02068977427005251)Node6:0)Node4:0,BLYMUB1:0.01036597601511323); 207s + for i in *.bf 207s + '[' -f F81.bf ']' 207s + hyphy F81.bf 207s Log Likelihood = -1187.54702793555; 207s Tree givenTree=(256:0.01194349931817215,(822:0.02944831511822758,159:0.004470548006066492)Node2:0.003652057115312472,((113:0.02244745718091993,9939:0.07632906548672694)Node6:0.00507764978158866,(6760:0.06903114752200892,((317:0.03751818519773164,6767:0.07086144671073689)Node12:0.01229344742288747,((135:0.02045618794857804,(529:0.03338016174521963,105r:0.01322043982245651)Node18:0.02586876645680794)Node16:0.005414265333512922,(719:0.02965903204975293,136:0.008234207161007853)Node21:0.04882998782707906)Node15:0.01525962110033743)Node11:0.01379934486338241)Node9:0.02422267836472632)Node5:0.02148378205726027); 207s + for i in *.bf 207s + '[' -f F81relrate.bf ']' 207s + hyphy F81relrate.bf 207s 207s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.001001418486; 207s Tree threeTaxaTree=(a:0.08501458081831741,b:0.07337612979570049,c:0.1653894109016897); 207s 207s 207s 1). With the outgroup at taxon #1, the P-value is:0.002155106158058695 207s Log Likelihood = -948.707253867892; 207s Tree threeTaxaTree=(a:0.08228741153904655,b:0.119450759858316,c:0.119450759858316); 207s 207s 207s 2). With the outgroup at taxon #2, the P-value is:0.008353404399320974 207s Log Likelihood = -947.479050125766; 207s Tree threeTaxaTree=(a:0.1250762630043411,b:0.07125949122322148,c:0.1250762630043411); 207s 207s 207s 3). With the outgroup at taxon #3, the P-value is:0.6669137053246262 207s Log Likelihood = -944.093618166699; 207s Tree threeTaxaTree=(a:0.07922729811878117,b:0.07922729811878117,c:0.165333983818582); 207s 207s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059583061; 207s Tree fourTaxaTree1=((1:0.1129103837257227,2:0.107343860013683)Node1:0.09978718076111803,3:0.3469443804232114,4:0.3219019795642176); 207s Tree fourTaxaTree2=((1:0.08585822862919713,2:0.09338072181116867)Node1:0.07364163086656983,3:0.3933120522865876,4:0.3801922663729329); 207s 207s 207s 1). Relative ratio constraint; the P-value is:0.6933531570010261 207s Log Likelihood = -2575.74610909567; 207s Global Parameters: 207s R=1.00729085341613; 207s 207s Tree fourTaxaTree1=((1:0.09948365505806882,2:0.09943037138794089)Node1:0.08696829308802421,3:0.3687235960126604,4:0.3489177338272059); 207s Tree fourTaxaTree2=((1:0.100073745135645,2:0.1000201454119401)Node1:0.08748414794664425,3:0.3709106903172302,4:0.3509873491072399); 207s + for i in *.bf 207s + '[' -f F81relratio.bf ']' 207s + hyphy F81relratio.bf 207s + for i in *.bf 207s + '[' -f HKY85.bf ']' 207s + hyphy HKY85.bf 207s Log Likelihood = -1152.88077773909; 207s Tree givenTree=(256:0.01162070182604088,(822:0.02979926451443584,159:0.004015046911942904)Node2:0.003749827223630768,((113:0.02130520770118562,9939:0.07785954801431182)Node6:0.004320565418539774,(6760:0.07315576754142032,((317:0.03809412646592474,6767:0.07101550063779899)Node12:0.006276164739972901,((135:0.01788112592444625,(529:0.03257791789990102,105r:0.01513878382158365)Node18:0.02833956064538017)Node16:0.007921503868834619,(719:0.02987628482584961,136:0.00804153730286988)Node21:0.04859310335914813)Node15:0.01599223438105079)Node11:0.01658044691131713)Node9:0.02665634421821494)Node5:0.02296564552436482); 207s + for i in *.bf 207s + '[' -f HKY852blocks.bf ']' 207s + hyphy HKY852blocks.bf 207s 207s ----- RESULTS ----- 207s + for i in *.bf 207s + '[' -f HKY852blocks2models.bf ']' 207s + hyphy HKY852blocks2models.bf 207s Log Likelihood = -6801.91478425276; 207s Tree actinTree1=(ZMU60513:0,ZMU60514:0.01050202321568921,((((((ZMU60511:0.01039488408135273,ZMU60510:0.02379070780713856)Node8:0.08348786107702381,OSRAC2:0.1885079102240996)Node7:0.05839366558942005,(OSRAC1:0.01536275994074223,SVSOAC1:0.07341325799891436)Node12:0.07295373451860043)Node6:0,((OSRAC3:0.07321302548671947,ZMU60507:0.06503975186773671)Node16:0.07977604215561537,ZMU60509:0.1288921885884091)Node15:0.001251872635464636)Node5:0.08269589050191273,(MZEACT1G:0.1142676217413272,OSRAC7:0.0341931097703487)Node20:0)Node4:0.1058973733340671,ZMU60508:0.01696789302960674)Node3:0.05975686204336134); 207s Tree actinTree2=(ZMU60513:0.01013471033128259,ZMU60514:0.02361992336180286,((((((ZMU60511:0.03958621037682149,ZMU60510:0.02871409626377734)Node8:0.0459917013426994,OSRAC2:0.1281527526633053)Node7:0.02274333471502154,(OSRAC1:0.04038736776829079,SVSOAC1:0.05533230239637962)Node12:0.09055757439546061)Node6:0.02100604348917753,((OSRAC3:0.108221164542607,ZMU60507:0.07346472812084469)Node16:0.05601779804320004,ZMU60509:0.1117227194511854)Node15:0.0291599894270592)Node5:0.04981252790522362,(MZEACT1G:0.1070039276414496,OSRAC7:0.09559155674444123)Node20:0.02268055914719592)Node4:0.04831150224458001,ZMU60508:0.02346330777492431)Node3:0.05651673682762296); 208s + for i in *.bf 208s + '[' -f HKY85relrate.bf ']' 208s + hyphy HKY85relrate.bf 208s 208s ----- RESULTS ----- 208s Log Likelihood = -6049.33413410755; 208s Tree actinTree1=(ZMU60513:0.01368111326830167,ZMU60514:0.06662165180548506,((((((ZMU60511:0.1014489610315025,ZMU60510:0.08940384587953119)Node8:0.2112347538259576,OSRAC2:0.3684206026894413)Node7:0.06392754822453442,(OSRAC1:0.04321367172357589,SVSOAC1:0.2447959878714145)Node12:0.4083947499795273)Node6:0.1002631510870106,((OSRAC3:0.1861737502599249,ZMU60507:0.3288459731518424)Node16:0.1590820363686745,ZMU60509:0.4442394027840464)Node15:0.04671167693415579)Node5:0.1895852966375731,(MZEACT1G:0.324493305604111,OSRAC7:0.247713489120728)Node20:0.009395678586464595)Node4:0.2662546000798074,ZMU60508:0.01033677340734289)Node3:0.223056294686429); 208s Tree actinTree2=(ZMU60513:0.004497206954537016,ZMU60514:0.004482860703023138,((((((ZMU60511:0.004483118612014198,ZMU60510:0.005992290361288377)Node8:0.004873742452637385,OSRAC2:0.04746326688188292)Node7:0.003177747582480156,(OSRAC1:0.01210015672457146,SVSOAC1:0.007446821280902099)Node12:0.02730445498714606)Node6:0,((OSRAC3:0.04645835124091833,ZMU60507:0.009174262025148719)Node16:0.0104545219968459,ZMU60509:0.02448226894659258)Node15:0)Node5:0.0192740564450552,(MZEACT1G:0.0338123940904346,OSRAC7:0.03062749757373966)Node20:0.006212161690449578)Node4:0.007802281177312584,ZMU60508:0.004488900142641823)Node3:0.01512222983434826); 208s 208s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371751632424; 208s Tree threeTaxaTree=(a:0.08473003175317764,b:0.07473137597643539,c:0.174064542689109); 208s 208s 208s 1). Outgroup at taxon #1 208s a). Transition rate test. P-Value = 0.02098226516725465 208s Log Likelihood = -924.035884021378; 208s Tree threeTaxaTree=(a:0.08099123330674669,b:0.1064970277501439,c:0.1431287422547734); 208s 208s b). Transversion rate test. P-Value = 0.03655174813200768 208s Log Likelihood = -923.55733986013; 208s Tree threeTaxaTree=(a:0.084385863180111,b:0.09108496720824998,c:0.1577932370277693); 208s 208s c). Both rates test. P-Value = 0.00632399828374719 208s Log Likelihood = -926.435155263498; 208s Tree threeTaxaTree=(a:0.08054167256686441,b:0.1248197388549912,c:0.1248197388549912); 208s 208s 208s 2). Outgroup at taxon #2 208s a). Transition rate test. P-Value = 0.02758028958440228 208s