0s autopkgtest [21:41:31]: starting date and time: 2025-03-15 21:41:31+0000 0s autopkgtest [21:41:31]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:41:31]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6sv7bfmx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade paml --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-13.secgroup --name adt-plucky-amd64-paml-20250315-210524-juju-7f2275-prod-proposed-migration-environment-20-12c2ac69-6de5-4f38-891b-72d554451989 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 63s autopkgtest [21:42:34]: testbed dpkg architecture: amd64 63s autopkgtest [21:42:34]: testbed apt version: 2.9.31ubuntu1 63s autopkgtest [21:42:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s autopkgtest [21:42:35]: testbed release detected to be: None 64s autopkgtest [21:42:35]: updating testbed package index (apt update) 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 65s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 65s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 65s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 65s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 65s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 65s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 65s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 65s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 65s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 65s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 66s Fetched 1265 kB in 1s (1419 kB/s) 67s Reading package lists... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s Calculating upgrade... 68s Calculating upgrade... 68s The following package was automatically installed and is no longer required: 68s libnl-genl-3-200 68s Use 'sudo apt autoremove' to remove it. 68s The following NEW packages will be installed: 68s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 68s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 68s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 68s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 68s The following packages will be upgraded: 68s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 68s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 68s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 68s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 68s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 68s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 68s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 68s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 68s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 68s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 68s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 68s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 68s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 68s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 68s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 68s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 68s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 68s parted pci.ids pciutils pinentry-curses python-apt-common python3 68s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 68s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 68s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 68s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 68s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 68s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 68s xz-utils 68s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 68s Need to get 829 MB of archives. 68s After this operation, 325 MB of additional disk space will be used. 68s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 69s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 69s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 69s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 69s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 69s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 69s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 69s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 69s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 69s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 69s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 69s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 69s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 69s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 69s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 69s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 69s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 69s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 69s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 69s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 69s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 69s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 70s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 70s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 70s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 70s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 70s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 70s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 70s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 70s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 70s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 70s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 70s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 70s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 70s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 70s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 70s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 70s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 70s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 70s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 70s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 70s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 70s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 70s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 70s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 70s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 70s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 70s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 70s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 70s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 70s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 70s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 70s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 70s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 70s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 70s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 70s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 70s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 70s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 70s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 70s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 70s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 70s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 70s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 70s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 70s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 70s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 70s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 71s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 71s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 71s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 71s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 71s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 71s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 71s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 71s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 71s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 71s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 71s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 71s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 71s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 71s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 71s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 71s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 71s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 71s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 71s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 71s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 71s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 71s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 71s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 71s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 71s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 71s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 71s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 71s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 71s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 71s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 71s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 71s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 71s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 71s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 72s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 72s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 72s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 72s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 72s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 72s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 72s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 97s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 97s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 97s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 97s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 97s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 97s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 97s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 97s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 99s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 100s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 106s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 106s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 106s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 106s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 106s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 106s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 107s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 107s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 107s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 107s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 107s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 107s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 107s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 107s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 107s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 107s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 107s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 107s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 107s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 108s Preconfiguring packages ... 108s Fetched 829 MB in 39s (21.2 MB/s) 108s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 115s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 115s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 115s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 115s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 115s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 115s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 115s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 115s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 115s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 115s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 115s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 115s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 115s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 115s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 115s Selecting previously unselected package libdebuginfod-common. 115s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 115s Unpacking libdebuginfod-common (0.192-4) ... 115s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 115s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 115s Setting up libsemanage-common (3.7-2.1build1) ... 115s (Reading database ... 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.../23-parted_3.6-5_amd64.deb ... 118s Unpacking parted (3.6-5) over (3.6-4build1) ... 118s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 118s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 118s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 118s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 118s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 118s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 118s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 118s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 118s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 118s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 118s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 118s Unpacking strace 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(2.44-3ubuntu1) over (2.44-2ubuntu1) ... 119s Preparing to unpack .../36-binutils_2.44-3ubuntu1_amd64.deb ... 119s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 119s Preparing to unpack .../37-binutils-common_2.44-3ubuntu1_amd64.deb ... 119s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 119s Preparing to unpack .../38-libsframe1_2.44-3ubuntu1_amd64.deb ... 119s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 119s Preparing to unpack .../39-hwdata_0.393-3_all.deb ... 119s Unpacking hwdata (0.393-3) over (0.392-1) ... 119s Selecting previously unselected package pnp.ids. 119s Preparing to unpack .../40-pnp.ids_0.393-3_all.deb ... 119s Unpacking pnp.ids (0.393-3) ... 119s Preparing to unpack .../41-linux-tools-common_6.14.0-10.10_all.deb ... 119s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ... 119s Selecting previously unselected package bpftool. 119s Preparing to unpack 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new version of config file /etc/mime.types ... 130s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 130s Setting up ubuntu-kernel-accessories (1.549) ... 130s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 130s Setting up pci.ids (0.0~2025.03.09-1) ... 130s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 130s Setting up apt-utils (2.9.33) ... 130s Setting up libdebuginfod-common (0.192-4) ... 132s Setting up exfatprogs (1.2.8-1) ... 132s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 132s Setting up bpftool (7.6.0+6.14.0-10.10) ... 132s Setting up libestr0:amd64 (0.1.11-2) ... 132s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 132s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 132s Setting up dosfstools (4.2-1.2) ... 132s Setting up rsyslog (8.2412.0-2ubuntu2) ... 132s info: The user `syslog' is already a member of `adm'. 132s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 132s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 132s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 132s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 132s Setting up systemd (257.3-1ubuntu3) ... 