Log Likelihood = -923.798808189923; 208s Tree threeTaxaTree=(a:0.1157945362947561,b:0.0710231672763683,c:0.1442792954111021); 208s 208s b). Transversion rate test. P-Value = 0.1106456954857765 208s Log Likelihood = -922.644238896077; 208s Tree threeTaxaTree=(a:0.09762132520456517,b:0.07463527366174004,c:0.1608971533992973); 208s 208s c). Both rates test. P-Value = 0.02199500082285188 208s Log Likelihood = -925.188691719246; 208s Tree threeTaxaTree=(a:0.1299135255623827,b:0.07078650465677661,c:0.1299135255623827); 208s 208s 208s 3). Outgroup at taxon #3 208s a). Transition rate test. P-Value = 0.9291732773304646 208s Log Likelihood = -921.37570190709; 208s Tree threeTaxaTree=(a:0.08354358737958395,b:0.07588180027038632,c:0.1740455829900139); 208s 208s b). Transversion rate test. P-Value = 0.5919879178907992 208s Log Likelihood = -921.515376857668; 208s Tree threeTaxaTree=(a:0.08115157531975309,b:0.07834973653854679,c:0.1740031943295483); 208s 208s c). Both rates test. P-Value = 0.8615417084585719 208s Log Likelihood = -921.520783442837; 208s Tree threeTaxaTree=(a:0.0797427566582293,b:0.0797427566582293,c:0.1740977267630993); 208s 208s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78444360128; 208s Tree fourTaxaTree1=((1:0.1138487045809995,2:0.1110122567337608)Node1:0.1041027812434805,3:0.3524784637033474,4:0.3311404591602357); 208s Tree fourTaxaTree2=((1:0.08605976045998506,2:0.09356337741977526)Node1:0.08032197435213155,3:0.385891426880159,4:0.3896179485372721); 208s 208s 208s 1). Relative ratio constraint on transitions; the P-value is:0.5738682609440525 208s Log Likelihood = -2541.23688168788; 208s Global Parameters: 208s R=0.8578541215383632; 208s 208s Tree fourTaxaTree1=((1:0.1087003096719766,2:0.09421907847385359)Node1:0.1116157058852775,3:0.3552439545342539,4:0.3552086892345077); 208s Tree fourTaxaTree2=((1:0.09037887537627746,2:0.1092097124826926)Node1:0.07302488882756823,3:0.3839571532719285,4:0.3656425327601758); 208s 208s 208s 2). Relative ratio constraint on transversions; the P-value is:0.5738472550933933 208s Log Likelihood = -2541.23694349417; 208s Global Parameters: 208s R=0.8589603715892914; 208s 208s Tree fourTaxaTree1=((1:0.1086716868936693,2:0.09419409914174939)Node1:0.1116642054312137,3:0.3552401464319628,4:0.3551648291482664); 208s Tree fourTaxaTree2=((1:0.0903996047664344,2:0.1092661814701359)Node1:0.07317145803537307,3:0.3840622417334454,4:0.365787126691511); 208s + for i in *.bf 208s + '[' -f HKY85relratio.bf ']' 208s + hyphy HKY85relratio.bf 208s 208s 208s 3). Relative ratio constraint on both rates; the P-value is:0.6565946568680778 208s Log Likelihood = -2543.19088078469; 208s Global Parameters: 208s R=0.9967217644791697; 208s 208s Tree fourTaxaTree1=((1:0.1004739282458528,2:0.1007148559674787)Node1:0.09256041076636634,3:0.371366834319677,4:0.3582398552835915); 208s Tree fourTaxaTree2=((1:0.1003279354876104,2:0.1007274698667217)Node1:0.09287222080919806,3:0.3698843409350728,4:0.3577786811818548); 208s + for i in *.bf 208s + '[' -f HKY85shared.bf ']' 208s + hyphy HKY85shared.bf 208s Log Likelihood = -1165.70301189119; 208s Global Parameters: 208s R=2.970526764066976; 208s 208s Tree givenTree=(256:0.01209242198680888,(822:0.0296096904559618,159:0.004652667075133809)Node2:0.003524577020351321,((113:0.02180310396607724,9939:0.07941957445876549)Node6:0.004909965762467951,(6760:0.07148879859256838,((317:0.03799252826569335,6767:0.07150930163009102)Node12:0.01178345155565053,((135:0.02022927441043865,(529:0.03405040226389042,105r:0.01304701782214643)Node18:0.02630176779799248)Node16:0.005817033318540698,(719:0.02973913484560455,136:0.008132528929219894)Node21:0.04877233126703942)Node15:0.01555697816688831)Node11:0.01396228515205485)Node9:0.02325904580437163)Node5:0.02145408623083264); 208s + for i in *.bf 208s + '[' -f JC69.bf ']' 208s + hyphy JC69.bf 208s Log Likelihood = -1230.82014326801; 208s Tree givenTree=(256:0.01105783470408406,(822:0.0337163664527533,159:0)Node2:0.007429579934259283,((113:0.02424611426527905,9939:0.0725802651184263)Node6:0.005767383812149995,(6760:0.0638269405763779,((317:0.04028429666635566,6767:0.06818598123703087)Node12:0.01439273294250011,((135:0.02427386729192116,(529:0.03328088534022183,105r:0.01296513381563256)Node18:0.01987484261181434)Node16:0.003608131256170868,(719:0.02788390238543526,136:0.009958341228777826)Node21:0.05117020263783743)Node15:0.01669617026509551)Node11:0.008546699816280461)Node9:0.02628932634763947)Node5:0.02193532028282088); 208s + for i in *.bf 208s + '[' -f K2P.bf ']' 208s + hyphy K2P.bf 208s Log Likelihood = -1198.26189205175; 208s Tree givenTree=(256:0.0117668465165985,(822:0.0292653940914878,159:0.004288526200384838)Node2:0.003666060737393463,((113:0.0236716381754644,9939:0.07263577424220546)Node6:0.003382417881682191,(6760:0.06224097903728203,((317:0.04072458677499916,6767:0.06833986513863637)Node12:0.01244235776566587,((135:0.02259380423047821,(529:0.03395470049514703,105r:0.01240299777923351)Node18:0.02142194109121085)Node16:0.004488574407829232,(719:0.02882049068762725,136:0.008836870553622599)Node21:0.05083308484288266)Node15:0.01733397884713602)Node11:0.01112113549461396)Node9:0.02821428231043235)Node5:0.02369793290158257); 208s + for i in *.bf 208s + '[' -f K2Pshared.bf ']' 208s + hyphy K2Pshared.bf 208s Log Likelihood = -1210.49419565614; 208s Global Parameters: 208s R=2.61677690422922; 208s 208s Tree givenTree=(256:0.01222052600796084,(822:0.02897524902103144,159:0.0047767594921817)Node2:0.003546476214582444,((113:0.0237609213031269,9939:0.07494541521469669)Node6:0.005887499660027141,(6760:0.0649116523386828,((317:0.03971077642678172,6767:0.06949275831976666)Node12:0.01422847207035552,((135:0.02389757841610578,(529:0.03395152381109477,105r:0.01263083620870724)Node18:0.02071510112051736)Node16:0.003965724802892091,(719:0.02813630817803825,136:0.009504474950289998)Node21:0.05080950687447722)Node15:0.01659145578218263)Node11:0.008799324573365243)Node9:0.02626396108843616)Node5:0.02011706663646625); 208s + for i in *.bf 208s + '[' -f MatrixIndexing.bf ']' 208s + hyphy MatrixIndexing.bf 208s 208s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 208s { 208s {0.3125820444693281, 0.8029450044974091, 0.6314596521275723, 0.2922574924985546, 0.161401936821966, 0.6386146286126726} 208s {0.07844261780344942, 0.8527969079680734, 0.4842203553962103, 0.4005766476971508, 0.3199580554664037, 0.9869275400384626} 208s {0.8224022951494908, 0.1079158017197428, 0.02765250718864903, 0.0939250015872356, 0.123407759033937, 0.143582639550693} 208s {0.6028853893752408, 0.2625994946022051, 0.3148843288223456, 0.1732412276727243, 0.3437260764985639, 0.1814901561433194} 208s {0.6735046079087781, 0.9130201712048194, 0.9571289475907406, 0.5862533302480013, 0.7283680247441791, 0.9207372744383144} 208s } 208s 208s 2). Accessing a second-row third-column element and a random element. 208s 208s matrix[1][2]=0.4842203553962103 208s matrix[4][3]=0.5862533302480013 208s 208s 3). Accessing the fourth row. 208s 208s matrix[3][-1]= 208s { 208s {0.6028853893752408, 0.2625994946022051, 0.3148843288223456, 0.1732412276727243, 0.3437260764985639, 0.1814901561433194} 208s } 208s 208s 4). Accessing the first column. 208s 208s matrix[-1][0]= 208s { 208s {0.3125820444693281} 208s {0.07844261780344942} 208s {0.8224022951494908} 208s {0.6028853893752408} 208s {0.6735046079087781} 208s } 208s 208s 5). Populating a matrix template (below the diagonal). 208s 208s { 208s {0, 0, 0, 0, 0, 0} 208s {1, 0, 0, 0, 0, 0} 208s {1, 1, 0, 0, 0, 0} 208s {1, 1, 1, 0, 0, 0} 208s {1, 1, 1, 1, 0, 0} 208s } 208s 208s 6). Extracting (by row) matrix elements using the template. 208s 208s { 208s {0.07844261780344942, 0.8224022951494908, 0.1079158017197428, 0.6028853893752408, 0.2625994946022051, 0.3148843288223456, 0.6735046079087781, 0.9130201712048194, 0.9571289475907406, 0.5862533302480013} 208s } 208s 208s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 208s 208s matrix[{{1,1}}][{{3,2}}]= 208s { 208s {0.8527969079680734, 0.4842203553962103} 208s {0.1079158017197428, 0.02765250718864903} 208s {0.2625994946022051, 0.3148843288223456} 208s } 208s 208s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 208s 208s 208s { 208s {0.09770753452462504, 1.644720680247344, 1.398741292265075, 1.085414441921543, 1.026050585209882, 1.407828643878102} 208s {0.006153244287858041, 0.7272625662399066, 1.234469352580032, 1.160461650680287, 1.102373157257842, 1.974025969286371} 208s {0.6763455350671502, 0.01164582026081484, 0.0007646611538182865, 1.008821905923162, 1.015229474989778, 1.020615974380344} 208s {0.3634707927221357, 0.06895849456533355, 0.09915214053789904, 0.03001252296555271, 1.118147615665097, 1.032938676776926} 208s {0.4536084568743569, 0.8336058330268776, 0.9160958223161587, 0.3436929672268721, 0.5305199794697371, 1.847757128540096} 208s } 208s + for i in *.bf 208s + '[' -f MolecularClockF81.bf ']' 208s + hyphy MolecularClockF81.bf 208s 208s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124421372; 208s Tree theTree=(HVRNASS:0.02574320256855454,(RICRSS3:0.05627851742798395,((ZMSUCS1:0.07161066928468893,(OSRSS1A:0.06059739725441392,(TASUCSYN1:0.02788097017899352,HVSSYNMR:0.02036991396821741)Internal1:0.05182308387639757)Node9:0.02015236147588837)Node7:0.1581547052281858,(MZESUS1:0.07665727571837029,ORRSS2:0.05437303153305795)Internal2:0.02506493312141303)Node6:0.03254782967988285)Node4:0.0590049435511152,TAAJ153:0.01372840481177689); 208s 208s 208s 1). Global Molecular Clock; the P-value is:0 208s Log Likelihood = -11927.6152937212; 208s Tree theTree=(HVRNASS:0.02157256601612202,(RICRSS3:0.1233391270223043,((ZMSUCS1:0.05658065876351052,(OSRSS1A:0.04751101925662449,(TASUCSYN1:0.01824591719415406,HVSSYNMR:0.01824591719415406)Internal1:0.02926510206247043)Node9:0.009069639506886022)Node7:0.05762932787233832,(MZESUS1:0.07014502507047848,ORRSS2:0.07014502507047848)Internal2:0.04406496156537035)Node6:0.009129140386455448)Node4:0.0271554254219784,TAAJ153:0.1504945524442827); 208s 208s 208s 2). Molecular Clock starting at Internal1; the P-value is:0.1603793692668972 208s Log Likelihood = -11476.6977648554; 208s Tree theTree=(HVRNASS:0.02574463805399199,(RICRSS3:0.05630537714760154,((ZMSUCS1:0.07170662802894455,(OSRSS1A:0.06051700985579202,(TASUCSYN1:0.02411838163024049,HVSSYNMR:0.02411838163024049)Internal1:0.0518064371902121)Node9:0.02017647165128062)Node7:0.1580963984079214,(MZESUS1:0.07663695130644277,ORRSS2:0.05441168181520002)Internal2:0.02507734912974911)Node6:0.03252990709623189)Node4:0.05896343352631034,TAAJ153:0.01372808144991367); 208s 208s 208s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610191699969754 208s Log Likelihood = -11479.841259083; 208s Tree theTree=(HVRNASS:0.02577199241771832,(RICRSS3:0.05650887182451454,((ZMSUCS1:0.0714810651525935,(OSRSS1A:0.06062414664017753,(TASUCSYN1:0.02412281661282775,HVSSYNMR:0.02412281661282775)Internal1:0.05166917557584396)Node9:0.02036314585801411)Node7:0.1580479241645817,(MZESUS1:0.06553054667663613,ORRSS2:0.06553054667663613)Internal2:0.02502100766961171)Node6:0.03235796154953852)Node4:0.05873963987451332,TAAJ153:0.01369897485123984); 208s + for i in *.bf 208s + '[' -f MolecularClockHKY85.bf ']' 208s + hyphy MolecularClockHKY85.bf 208s 208s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013283038; 208s Tree theTree=(HVRNASS:0.02587743457443942,(RICRSS3:0.05729290966256458,((ZMSUCS1:0.07272534704665261,(OSRSS1A:0.06094885889423878,(TASUCSYN1:0.0274215052323902,HVSSYNMR:0.02081976368952715)Node11:0.05283851203645621)Node9:0.02050493694741961)Node7:0.1590019762384745,(MZESUS1:0.07762137158169617,ORRSS2:0.05413759348131894)Node14:0.02601795305008483)Node6:0.03166526586491966)Node4:0.06041305598989313,TAAJ153:0.01384598063765552); 208s 208s 208s 1). Global Molecular Clock on transition rates; the P-value is:0 208s Log Likelihood = -11434.7016033505; 208s Tree theTree=(HVRNASS:0.02319732345917447,(RICRSS3:0.08334082646277663,((ZMSUCS1:0.06367263689382201,(OSRSS1A:0.05485168593181718,(TASUCSYN1:0.02325513670224505,HVSSYNMR:0.01890603068464118)Node11:0.04016830271520158)Node9:0.01328536077718002)Node7:0.1273995968145573,(MZESUS1:0.07240242164513809,ORRSS2:0.06226501706007253)Node14:0.03460944097224466)Node6:0.02068820539812524)Node4:0.0389942521914492,TAAJ153:0.08890802688190375); 208s 208s 208s 2). Global Molecular Clock on transversion rates; the P-value is:0 208s Log Likelihood = -11497.3782378614; 208s Tree theTree=(HVRNASS:0.02484203947298438,(RICRSS3:0.09397047508063444,((ZMSUCS1:0.06899532712237967,(OSRSS1A:0.05468071241477943,(TASUCSYN1:0.02277218833670913,HVSSYNMR:0.02034632951245292)Node11:0.04374488950975081)Node9:0.01674196535254953)Node7:0.09971736090270263,(MZESUS1:0.07446775530660792,ORRSS2:0.06134915824606269)Node14:0.03386699677794925)Node6:0.02080023539102577)Node4:0.05008131208856946,TAAJ153:0.07305847922015964); 208s 208s 208s 3). Global Molecular Clock on both rates; the P-value is:0 208s Log Likelihood = -11703.6261633936; 208s Tree theTree=(HVRNASS:0.02209790524913105,(RICRSS3:0.1239838041625247,((ZMSUCS1:0.0580005191388791,(OSRSS1A:0.04854685895429329,(TASUCSYN1:0.01832952130566496,HVSSYNMR:0.01832952130566496)Node11:0.03021733764862832)Node9:0.009453660184585806)Node7:0.05732732377110523,(MZESUS1:0.07025388165506863,ORRSS2:0.07025388165506863)Node14:0.04507396125491571)Node6:0.008655961252540395)Node4:0.02800717113897166,TAAJ153:0.1519909753014964); 208s + for i in *.bf 208s + '[' -f Non-Rev.bf ']' 208s + hyphy Non-Rev.bf 209s Log Likelihood = -1152.79155846598; 209s Global Parameters: 209s GC=0.2646611492313629; 209s CG=0.1880506483131626; 209s GA=1.896680642221536; 209s CT=1.250125933746513; 209s GT=0.08600265690748626; 209s CA=0.9151772643703251; 209s AT=0.4274999277523984; 209s AG=1.573251948155159; 209s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2573386317899553; 209s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.026482009726261; 209s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.7850690065246353; 209s 209s Tree