132s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 132s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 132s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 132s Setting up libparted2t64:amd64 (3.6-5) ... 132s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 132s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 132s Setting up linux-headers-generic (6.14.0-10.10) ... 132s Setting up libjemalloc2:amd64 (5.3.0-3) ... 132s Setting up locales (2.41-1ubuntu1) ... 132s Installing new version of config file /etc/locale.alias ... 133s Generating locales (this might take a while)... 134s en_US.UTF-8... done 134s Generation complete. 134s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 134s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 134s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 134s Installing new version of config file /etc/apparmor.d/fusermount3 ... 134s Installing new version of config file /etc/apparmor.d/lsusb ... 134s Installing new version of config file /etc/apparmor.d/openvpn ... 135s Reloading AppArmor profiles 137s Setting up libftdi1-2:amd64 (1.5-8build1) ... 137s Setting up libglib2.0-data (2.84.0-1) ... 137s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 137s Setting up libncurses6:amd64 (6.5+20250216-2) ... 137s Setting up strace (6.13+ds-1ubuntu1) ... 137s Setting up xz-utils (5.6.4-1) ... 137s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 137s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 138s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 138s Setting up udev (257.3-1ubuntu3) ... 138s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 140s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 140s Setting up libpci3:amd64 (1:3.13.0-2) ... 140s Setting up whiptail (0.52.24-4ubuntu2) ... 140s Setting up python-apt-common (2.9.9build1) ... 140s Setting up pnp.ids (0.393-3) ... 140s Setting up libnl-3-200:amd64 (3.7.0-1) ... 140s Setting up python3.13-minimal (3.13.2-2) ... 141s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 141s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 141s Setting up libc-dev-bin (2.41-1ubuntu1) ... 141s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 141s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 141s Setting up rsync (3.4.1+ds1-3) ... 142s rsync.service is a disabled or a static unit not running, not starting it. 142s Setting up python3.13-gdbm (3.13.2-2) ... 142s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 142s Setting up systemd-resolved (257.3-1ubuntu3) ... 143s Setting up initramfs-tools-bin (0.146ubuntu1) ... 143s Setting up ncurses-term (6.5+20250216-2) ... 143s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 143s Setting up libpython3.13:amd64 (3.13.2-2) ... 143s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 143s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 143s Setting up systemd-sysv (257.3-1ubuntu3) ... 143s Setting up linux-headers-virtual (6.14.0-10.10) ... 143s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 143s Setting up python3.13 (3.13.2-2) ... 143s Setting up htop (3.4.0-2) ... 143s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 146s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 146s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 146s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 146s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 146s Setting up parted (3.6-5) ... 146s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 146s Setting up python3 (3.13.2-2) ... 146s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 146s Setting up python3-markupsafe (2.1.5-1build4) ... 146s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 148s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 148s Setting up hwdata (0.393-3) ... 148s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 149s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 149s No schema files found: doing nothing. 149s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 149s Setting up linux-perf (6.14.0-10.10) ... 149s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 149s Setting up pciutils (1:3.13.0-2) ... 149s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 149s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 149s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 149s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 149s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 149s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 149s Setting up curl (8.12.1-3ubuntu1) ... 149s Setting up linux-image-virtual (6.14.0-10.10) ... 149s Setting up initramfs-tools-core (0.146ubuntu1) ... 149s Setting up linux-tools-common (6.14.0-10.10) ... 149s Setting up python3-systemd (235-1build6) ... 149s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 149s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 149s Setting up linux-image-generic (6.14.0-10.10) ... 149s Setting up python3-dbus (1.3.2-5build5) ... 149s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 149s Setting up initramfs-tools (0.146ubuntu1) ... 