givenTree=(256:0.01342247413452693,(822:0.02847841113168868,159:0.006070363719122137)Node2:0.003451377406769239,((113:0.02186140110161882,9939:0.07931516999811256)Node6:0.004996210486770037,(6760:0.07323235800381354,((317:0.04006907352700852,6767:0.06982114365379638)Node12:0.01161176816996447,((135:0.0215556153190308,(529:0.03497251249572147,105r:0.01424241222689641)Node18:0.02377532456125624)Node16:0.005234661259424786,(719:0.02861552420274574,136:0.009578684982477475)Node21:0.04928912247100518)Node15:0.01635353536220016)Node11:0.01271954937522245)Node9:0.02194824451742275)Node5:0.02031592692001932); 209s + for i in *.bf 209s + '[' -f PBootstrapHetRates.bf ']' 209s + hyphy PBootstrapHetRates.bf 209s 209s ----ORIGINAL DATA---- 209s Log Likelihood = -1127.31560536389; 209s Global Parameters: 209s alpha=0.318903661364874; 209s kappa=0.3236251153932033; 209s 209s Tree givenTree=(256:0.01258515195286014,(822:0.03175356558495591,159:0.004692747342476685)Node2:0.003777499490449313,((113:0.02291471891534015,9939:0.09712474689339325)Node6:0.001964058262546234,(6760:0.08715359252891673,((317:0.04570220836308511,6767:0.08106974545339699)Node12:0.007409621819652962,((135:0.018636646919929,(529:0.0369383857434715,105r:0.01499292845477245)Node18:0.03033508405649344)Node16:0.007147322073341072,(719:0.03339504194476876,136:0.007167255439850933)Node21:0.05751745057914805)Node15:0.01788805604870618)Node11:0.01884118206937395)Node9:0.02369235179374087)Node5:0.02500575626841894); 209s 209s Using the seed: 209s 1711263893 209s Category variable name: TRUE 209s Site Rate 209s 0 0.00000 209s 1 0.00000 209s 2 0.00000 209s 3 0.00000 209s 4 0.00000 209s 5 0.00000 209s 6 0.00001 209s 7 0.00002 209s 8 0.00003 209s 9 0.00003 209s 10 0.00004 209s 11 0.00005 209s 12 0.00006 209s 13+ for i in *.bf 209s + '[' -f REV.bf ']' 209s + hyphy REV.bf 209s 0.00011 209s 14 0.00014 209s 15 0.00016 209s 16 0.00022 209s 17 0.00030 209s 18 0.00031 209s 19 0.00040 209s 20 0.00056 209s 21 0.00056 209s 22 0.00096 209s 23 0.00115 209s 24 0.00121 209s 25 0.00121 209s 26 0.00127 209s 27 0.00158 209s 28 0.00169 209s 29 0.00183 209s 30 0.00186 209s 31 0.00308 209s 32 0.00342 209s 33 0.00346 209s 34 0.00382 209s 35 0.00410 209s 36 0.00422 209s 37 0.00499 209s 38 0.00500 209s 39 0.00583 209s 40 0.00623 209s 41 0.00696 209s 42 0.00697 209s 43 0.00717 209s 44 0.00751 209s 45 0.00766 209s 46 0.00772 209s 47 0.00828 209s 48 0.00893 209s 49 0.00898 209s 50 0.00928 209s 51 0.00935 209s 52 0.00951 209s 53 0.00961 209s 54 0.01189 209s 55 0.01261 209s 56 0.01289 209s 57 0.01388 209s 58 0.01513 209s 59 0.01543 209s 60 0.01837 209s 61 0.01889 209s 62 0.02000 209s 63 0.02002 209s 64 0.02042 209s 65 0.02043 209s 66 0.02078 209s 67 0.02286 209s 68 0.02462 209s 69 0.02470 209s 70 0.02476 209s 71 0.02703 209s 72 0.03062 209s 73 0.03167 209s 74 0.03233 209s 75 0.03499 209s 76 0.03570 209s 77 0.03711 209s 78 0.03810 209s 79 0.03833 209s 80 0.04005 209s 81 0.04190 209s 82 0.04195 209s 83 0.05028 209s 84 0.05273 209s 85 0.05497 209s 86 0.05586 209s 87 0.05657 209s 88 0.05881 209s 89 0.06016 209s 90 0.06168 209s 91 0.06608 209s 92 0.06969 209s 93 0.07226 209s 94 0.07234 209s 95 0.07265 209s 96 0.07479 209s 97 0.07719 209s 98 0.07761 209s 99 0.07954 209s 100 0.08435 209s 101 0.10115 209s 102 0.10303 209s 103 0.10469 209s 104 0.11044 209s 105 0.11275 209s 106 0.12123 209s 107 0.12758 209s 108 0.12940 209s 109 0.13116 209s 110 0.13125 209s 111 0.13908 209s 112 0.14091 209s 113 0.14448 209s 114 0.14582 209s 115 0.15020 209s 116 0.17021 209s 117 0.17731 209s 118 0.18375 209s 119 0.18944 209s 120 0.18944 209s 121 0.18988 209s 122 0.19886 209s 123 0.20204 209s 124 0.20251 209s 125 0.20296 209s 126 0.20416 209s 127 0.20484 209s 128 0.20826 209s 129 0.21172 209s 130 0.21880 209s 131 0.22452 209s 132 0.22847 209s 133 0.22904 209s 134 0.23149 209s 135 0.23481 209s 136 0.24779 209s 137 0.24831 209s 138 0.26003 209s 139 0.26146 209s 140 0.26353 209s 141 0.26666 209s 142 0.27328 209s 143 0.28707 209s 144 0.29080 209s 145 0.30231 209s 146 0.30693 209s 147 0.31114 209s 148 0.32060 209s 149 0.32418 209s 150 0.32803 209s 151 0.33972 209s 152 0.37197 209s 153 0.37228 209s 154 0.37494 209s 155 0.37804 209s 156 0.37859 209s 157 0.38254 209s 158 0.39796 209s 159 0.41950 209s 160 0.42126 209s 161 0.42452 209s 162 0.45413 209s 163 0.46656 209s 164 0.47262 209s 165 0.49420 209s 166 0.50055 209s 167 0.51221 209s 168 0.51525 209s 169 0.54450 209s 170 0.54650 209s 171 0.55128 209s 172 0.58308 209s 173 0.58795 209s 174 0.63514 209s 175 0.63542 209s 176 0.63639 209s 177 0.66389 209s 178 0.66536 209s 179 0.67951 209s 180 0.68062 209s 181 0.72109 209s 182 0.72853 209s 183 0.76962 209s 184 0.77090 209s 185 0.77224 209s 186 0.77526 209s 187 0.78436 209s 188 0.80768 209s 189 0.83144 209s 190 0.83179 209s 191 0.83997 209s 192 0.84234 209s 193 0.85050 209s 194 0.85206 209s 195 0.86783 209s 196 0.87390 209s 197 0.90742 209s 198 0.91643 209s 199 0.91723 209s 200 0.91883 209s 201 0.91900 209s 202 0.92169 209s 203 0.92894 209s 204 0.95872 209s 205 0.96542 209s 206 0.97182 209s 207 1.06002 209s 208 1.06321 209s 209 1.06898 209s 210 1.18183 209s 211 1.23726 209s 212 1.23981 209s 213 1.26217 209s 214 1.32001 209s 215 1.33098 209s 216 1.40276 209s 217 1.40916 209s 218 1.50232 209s 219 1.50264 209s 220 1.50806 209s 221 1.52227 209s 222 1.53817 209s 223 1.54400 209s 224 1.58077 209s 225 1.58895 209s 226 1.60036 209s 227 1.77794 209s 228 1.78616 209s 229 1.78730 209s 230 1.80132 209s 231 1.90046 209s 232 1.91905 209s 233 1.98062 209s 234 1.98067 209s 235 2.00132 209s 236 2.00814 209s 237 2.16649 209s 238 2.28611 209s 239 2.35298 209s 240 2.44968 209s 241 2.52950 209s 242 2.54342 209s 243 2.73223 209s 244 2.85482 209s 245 2.85686 209s 246 2.87370 209s 247 2.91022 209s 248 3.01953 209s 249 3.12670 209s 250 3.28744 209s 251 3.45269 209s 252 3.48688 209s 253 3.67943 209s 254 3.83093 209s 255 4.08208 209s 256 4.08696 209s 257 4.09810 209s 258 4.26093 209s 259 4.56720 209s 260 4.90641 209s 261 4.94273 209s 262 5.34406 209s 263 5.66551 209s 264 5.80293 209s 265 6.32956 209s 266 6.90739 209s 267 8.45199 209s 268 9.85518 209s 269 9.94785 209s 270 13.06203 209s 271 15.39952 209s 272 16.05000 209s 209s Mean = 1.034208287682586 209s Var = 4.490308387307267 (1/alpha) = 3.135743238945911 209s Log Likelihood = -1100.00325192676; 209s Tree givenTree=(256:0.02246871958920071,(822:0.01867826392010883,159:0.01469054619642481)Node2:0.003780037041493445,((113:0.01829386361698467,9939:0.07804102019026828)Node6:0.007456157729891971,(6760:0.07113581697010701,((317:0.0371908451117874,6767:0.07206937237146221)Node12:0.01019126092445315,((135:0.02036489328864084,(529:0.03424008693126637,105r:0.01130058987905245)Node18:0.02851169007030497)Node16:0.006571243076489387,(719:0.02830813236724508,136:0.009595583712718415)Node21:0.04404095929135449)Node15:0.01655093024567787)Node11:0.01315865370683736)Node9:0.02915628572885135)Node5:0.009980421685718468); 209s + for i in *.bf 209s + '[' -f REVshared.bf ']' 209s + hyphy REVshared.bf 209s Log Likelihood = -1156.62540457054; 209s Global Parameters: 209s AT=0.3620864498928175; 209s GT=0.4597052870130426; 209s CG=0.2460538484483357; 209s AG=1.843831882122668; 209s CT=1.197638246713696; 209s 209s Tree