149s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 149s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 149s update-initramfs: deferring update (trigger activated) 149s Setting up linux-generic (6.14.0-10.10) ... 149s Setting up ubuntu-minimal (1.549) ... 149s Setting up python3-apt (2.9.9build1) ... 149s Setting up python3-bcrypt (4.2.0-2.1build1) ... 149s Setting up python3-yaml (6.0.2-1build2) ... 150s Setting up libfwupd3:amd64 (2.0.6-4) ... 150s Setting up python3-lazr.uri (1.0.6-6) ... 150s Setting up binutils (2.44-3ubuntu1) ... 150s Setting up ubuntu-standard (1.549) ... 150s Setting up cloud-init-base (25.1-0ubuntu3) ... 151s Setting up linux-virtual (6.14.0-10.10) ... 151s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 151s Setting up python3-gi (3.50.0-4build1) ... 151s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 151s Setting up fwupd (2.0.6-4) ... 152s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 152s fwupd.service is a disabled or a static unit not running, not starting it. 152s Setting up cloud-init (25.1-0ubuntu3) ... 152s Processing triggers for man-db (2.13.0-1) ... 154s Processing triggers for dbus (1.16.2-1ubuntu1) ... 154s Processing triggers for shared-mime-info (2.4-5) ... 154s Warning: program compiled against libxml 212 using older 209 154s Processing triggers for libc-bin (2.41-1ubuntu1) ... 154s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 154s /etc/kernel/postinst.d/initramfs-tools: 154s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 154s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 165s /etc/kernel/postinst.d/zz-update-grub: 165s Sourcing file `/etc/default/grub' 165s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 165s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 165s Generating grub configuration file ... 165s Found linux image: /boot/vmlinuz-6.14.0-10-generic 165s Found initrd image: /boot/initrd.img-6.14.0-10-generic 165s Found linux image: /boot/vmlinuz-6.12.0-16-generic 165s Found initrd image: /boot/initrd.img-6.12.0-16-generic 165s Found linux image: /boot/vmlinuz-6.11.0-8-generic 165s Found initrd image: /boot/initrd.img-6.11.0-8-generic 165s Warning: os-prober will not be executed to detect other bootable partitions. 165s Systems on them will not be added to the GRUB boot configuration. 165s Check GRUB_DISABLE_OS_PROBER documentation entry. 165s Adding boot menu entry for UEFI Firmware Settings ... 165s done 165s Processing triggers for initramfs-tools (0.146ubuntu1) ... 165s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 165s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 177s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Solving dependencies... 178s The following packages will be REMOVED: 178s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 178s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 178s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 178s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 178s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 178s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 178s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 178s linux-tools-6.12.0-16-generic* 178s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 178s After this operation, 545 MB disk space will be freed. 178s (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 ... 148643 files and directories currently installed.) 178s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 178s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 178s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 178s Removing libpython3.12t64:amd64 (3.12.9-1) ... 178s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 178s Removing libnsl2:amd64 (1.3.0-3build3) ... 178s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 179s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 179s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 181s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 182s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 184s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 184s /etc/kernel/postrm.d/initramfs-tools: 184s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 184s /etc/kernel/postrm.d/zz-update-grub: 184s Sourcing file `/etc/default/grub' 184s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 184s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 184s Generating grub configuration file ... 184s Found linux image: /boot/vmlinuz-6.14.0-10-generic 184s Found initrd image: /boot/initrd.img-6.14.0-10-generic 185s Found linux image: /boot/vmlinuz-6.12.0-16-generic 185s Found initrd image: /boot/initrd.img-6.12.0-16-generic 185s Warning: os-prober will not be executed to detect other bootable partitions. 185s Systems on them will not be added to the GRUB boot configuration. 185s Check GRUB_DISABLE_OS_PROBER documentation entry. 185s Adding boot menu entry for UEFI Firmware Settings ... 185s done 185s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 185s W: Removing the running kernel 185s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 185s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 185s /etc/kernel/postrm.d/initramfs-tools: 185s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 185s /etc/kernel/postrm.d/zz-update-grub: 185s Sourcing file `/etc/default/grub' 185s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 185s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 185s Generating grub configuration file ... 185s Found linux image: /boot/vmlinuz-6.14.0-10-generic 185s Found initrd image: /boot/initrd.img-6.14.0-10-generic 186s Warning: os-prober will not be executed to detect other bootable partitions. 186s Systems on them will not be added to the GRUB boot configuration. 186s Check GRUB_DISABLE_OS_PROBER documentation entry. 186s Adding boot menu entry for UEFI Firmware Settings ... 186s done 186s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 186s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 188s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 188s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 188s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 188s Processing triggers for libc-bin (2.41-1ubuntu1) ... 188s (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 ... 76972 files and directories currently installed.) 188s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 188s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 188s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 188s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 188s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 188s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 188s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 188s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 188s autopkgtest [21:44:39]: upgrading testbed (apt dist-upgrade and autopurge) 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 190s Entering ResolveByKeep 190s 190s Calculating upgrade... 190s The following packages will be upgraded: 190s libc-bin libc-dev-bin libc6 libc6-dev locales 190s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Need to get 10.5 MB of archives. 190s After this operation, 1024 B of additional disk space will be used. 190s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 191s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 191s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 191s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 191s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 192s Preconfiguring packages ... 192s Fetched 10.5 MB in 1s (11.5 MB/s) 192s (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 ... 76968 files and directories currently installed.) 192s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 192s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 192s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 192s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 192s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 192s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 192s Setting up libc6:amd64 (2.41-1ubuntu2) ... 192s (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 ... 76968 files and directories currently installed.) 192s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 192s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 192s Setting up libc-bin (2.41-1ubuntu2) ... 192s (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 ... 76968 files and directories currently installed.) 192s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 192s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 193s Setting up locales (2.41-1ubuntu2) ... 193s Generating locales (this might take a while)... 195s en_US.UTF-8... done 195s Generation complete. 195s Setting up libc-dev-bin (2.41-1ubuntu2) ... 195s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 195s Processing triggers for man-db (2.13.0-1) ... 196s Processing triggers for systemd (257.3-1ubuntu3) ... 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Starting pkgProblemResolver with broken count: 0 197s Starting 2 pkgProblemResolver with broken count: 0 197s Done 198s Solving dependencies... 198s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s autopkgtest [21:44:49]: rebooting testbed after setup commands that affected boot 221s autopkgtest [21:45:12]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 224s autopkgtest [21:45:15]: @@@@@@@@@@@@@@@@@@@@ apt-source paml 226s Get:1 http://ftpmaster.internal/ubuntu plucky/universe paml 4.9j+dfsg-6 (dsc) [2244 B] 226s Get:2 http://ftpmaster.internal/ubuntu plucky/universe paml 4.9j+dfsg-6 (tar) [1375 kB] 226s Get:3 http://ftpmaster.internal/ubuntu plucky/universe paml 4.9j+dfsg-6 (diff) [8604 B] 226s gpgv: Signature made Wed Feb 26 22:07:37 2025 UTC 226s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 226s gpgv: issuer "emollier@debian.org" 226s gpgv: Can't check signature: No public key 226s dpkg-source: warning: cannot verify inline signature for ./paml_4.9j+dfsg-6.dsc: no acceptable signature found 226s autopkgtest [21:45:17]: testing package paml version 4.9j+dfsg-6 227s autopkgtest [21:45:18]: build not needed 227s autopkgtest [21:45:18]: test run-unit-test: preparing testbed 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s Starting pkgProblemResolver with broken count: 0 229s Starting 2 pkgProblemResolver with broken count: 0 229s Done 229s The following NEW packages will be installed: 229s paml paml-doc 229s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 229s Need to get 1673 kB of archives. 