givenTree=(256:0.01208251220644581,(822:0.029737488493712,159:0.004672259626667204)Node2:0.003488371623634371,((113:0.02208107701492746,9939:0.07975700593153943)Node6:0.004709009765687309,(6760:0.07205505045490256,((317:0.03911304112716218,6767:0.0710717819219864)Node12:0.01083325224437629,((135:0.02050380402747335,(529:0.03438702674090106,105r:0.01467793485721706)Node18:0.02467636231794451)Node16:0.005560945661843388,(719:0.02873587733291043,136:0.009469209764284033)Node21:0.04910009406359832)Node15:0.01584220722126514)Node11:0.0142658080884724)Node9:0.02297074317769743)Node5:0.02144991115727102); 209s + for i in *.bf 209s + '[' -f ReplicateConstraint1.bf ']' 209s + hyphy ReplicateConstraint1.bf 209s 1).Unconstrained HKY85 209s 209s Log Likelihood = -1152.88; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.317.trvs 209s Parameter 2 : hivTree.317.trst 209s Parameter 3 : hivTree.6767.trvs 209s Parameter 4 : hivTree.6767.trst 209s Parameter 5 : hivTree.Node2.trvs 209s Parameter 6 : hivTree.Node2.trst 209s Parameter 7 : hivTree.135.trvs 209s Parameter 8 : hivTree.135.trst 209s Parameter 9 : hivTree.529.trvs 209s Parameter 10 : hivTree.529.trst 209s Parameter 11 : hivTree.105r.trvs 209s Parameter 12 : hivTree.105r.trst 209s Parameter 13 : hivTree.Node8.trvs 209s Parameter 14 : hivTree.Node8.trst 209s Parameter 15 : hivTree.iNode1.trvs 209s Parameter 16 : hivTree.iNode1.trst 209s Parameter 17 : hivTree.719.trvs 209s Parameter 18 : hivTree.719.trst 209s Parameter 19 : hivTree.136.trvs 209s Parameter 20 : hivTree.136.trst 209s Parameter 21 : hivTree.Node11.trvs 209s Parameter 22 : hivTree.Node11.trst 209s Parameter 23 : hivTree.Node5.trvs 209s Parameter 24 : hivTree.Node5.trst 209s Parameter 25 : hivTree.Node1.trvs 209s Parameter 26 : hivTree.Node1.trst 209s Parameter 27 : hivTree.6760.trvs 209s Parameter 28 : hivTree.6760.trst 209s Parameter 29 : hivTree.113.trvs 209s Parameter 30 : hivTree.113.trst 209s Parameter 31 : hivTree.9939.trvs 209s Parameter 32 : hivTree.9939.trst 209s Parameter 33 : hivTree.Node16.trvs 209s Parameter 34 : hivTree.Node16.trst 209s Parameter 35 : hivTree.256.trvs 209s Parameter 36 : hivTree.256.trst 209s Parameter 37 : hivTree.822.trvs 209s Parameter 38 : hivTree.822.trst 209s Parameter 39 : hivTree.159.trvs 209s Parameter 40 : hivTree.159.trst 209s Parameter 41 : hivTree.Node21.trvs 209s Parameter 42 : hivTree.Node21.trst 209s Parameter 43 : hivTree.iNode2.trvs 209s Parameter 44 : hivTree.iNode2.trst 209s Parameter 45 : hivTree.Node15.trvs 209s Parameter 46 : hivTree.Node15.trst 209s 209s 2).HKY85 constrained to F81 209s 209s Log Likelihood = -1187.55; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.317.trvs 209s Parameter 2 : hivTree.6767.trvs 209s Parameter 3 : hivTree.Node2.trvs 209s Parameter 4 : hivTree.135.trvs 209s Parameter 5 : hivTree.529.trvs 209s Parameter 6 : hivTree.105r.trvs 209s Parameter 7 : hivTree.Node8.trvs 209s Parameter 8 : hivTree.iNode1.trvs 209s Parameter 9 : hivTree.719.trvs 209s Parameter 10 : hivTree.136.trvs 209s Parameter 11 : hivTree.Node11.trvs 209s Parameter 12 : hivTree.Node5.trvs 209s Parameter 13 : hivTree.Node1.trvs 209s Parameter 14 : hivTree.6760.trvs 209s Parameter 15 : hivTree.113.trvs 209s Parameter 16 : hivTree.9939.trvs 209s Parameter 17 : hivTree.Node16.trvs 209s Parameter 18 : hivTree.256.trvs 209s Parameter 19 : hivTree.822.trvs 209s Parameter 20 : hivTree.159.trvs 209s Parameter 21 : hivTree.Node21.trvs 209s Parameter 22 : hivTree.iNode2.trvs 209s Parameter 23 : hivTree.Node15.trvs 209s 209s Constrained Parameters List 209s 209s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 209s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 209s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 209s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 209s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 209s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 209s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 209s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 209s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 209s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 209s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 209s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 209s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 209s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 209s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 209s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 209s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 209s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 209s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 209s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 209s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 209s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 209s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 209s 209s 3).HKY85 constrained to F81 on internal branches 209s 209s Log Likelihood = -1167.99; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.Node2.trvs 209s Parameter 2 : hivTree.Node8.trvs 209s Parameter 3 : hivTree.iNode1.trvs 209s Parameter 4 : hivTree.Node11.trvs 209s Parameter 5 : hivTree.Node5.trvs 209s Parameter 6 : hivTree.Node1.trvs 209s Parameter 7 : hivTree.Node16.trvs 209s Parameter 8 : hivTree.Node21.trvs 209s Parameter 9 : hivTree.iNode2.trvs 209s Parameter 10 : hivTree.Node15.trvs 209s Parameter 11 : hivTree.317.trst 209s Parameter 12 : hivTree.317.trvs 209s Parameter 13 : hivTree.6767.trvs 209s Parameter 14 : hivTree.6767.trst 209s Parameter 15 : hivTree.135.trst 209s Parameter 16 : hivTree.135.trvs 209s Parameter 17 : hivTree.529.trvs 209s Parameter 18 : hivTree.529.trst 209s Parameter 19 : hivTree.105r.trst 209s Parameter 20 : hivTree.105r.trvs 209s Parameter 21 : hivTree.719.trvs 209s Parameter 22 : hivTree.719.trst 209s Parameter 23 : hivTree.136.trvs 209s Parameter 24 : hivTree.136.trst 209s Parameter 25 : hivTree.6760.trvs 209s Parameter 26 : hivTree.6760.trst 209s Parameter 27 : hivTree.113.trvs 209s Parameter 28 : hivTree.113.trst 209s Parameter 29 : hivTree.9939.trst 209s Parameter 30 : hivTree.9939.trvs 209s Parameter 31 : hivTree.256.trvs 209s Parameter 32 : hivTree.256.trst 209s Parameter 33 : hivTree.822.trvs 209s Parameter 34 : hivTree.822.trst 209s Parameter 35 : hivTree.159.trst 209s Parameter 36 : hivTree.159.trvs 209s 209s Constrained Parameters List 209s 209s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 209s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 209s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 209s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 209s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 209s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 209s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 209s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 209s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 209s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 209s 209s 4).HKY85 with shared ratio. 