229s After this operation, 8376 kB of additional disk space will be used. 229s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 paml amd64 4.9j+dfsg-6 [670 kB] 230s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 paml-doc all 4.9j+dfsg-6 [1002 kB] 230s Fetched 1673 kB in 1s (2579 kB/s) 230s Selecting previously unselected package paml. 230s (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 ... 76968 files and directories currently installed.) 230s Preparing to unpack .../paml_4.9j+dfsg-6_amd64.deb ... 230s Unpacking paml (4.9j+dfsg-6) ... 230s Selecting previously unselected package paml-doc. 230s Preparing to unpack .../paml-doc_4.9j+dfsg-6_all.deb ... 230s Unpacking paml-doc (4.9j+dfsg-6) ... 231s Setting up paml-doc (4.9j+dfsg-6) ... 231s Setting up paml (4.9j+dfsg-6) ... 232s autopkgtest [21:45:23]: test run-unit-test: [----------------------- 232s Test 1 233s 233s CODONML in paml version 4.9j, October 2019 233s 233s ---------------------------------------------- 233s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 233s TTC | TCC | TAC | TGC 233s Leu L TTA | TCA | *** * TAA | *** * TGA 233s TTG | TCG | TAG | Trp W TGG 233s ---------------------------------------------- 233s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 233s CTC | CCC | CAC | CGC 233s CTA | CCA | Gln Q CAA | CGA 233s CTG | CCG | CAG | CGG 233s ---------------------------------------------- 233s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 233s ATC | ACC | AAC | AGC 233s ATA | ACA | Lys K AAA | Arg R AGA 233s Met M ATG | ACG | AAG | AGG 233s ---------------------------------------------- 233s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 233s GTC | GCC | GAC | GGC 233s GTA | GCA | Glu E GAA | GGA 233s GTG | GCG | GAG | GGG 233s ---------------------------------------------- 233s Nice code, uuh? 233s NSsites batch run (ncatG as in YNGP2000): 0 1 2 233s ns = 13 ls = 273 233s Reading sequences, sequential format.. 233s Reading seq # 1: U68496 Reading seq # 2: U68497 Reading seq # 3: U68498 Reading seq # 4: U68499 Reading seq # 5: U68500 Reading seq # 6: U68501 Reading seq # 7: U68502 Reading seq # 8: U68503 Reading seq # 9: U68504 Reading seq #10: U68505 Reading seq #11: U68506 Reading seq #12: U68507 Reading seq #13: U68508 233s Sequences read.. 233s Counting site patterns.. 0:00 233s Compressing, 79 patterns at 91 / 91 sites (100.0%), 0:00 233s Collecting fpatt[] & pose[], 79 patterns at 91 / 91 sites (100.0%), 0:00 233s Counting codons.. 233s 233s 624 bytes for distance 233s 77104 bytes for conP 233s 6952 bytes for fhK 233s 5000000 bytes for space 233s 233s 233s Model 0: one-ratio 233s 233s TREE # 1 233s (1, 2, ((3, (4, 5)), (6, (7, (8, ((((9, 11), 10), 12), 13)))))); MP score: 136 233s 424072 bytes for conP, adjusted 233s 233s 0.029123 0.101972 0.018821 0.101264 0.096855 0.023405 0.099514 0.079037 0.106845 0.100399 0.103472 0.010639 0.063385 0.068450 0.011908 0.080575 0.027716 0.031611 0.094182 0.064862 0.061158 0.053308 0.054399 0.300000 1.300000 233s 233s ntime & nrate & np: 23 2 25 233s 233s Bounds (np=25): 233s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 233s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 233s 233s np = 25 233s lnL0 = -1274.355065 233s 233s Iterating by ming2 233s Initial: fx= 1274.355065 233s x= 0.02912 0.10197 0.01882 0.10126 0.09686 0.02341 0.09951 0.07904 0.10685 0.10040 0.10347 0.01064 0.06339 0.06845 0.01191 0.08057 0.02772 0.03161 0.09418 0.06486 0.06116 0.05331 0.05440 0.30000 1.30000 233s 233s 1 h-m-p 0.0000 0.0014 1126.4881 +++YCYCCC 1214.066579 5 0.0004 41 | 0/25 233s 2 h-m-p 0.0002 0.0011 200.5824 ++ 1187.899458 m 0.0011 69 | 0/25 233s 3 h-m-p 0.0000 0.0001 1410.9143 +YYCCC 1184.046364 4 0.0000 104 | 0/25 233s 4 h-m-p 0.0001 0.0005 362.7044 +YYCCC 1175.725931 4 0.0004 139 | 0/25 233s 5 h-m-p 0.0000 0.0001 760.3202 +CCC 1172.937183 2 0.0001 172 | 0/25 233s 6 h-m-p 0.0002 0.0088 329.2303 +CYCCC 1162.956821 4 0.0009 208 | 0/25 233s 7 h-m-p 0.0007 0.0034 87.1309 YCC 1159.620928 2 0.0014 239 | 0/25 233s 8 h-m-p 0.0009 0.0045 52.6147 YCCCC 1157.860358 4 0.0018 274 | 0/25 233s 9 h-m-p 0.0008 0.0039 47.6964 CYC 1157.415247 2 0.0008 305 | 0/25 233s 10 h-m-p 0.0021 0.0138 17.3861 YC 1157.266040 1 0.0012 334 | 0/25 233s 11 h-m-p 0.0021 0.0176 10.2275 CCC 1157.124203 2 0.0028 366 | 0/25 240s 12 h-m-p 0.0014 0.0355 20.7058 +CCCC 1156.408516 3 0.0070 401 | 0/25 240s 13 h-m-p 0.0012 0.0086 120.4954 CYCCC 1154.950288 4 0.0023 436 | 0/25 240s 14 h-m-p 0.0012 0.0060 133.1196 YYC 1154.307015 2 0.0010 466 | 0/25 240s 15 h-m-p 0.0036 0.0180 22.0456 YC 1154.122271 1 0.0017 495 | 0/25 240s 16 h-m-p 0.0062 0.0477 6.0889 YCC 1154.007335 2 0.0030 526 | 0/25 240s 17 h-m-p 0.0030 0.0382 6.0697 +YYC 1153.286022 2 0.0091 557 | 0/25 240s 18 h-m-p 0.0018 0.0113 31.2181 +YYYC 1149.308540 3 0.0068 589 | 0/25 240s 19 h-m-p 0.0004 0.0022 152.4244 +YYCCC 1145.189181 4 0.0015 624 | 0/25 240s 20 h-m-p 0.0012 0.0058 24.1837 YYCC 1144.990412 3 0.0009 656 | 0/25 240s 21 h-m-p 0.0017 0.0083 12.4297 YC 1144.948459 1 0.0007 685 | 0/25 240s 22 h-m-p 0.0018 0.0225 4.8015 CCC 1144.928113 