209s 209s Log Likelihood = -1165.7; 209s 209s Independent Parameters List 209s 209s Parameter 1 : R 209s Parameter 2 : hivTree.317.trst 209s Parameter 3 : hivTree.6767.trst 209s Parameter 4 : hivTree.Node2.trst 209s Parameter 5 : hivTree.135.trst 209s Parameter 6 : hivTree.529.trst 209s Parameter 7 : hivTree.105r.trst 209s Parameter 8 : hivTree.Node8.trst 209s Parameter 9 : hivTree.iNode1.trst 209s Parameter 10 : hivTree.719.trst 209s Parameter 11 : hivTree.136.trst 209s Parameter 12 : hivTree.Node11.trst 209s Parameter 13 : hivTree.Node5.trst 209s Parameter 14 : hivTree.Node1.trst 209s Parameter 15 : hivTree.6760.trst 209s Parameter 16 : hivTree.113.trst 209s Parameter 17 : hivTree.9939.trst 209s Parameter 18 : hivTree.Node16.trst 209s Parameter 19 : hivTree.256.trst 209s Parameter 20 : hivTree.822.trst 209s Parameter 21 : hivTree.159.trst 209s Parameter 22 : hivTree.Node21.trst 209s Parameter 23 : hivTree.iNode2.trst 209s Parameter 24 : hivTree.Node15.trst 209s 209s Constrained Parameters List 209s 209s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 209s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 209s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 209s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 209s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 209s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 209s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 209s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 209s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 209s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 209s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 209s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 209s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 209s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 209s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 209s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 209s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 209s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 209s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 209s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 209s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 209s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 209s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 209s + '[' -f ReplicateConstraint2.bf ']' 209s + hyphy ReplicateConstraint2.bf 209s 1).Unconstrained HKY85 209s 209s Log Likelihood = -1152.88; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.317.trvs 209s Parameter 2 : hivTree.317.trst 209s Parameter 3 : hivTree.6767.trvs 209s Parameter 4 : hivTree.6767.trst 209s Parameter 5 : hivTree.Node2.trvs 209s Parameter 6 : hivTree.Node2.trst 209s Parameter 7 : hivTree.135.trvs 209s Parameter 8 : hivTree.135.trst 209s Parameter 9 : hivTree.529.trvs 209s Parameter 10 : hivTree.529.trst 209s Parameter 11 : hivTree.105r.trvs 209s Parameter 12 : hivTree.105r.trst 209s Parameter 13 : hivTree.Node8.trvs 209s Parameter 14 : hivTree.Node8.trst 209s Parameter 15 : hivTree.iNode1.trvs 209s Parameter 16 : hivTree.iNode1.trst 209s Parameter 17 : hivTree.719.trvs 209s Parameter 18 : hivTree.719.trst 209s Parameter 19 : hivTree.136.trvs 209s Parameter 20 : hivTree.136.trst 209s Parameter 21 : hivTree.Node11.trvs 209s Parameter 22 : hivTree.Node11.trst 209s Parameter 23 : hivTree.Node5.trvs 209s Parameter 24 : hivTree.Node5.trst 209s Parameter 25 : hivTree.Node1.trvs 209s Parameter 26 : hivTree.Node1.trst 209s Parameter 27 : hivTree.6760.trvs 209s Parameter 28 : hivTree.6760.trst 209s Parameter 29 : hivTree.113.trvs 209s Parameter 30 : hivTree.113.trst 209s Parameter 31 : hivTree.9939.trvs 209s Parameter 32 : hivTree.9939.trst 209s Parameter 33 : hivTree.Node16.trvs 209s Parameter 34 : hivTree.Node16.trst 209s Parameter 35 : hivTree.256.trvs 209s Parameter 36 : hivTree.256.trst 209s Parameter 37 : hivTree.822.trvs 209s Parameter 38 : hivTree.822.trst 209s Parameter 39 : hivTree.159.trvs 209s Parameter 40 : hivTree.159.trst 209s Parameter 41 : hivTree.Node21.trvs 209s Parameter 42 : hivTree.Node21.trst 209s Parameter 43 : hivTree.iNode2.trvs 209s Parameter 44 : hivTree.iNode2.trst 209s Parameter 45 : hivTree.Node15.trvs 209s Parameter 46 : hivTree.Node15.trst 209s 209s 2).HKY85 constrained to F81 on the "iNode1" subtree 209s 209s Log Likelihood = -1157.82; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.135.trvs 209s Parameter 2 : hivTree.529.trvs 209s Parameter 3 : hivTree.105r.trvs 209s Parameter 4 : hivTree.Node8.trvs 209s Parameter 5 : hivTree.317.trvs 209s Parameter 6 : hivTree.317.trst 209s Parameter 7 : hivTree.6767.trst 209s Parameter 8 : hivTree.6767.trvs 209s Parameter 9 : hivTree.Node2.trst 209s Parameter 10 : hivTree.Node2.trvs 209s Parameter 11 : hivTree.iNode1.trvs 209s Parameter 12 : hivTree.iNode1.trst 209s Parameter 13 : hivTree.719.trvs 209s Parameter 14 : hivTree.719.trst 209s Parameter 15 : hivTree.136.trvs 209s Parameter 16 : hivTree.136.trst 209s Parameter 17 : hivTree.Node11.trvs 209s Parameter 18 : hivTree.Node11.trst 209s Parameter 19 : hivTree.Node5.trvs 209s Parameter 20 : hivTree.Node5.trst 209s Parameter 21 : hivTree.Node1.trvs 209s Parameter 22 : hivTree.Node1.trst 209s Parameter 23 : hivTree.6760.trvs 209s Parameter 24 : hivTree.6760.trst 209s Parameter 25 : hivTree.113.trvs 209s Parameter 26 : hivTree.113.trst 209s Parameter 27 : hivTree.9939.trvs 209s Parameter 28 : hivTree.9939.trst 209s Parameter 29 : hivTree.Node16.trvs 209s Parameter 30 : hivTree.Node16.trst 209s Parameter 31 : hivTree.256.trvs 209s Parameter 32 : hivTree.256.trst 209s Parameter 33 : hivTree.822.trvs 209s Parameter 34 : hivTree.822.trst 209s Parameter 35 : hivTree.159.trvs 209s Parameter 36 : hivTree.159.trst 209s Parameter 37 : hivTree.Node21.trvs 209s Parameter 38 : hivTree.Node21.trst 209s Parameter 39 : hivTree.iNode2.trvs 209s Parameter 40 : hivTree.iNode2.trst 209s Parameter 41 : hivTree.Node15.trvs 209s Parameter 42 : hivTree.Node15.trst 209s 209s Constrained Parameters List 209s 209s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 209s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 209s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 209s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 209s 209s 3).HKY85 constrained to F81 on the "iNode1" branch 209s 209s Log Likelihood = -1152.88; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.317.trvs 209s Parameter 2 : hivTree.317.trst 209s Parameter 3 : hivTree.6767.trvs 209s Parameter 4 : hivTree.6767.trst 209s Parameter 5 : hivTree.Node2.trvs 209s Parameter 6 : hivTree.Node2.trst 209s Parameter 7 : hivTree.135.trvs 209s Parameter 8 : hivTree.135.trst 209s Parameter 9 : hivTree.529.trvs 209s Parameter 10 : hivTree.529.trst 209s Parameter 11 : hivTree.105r.trvs 209s Parameter 12 : hivTree.105r.trst 209s Parameter 13 : hivTree.Node8.trvs 209s Parameter 14 : hivTree.Node8.trst 209s Parameter 15 : hivTree.iNode1.trvs 209s Parameter 16 : hivTree.iNode1.trst 209s Parameter 17 : hivTree.719.trvs 209s Parameter 18 : hivTree.719.trst 209s Parameter 19 : hivTree.136.trvs 209s Parameter 20 : hivTree.136.trst 209s Parameter 21 : hivTree.Node11.trvs 209s Parameter 22 : hivTree.Node11.trst 209s Parameter 23 : hivTree.Node5.trvs 209s Parameter 24 : hivTree.Node5.trst 209s Parameter 25 : hivTree.Node1.trvs 209s Parameter 26 : hivTree.Node1.trst 209s Parameter 27 : hivTree.6760.trvs 209s Parameter 28 : hivTree.6760.trst 209s Parameter 29 : hivTree.113.trvs 209s Parameter 30 : hivTree.113.trst 209s Parameter 31 : hivTree.9939.trvs 209s Parameter 32 : hivTree.9939.trst 209s Parameter 33 : hivTree.Node16.trvs 209s Parameter 34 : hivTree.Node16.trst 209s Parameter 35 : hivTree.256.trvs 209s Parameter 36 : hivTree.256.trst 209s Parameter 37 : hivTree.822.trvs 209s Parameter 38 : hivTree.822.trst 209s Parameter 39 : hivTree.159.trvs 209s Parameter 40 : hivTree.159.trst 209s Parameter 41 : hivTree.Node21.trvs 209s Parameter 42 : hivTree.Node21.trst 209s Parameter 43 : hivTree.iNode2.trvs 209s Parameter 44 : hivTree.iNode2.trst 209s Parameter 45 : hivTree.Node15.trvs 209s Parameter 46 : hivTree.Node15.trst 209s 209s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 209s 209s Log Likelihood = -1152.88; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.317.trvs 209s Parameter 2 : hivTree.317.trst 209s Parameter 3 : hivTree.6767.trvs 209s Parameter 4 : hivTree.6767.trst 209s Parameter 5 : hivTree.Node2.trvs 209s Parameter 6 : hivTree.Node2.trst 209s Parameter 7 : hivTree.135.trvs 209s Parameter 8 : hivTree.135.trst 209s Parameter 9 : hivTree.529.trvs 209s Parameter 10 : hivTree.529.trst 209s Parameter 11 : hivTree.105r.trvs 209s Parameter 12 : hivTree.105r.trst 209s Parameter 13 : hivTree.Node8.trvs 209s Parameter 14 : hivTree.Node8.trst 209s Parameter 15 : hivTree.iNode1.trvs 209s Parameter 16 : hivTree.iNode1.trst 209s Parameter 17 : hivTree.719.trvs 209s Parameter 18 : hivTree.719.trst 209s Parameter 19 : hivTree.136.trvs 209s Parameter 20 : hivTree.136.trst 209s Parameter 21 : hivTree.Node11.trvs 209s Parameter 22 : hivTree.Node11.trst 209s Parameter 23 : hivTree.Node5.trvs 209s Parameter 24 : hivTree.Node5.trst 209s Parameter 25 : hivTree.Node1.trvs 209s Parameter 26 : hivTree.Node1.trst 209s Parameter 27 : hivTree.6760.trvs 209s Parameter 28 : hivTree.6760.trst 209s Parameter 29 : hivTree.113.trvs 209s Parameter 30 : hivTree.113.trst 209s Parameter 31 : hivTree.9939.trvs 209s Parameter 32 : hivTree.9939.trst 209s Parameter 33 : hivTree.Node16.trvs 209s Parameter 34 : hivTree.Node16.trst 209s Parameter 35 : hivTree.256.trvs 209s Parameter 36 : hivTree.256.trst 209s Parameter 37 : hivTree.822.trvs 209s Parameter 38 : hivTree.822.trst 209s Parameter 39 : hivTree.159.trvs 209s Parameter 40 : hivTree.159.trst 209s Parameter 41 : hivTree.Node21.trvs 209s Parameter 42 : hivTree.Node21.trst 209s Parameter 43 : hivTree.iNode2.trvs 209s Parameter 44 : hivTree.iNode2.trst 209s Parameter 45 : hivTree.Node15.trvs 209s Parameter 46 : hivTree.Node15.trst 209s 209s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 209s 209s Log Likelihood = -1152.88; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.317.trvs 209s Parameter 2 : hivTree.317.trst 209s Parameter 3 : hivTree.6767.trvs 209s Parameter 4 : hivTree.6767.trst 209s Parameter 5 : hivTree.Node2.trvs 209s Parameter 6 : hivTree.Node2.trst 209s Parameter 7 : hivTree.135.trvs 209s Parameter 8 : hivTree.135.trst 209s Parameter 9 : hivTree.529.trvs 209s Parameter 10 : hivTree.529.trst 209s Parameter 11 : hivTree.105r.trvs 209s Parameter 12 : hivTree.105r.trst 209s Parameter 13 : hivTree.Node8.trvs 209s Parameter 14 : hivTree.Node8.trst 209s Parameter 15 : hivTree.iNode1.trvs 209s Parameter 16 : hivTree.iNode1.trst 209s Parameter 17 : hivTree.719.trvs 209s Parameter 18 : hivTree.719.trst 209s Parameter 19 : hivTree.136.trvs 209s Parameter 20 : hivTree.136.trst 209s Parameter 21 : hivTree.Node11.trvs 209s Parameter 22 : hivTree.Node11.trst 209s Parameter 23 : hivTree.Node5.trvs 209s Parameter 24 : hivTree.Node5.trst 209s Parameter 25 : hivTree.Node1.trvs 209s Parameter 26 : hivTree.Node1.trst 209s Parameter 27 : hivTree.6760.trvs 209s Parameter 28 : hivTree.6760.trst 209s Parameter 29 : hivTree.113.trvs 209s Parameter 30 : hivTree.113.trst 209s Parameter 31 : hivTree.9939.trvs 209s Parameter 32 : hivTree.9939.trst 209s Parameter 33 : hivTree.Node16.trvs 209s Parameter 34 : hivTree.Node16.trst 209s Parameter 35 : hivTree.256.trvs 209s Parameter 36 : hivTree.256.trst 209s Parameter 37 : hivTree.822.trvs 209s Parameter 38 : hivTree.822.trst 209s Parameter 39 : hivTree.159.trvs 209s Parameter 40 : hivTree.159.trst 209s Parameter 41 : hivTree.Node21.trvs 209s Parameter 42 : hivTree.Node21.trst 209s Parameter 43 : hivTree.iNode2.trvs 209s Parameter 44 : hivTree.iNode2.trst 209s Parameter 45 : hivTree.Node15.trvs 209s Parameter 46 : hivTree.Node15.trst 209s 209s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 209s 209s Log Likelihood = -1157.82; 209s 209s Independent Parameters List 209s 209s Parameter 1 : hivTree.135.trst 209s Parameter 2 : hivTree.529.trst 209s Parameter 3 : hivTree.105r.trst 209s Parameter 4 : hivTree.Node8.trst 209s Parameter 5 : hivTree.317.trvs 209s Parameter 6 : hivTree.317.trst 209s Parameter 7 : hivTree.6767.trst 209s Parameter 8 : hivTree.6767.trvs 209s Parameter 9 : hivTree.Node2.trst 209s Parameter 10 : hivTree.Node2.trvs 209s Parameter 11 : hivTree.iNode1.trvs 209s Parameter 12 : hivTree.iNode1.trst 209s Parameter 13 : hivTree.719.trvs 209s Parameter 14 : hivTree.719.trst 209s Parameter 15 : hivTree.136.trvs 209s Parameter 16 : hivTree.136.trst 209s Parameter 17 : hivTree.Node11.trvs 209s Parameter 18 : hivTree.Node11.trst 209s Parameter 19 : hivTree.Node5.trvs 209s Parameter 20 : hivTree.Node5.trst 209s Parameter 21 : hivTree.Node1.trvs 209s Parameter 22 : hivTree.Node1.trst 209s Parameter 23 : hivTree.6760.trvs 209s Parameter 24 : hivTree.6760.trst 209s Parameter 25 : hivTree.113.trvs 209s Parameter 26 : hivTree.113.trst 209s Parameter 27 : hivTree.9939.trvs 209s Parameter 28 : hivTree.9939.trst 209s Parameter 29 : hivTree.Node16.trvs 209s Parameter 30 : hivTree.Node16.trst 209s Parameter 31 : hivTree.256.trvs 209s Parameter 32 : hivTree.256.trst 209s Parameter 33 : hivTree.822.trvs 209s Parameter 34 : hivTree.822.trst 209s Parameter 35 : hivTree.159.trvs 209s Parameter 36 : hivTree.159.trst 209s Parameter 37 : hivTree.Node21.trvs 209s Parameter 38 : hivTree.Node21.trst 209s Parameter 39 : hivTree.iNode2.trvs 209s Parameter 40 : hivTree.iNode2.trst 209s Parameter 41 : hivTree.Node15.trvs 209s Parameter 42 : hivTree.Node15.trst 209s 209s Constrained Parameters List 209s 209s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 209s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 209s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 209s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 209s + '[' -f aa.bf ']' 209s + hyphy aa.bf 210s Log Likelihood = -1134.73158903811; 210s Tree theTree=(((Langur:0.07430929885972404,Baboon:0.03832849634012803)Node2:0.0233919252843166,Human:0.05949976654865775)Node1:0.0200665584749996,Rat:0.2458809231757731,(Cow:0.2552868234106432,Horse:0.5627637317168085)Node7:0.07060308955953205); 210s + for i in *.bf 210s + '[' -f definitions2.bf ']' 210s + hyphy definitions2.bf 210s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 210s 210s Sample by MEAN: 210s 210s Sample mean = 0.5 (sample variance = 0.2450374540764348) 210s 210s Rate[0]= 0.06847689 (weight=0.2500000) 210s Rate[1]= 0.23837593 (weight=0.2500000) 210s Rate[2]= 0.50000000 (weight=0.2500000) 210s Rate[3]= 1.19314718 (weight=0.2500000) 210s ------------------------------------------------ 210s 210s Sample by MEDIAN: 210s 210s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 210s 210s Rate[0]= 0.06676570 (weight=0.2500000) 210s Rate[1]= 0.23500181 (weight=0.2500000) 210s Rate[2]= 0.49041463 (weight=0.2500000) 210s Rate[3]= 1.03972077 (weight=0.2500000) 210s ------------------------------------------------ 210s 210s Sample by SCALED_MEDIAN: 210s 210s Sample mean = 0.5 (sample variance = 0.2154404122636025) 210s 210s Rate[0]= 0.07289218 (weight=0.2500000) 210s Rate[1]= 0.25656580 (weight=0.2500000) 210s Rate[2]= 0.53541552 (weight=0.2500000) 210s Rate[3]= 1.13512650 (weight=0.2500000) 210s ------------------------------------------------ 210s 210s Sample by MEAN (numerical averaging): 210s 210s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 210s 210s Rate[0]= 0.06846096 (weight=0.2500000) 210s Rate[1]= 0.23834015 (weight=0.2500000) 210s Rate[2]= 0.49996411 (weight=0.2500000) 210s Rate[3]= 1.19314889 (weight=0.2500000) 210s ------------------------------------------------ 210s 210s Sample by MEAN (numerical CDF and averaging): 210s 210s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 210s 210s Rate[0]= 0.06849282 (weight=0.2500000) 210s Rate[1]= 0.23835613 (weight=0.2500000) 210s Rate[2]=+ for i in *.bf 210s + '[' -f definitions3.bf ']' 210s + hyphy definitions3.bf 210s + for i in *.bf 210s + '[' -f displayFunction.bf ']' 210s + hyphy displayFunction.bf 210s + for i in *.bf 210s + '[' -f profile_test.bf ']' 210s + hyphy profile_test.bf 210s 0.49994751 (weight=0.2500000) 210s Rate[3]= 1.19311765 (weight=0.2500000) 210s ------------------------------------------------ 210s 2). Equiprobable rates sampled from Exponential with lambda = 2 210s 210s Sample by MEDIAN (3 rate classes): 210s 210s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 210s 210s Rate[0]= 0.09116078 (weight=0.3333333) 210s Rate[1]= 0.34657359 (weight=0.3333333) 210s Rate[2]= 0.89587973 (weight=0.3333333) 210s ------------------------------------------------ 210s 210s Sample by MEDIAN (9 rate classes): 210s 210s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 210s 210s Rate[0]= 0.02857921 (weight=0.1111111) 210s Rate[1]= 0.09116078 (weight=0.1111111) 210s Rate[2]= 0.16271120 (weight=0.1111111) 210s Rate[3]= 0.24623824 (weight=0.1111111) 210s Rate[4]= 0.34657359 (weight=0.1111111) 210s Rate[5]= 0.47223080 (weight=0.1111111) 210s Rate[6]= 0.64046692 (weight=0.1111111) 210s Rate[7]= 0.89587973 (weight=0.1111111) 210s Rate[8]= 1.44518588 (weight=0.1111111) 210s ------------------------------------------------ 210s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 210s 210s Sample by MEAN (10 rate classes): 210s 210s Sample mean = 1 (sample variance = 0.1057310289486733) 210s 210s Rate[0]= 0.52447499 (weight=0.1000000) 210s Rate[1]= 0.67866972 (weight=0.1000000) 210s Rate[2]= 0.77209919 (weight=0.1000000) 210s Rate[3]= 0.85214884 (weight=0.1000000) 210s Rate[4]= 0.92850815 (weight=0.1000000) 210s Rate[5]= 1.00664500 (weight=0.1000000) 210s Rate[6]= 1.09192933 (weight=0.1000000) 210s Rate[7]= 1.19267960 (weight=0.1000000) 210s Rate[8]= 1.32858029 (weight=0.1000000) 210s Rate[9]= 1.62426489 (weight=0.1000000) 210s ------------------------------------------------ 210s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 210s 210s Sample by MEAN (10 rate classes): 210s 210s Sample mean = 2 (sample variance = 0.04259071282256012) 210s 210s Rate[0]= 1.66431246 (weight=0.1000000) 210s Rate[1]= 1.79212822 (weight=0.1000000) 210s Rate[2]= 1.86123411 (weight=0.1000000) 210s Rate[3]= 1.91722052 (weight=0.1000000) 210s Rate[4]= 1.96832799 (weight=0.1000000) 210s Rate[5]= 2.01862937 (weight=0.1000000) 210s Rate[6]= 2.07152664 (weight=0.1000000) 210s Rate[7]= 2.13166629 (weight=0.1000000) 210s Rate[8]= 2.20930216 (weight=0.1000000) 210s Rate[9]= 2.36565224 (weight=0.1000000) 210s ------------------------------------------------ 210s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 210s 210s Sample by MEAN (8 rate classes): 210s 210s Sample mean = 0.5 (sample variance = 0.09375000225643569) 210s 210s Rate[0]= 0.06250000 (weight=0.1250000) 210s Rate[1]= 0.18750000 (weight=0.1250000) 210s Rate[2]= 0.31250001 (weight=0.1250000) 210s Rate[3]= 0.43750001 (weight=0.1250000) 210s Rate[4]= 0.56249993 (weight=0.1250000) 210s Rate[5]= 0.68750001 (weight=0.1250000) 210s Rate[6]= 0.81250002 (weight=0.1250000) 210s Rate[7]= 0.93750002 (weight=0.1250000) 210s ------------------------------------------------ 210s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 210s 210s Sample by MEAN (8 rate classes): 210s 210s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 210s 210s Rate[0]= 2.17658588 (weight=0.1250000) 210s Rate[1]= 2.55230783 (weight=0.1250000) 210s Rate[2]= 2.75432532 (weight=0.1250000) 210s Rate[3]= 2.92101185 (weight=0.1250000) 210s Rate[4]= 3.07898815 (weight=0.1250000) 210s Rate[5]= 3.24567468 (weight=0.1250000) 210s Rate[6]= 3.44769217 (weight=0.1250000) 210s Rate[7]= 3.82341415 (weight=0.1250000) 210s ------------------------------------------------ 210s 210s 210s Sample mean = 1 (sample variance = 0.9920002887656187) 210s 210s Rate[0]= 0.05175536 (weight=0.1000000) 210s Rate[1]= 0.16309623 (weight=0.1000000) 210s Rate[2]= 0.28842380 (weight=0.1000000) 210s Rate[3]= 0.43177086 (weight=0.1000000) 210s Rate[4]= 0.59921784 (weight=0.1000000) 210s Rate[5]= 0.80057298 (weight=0.1000000) 210s Rate[6]= 1.05324451 (weight=0.1000000) 210s Rate[7]= 1.39304259 (weight=0.1000000) 210s Rate[8]= 1.91629073 (weight=0.1000000) 210s Rate[9]= 3.30258509 (weight=0.1000000) 210s ------------------------------------------------ 210s 210s Total run time (seconds) : 0.000000 210s Total number of steps : 1500005 210s 210s 1 : s=0; 210s Call count: 1 210s Time (seconds): 9e-12 210s 2 : m={5,1}; 210s Call count: 1 210s Time (seconds): 1.5e-11 210s 3 : k=0; 210s Call count: 1 210s Time (seconds): 1e-12 210s 4 : Branch under condition 'k<250000' 210s to 210s s=s+k; 210s else 210s #profilePAUSE, ; 210s Call count: 250001 210s Time (seconds): 3.092900000001022e-08 210s 5 : s=s+k; 210s Call count: 250000 210s Time (seconds): 3.593500000001533e-08 210s 6 : t=Random(0,5); 210s Call count: 250000 210s Time (seconds): 3.715800000001598e-08 210s 7 : m[t]=m[t]+1; 210s Call count: 250000 210s Time (seconds): 9.750000000007646e-08 210s 8 : k=k+1; 210s Call count: 250000 210s Time (seconds): 4.053400000001963e-08 210s 9 : Go to step 4 210s Call count: 250000 210s Time (seconds): 1.048699999999876e-08 210s 10 : #profilePAUSE, ; 210s Call count: 1 210s Time (seconds): 0 210s + for i in *.bf 210s + '[' -f shared.bf ']' 210s + hyphy shared.bf 210s + rm -f '*messages.log*' '*errors.log*' 210s autopkgtest [06:41:22]: test run-unit-tests: -----------------------] 211s autopkgtest [06:41:23]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 211s run-unit-tests PASS 211s autopkgtest [06:41:23]: @@@@@@@@@@@@@@@@@@@@ summary 211s run-unit-tests PASS 222s Creating nova instance adt-noble-s390x-hyphy-20240324-063752-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240324.img (UUID e13d5247-1289-46d4-b3a9-3aa9fa45fdc9)...