2 0.0015 717 | 0/25 240s 23 h-m-p 0.0036 0.0641 1.9751 YC 1144.879444 1 0.0067 746 | 0/25 240s 24 h-m-p 0.0030 0.0407 4.4404 YC 1144.725260 1 0.0050 775 | 0/25 240s 25 h-m-p 0.0032 0.0270 6.8516 +YCCC 1143.837850 3 0.0094 809 | 0/25 240s 26 h-m-p 0.0021 0.0105 27.7829 CCC 1143.198394 2 0.0021 841 | 0/25 240s 27 h-m-p 0.0337 0.1683 1.0757 YC 1143.181707 1 0.0063 870 | 0/25 240s 28 h-m-p 0.0049 0.5904 1.3964 +++YYC 1140.428026 2 0.2726 903 | 0/25 240s 29 h-m-p 0.9805 4.9023 0.3605 CYCCC 1138.970282 4 0.7433 938 | 0/25 240s 30 h-m-p 1.2963 6.4817 0.1042 YYC 1138.444753 2 1.0733 993 | 0/25 240s 31 h-m-p 1.6000 8.0000 0.0237 CCC 1138.282437 2 1.8525 1050 | 0/25 240s 32 h-m-p 1.6000 8.0000 0.0116 CC 1138.165662 1 2.1072 1105 | 0/25 240s 33 h-m-p 1.6000 8.0000 0.0094 CCC 1138.039182 2 2.1658 1162 | 0/25 240s 34 h-m-p 1.2605 8.0000 0.0162 YCCC 1137.882616 3 2.6387 1220 | 0/25 240s 35 h-m-p 1.6000 8.0000 0.0127 CCC 1137.789217 2 2.2824 1277 | 0/25 240s 36 h-m-p 1.6000 8.0000 0.0139 CC 1137.727530 1 1.9304 1332 | 0/25 240s 37 h-m-p 1.6000 8.0000 0.0063 CC 1137.706521 1 1.3057 1387 | 0/25 240s 38 h-m-p 1.6000 8.0000 0.0044 CC 1137.696481 1 1.7827 1442 | 0/25 240s 39 h-m-p 1.6000 8.0000 0.0036 CC 1137.692480 1 1.7270 1497 | 0/25 240s 40 h-m-p 0.9596 8.0000 0.0064 +YC 1137.689780 1 2.4481 1552 | 0/25 240s 41 h-m-p 1.6000 8.0000 0.0012 CC 1137.689002 1 1.8760 1607 | 0/25 240s 42 h-m-p 1.0939 8.0000 0.0021 YC 1137.688579 1 2.0732 1661 | 0/25 240s 43 h-m-p 1.5805 8.0000 0.0027 CC 1137.688260 1 2.0001 1716 | 0/25 240s 44 h-m-p 1.6000 8.0000 0.0008 C 1137.688193 0 1.4604 1769 | 0/25 240s 45 h-m-p 1.6000 8.0000 0.0002 Y 1137.688190 0 1.2423 1822 | 0/25 240s 46 h-m-p 1.6000 8.0000 0.0000 Y 1137.688190 0 1.0767 1875 | 0/25 240s 47 h-m-p 1.6000 8.0000 0.0000 Y 1137.688190 0 1.2428 1928 | 0/25 240s 48 h-m-p 1.6000 8.0000 0.0000 C 1137.688190 0 1.3430 1981 | 0/25 240s 49 h-m-p 1.6000 8.0000 0.0000 Y 1137.688190 0 0.4000 2034 | 0/25 240s 50 h-m-p 0.5768 8.0000 0.0000 Y 1137.688190 0 0.2844 2087 | 0/25 240s 51 h-m-p 0.3619 8.0000 0.0000 -----C 1137.688190 0 0.0001 2145 240s Out.. 240s lnL = -1137.688190 240s 2146 lfun, 2146 eigenQcodon, 49358 P(t) 240s 240s Time used: 0:08 240s 240s 240s Model 1: NearlyNeutral 240s 240s TREE # 1 240s (1, 2, ((3, (4, 5)), (6, (7, (8, ((((9, 11), 10), 12), 13)))))); MP score: 136 240s 0.070043 0.038852 0.096272 0.022832 0.036157 0.051290 0.035036 0.096865 0.064612 0.085826 0.039423 0.011118 0.106901 0.055362 0.102471 0.091478 0.025095 0.016377 0.061227 0.022693 0.010049 0.093511 0.033850 2.471747 0.596912 0.141299 240s 240s ntime & nrate & np: 23 2 26 240s 240s Bounds (np=26): 240s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000010 0.000001 251s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 0.999990 1.000000 251s Qfactor_NS = 5.350420 251s 251s np = 26 251s lnL0 = -1174.119343 251s 251s Iterating by ming2 251s Initial: fx= 1174.119343 251s x= 0.07004 0.03885 0.09627 0.02283 0.03616 0.05129 0.03504 0.09686 0.06461 0.08583 0.03942 0.01112 0.10690 0.05536 0.10247 0.09148 0.02510 0.01638 0.06123 0.02269 0.01005 0.09351 0.03385 2.47175 0.59691 0.14130 251s 251s 1 h-m-p 0.0000 0.0010 1011.3989 ++YCYCCC 1128.195760 5 0.0003 41 | 0/26 251s 2 h-m-p 0.0002 0.0011 132.6678 +CYCCC 1119.193721 4 0.0009 78 | 0/26 251s 3 h-m-p 0.0001 0.0006 206.3110 YCYC 1117.304606 3 0.0002 111 | 0/26 251s 4 h-m-p 0.0003 0.0013 90.2709 YCYC 1116.048911 3 0.0005 144 | 0/26 251s 5 h-m-p 0.0005 0.0027 34.5846 YCCC 1115.587400 3 0.0010 178 | 0/26 251s 6 h-m-p 0.0012 0.0106 28.1328 YCCC 1115.429487 3 0.0007 212 | 0/26 251s 7 h-m-p 0.0010 0.0060 19.9577 CC 1115.317612 1 0.0010 243 | 0/26 251s 8 h-m-p 0.0013 0.0264 15.5685 YC 1115.178679 1 0.0023 273 | 0/26 251s 9 h-m-p 0.0021 0.0122 16.7841 YCC 1115.115298 2 0.0012 305 | 0/26 251s 10 h-m-p 0.0032 0.0236 6.2079 YC 1115.096330 1 0.0015 335 | 0/26 251s 11 h-m-p 0.0018 0.0401 5.2261 YC 1115.087974 1 0.0011 365 | 0/26 251s 12 h-m-p 0.0021 0.0509 2.7998 YC 1115.084664 1 0.0013 395 | 0/26 251s 13 h-m-p 0.0020 0.2196 1.7234 YC 1115.082991 1 0.0014 425 | 0/26 251s 14 h-m-p 0.0015 0.4955 1.6128 +CC 1115.073786 1 0.0092 457 | 0/26 251s 15 h-m-p 0.0015 0.0878 10.0846 +CC 1115.040947 1 0.0052 489 | 0/26 251s 16 h-m-p 0.0018 0.0198 28.4486 YC 1114.975737 1 0.0037 519 | 0/26 251s 17 h-m-p 0.0020 0.0102 27.6876 YC 1114.951860 1 0.0014 549 | 0/26 251s 18 h-m-p 0.0075 0.1104 5.1197 C 1114.945914 0 0.0019 578 | 0/26 251s 19 h-m-p 0.0079 0.1695 1.2513 CC 1114.944518 1 0.0018 609 | 0/26 251s 20 h-m-p 0.0059 0.1445 0.3736 YC 1114.939702 1 0.0101 639 | 0/26 251s 21 h-m-p 0.0019 0.0825 1.9316 +CC 1114.909255 1 0.0081 697 | 0/26 251s 22 h-m-p 0.0018 0.0652 8.5907 +CC 1114.747036 1 0.0089 729 | 0/26 251s 23 h-m-p 0.0062 0.0310 5.5044 CC 1114.732878 1 0.0017 760 | 0/26 251s 24 h-m-p 0.0153 0.2290 0.6005 -C 1114.732680 0 0.0011 790 | 0/26 251s 25 h-m-p 0.0063 1.1428 0.0995 C 1114.732531 0 0.0068 845 | 0/26 251s 26 h-m-p 0.0131 1.8052 0.0512 +CC 1114.726029 1 0.0818 903 | 0/26 251s 27 h-m-p 0.0031 0.0526 1.3712 YC 1114.697439 1 0.0060 959 | 0/26 251s 28 h-m-p 0.0040 0.0797 2.0641 CC 1114.693933 1 0.0015 990 | 0/26 251s 29 h-m-p 0.9016 8.0000 0.0033 +CC 1114.672848 1 3.1462 1022 | 0/26 251s 30 h-m-p 1.6000 8.0000 0.0055 YCC 1114.643950 2 2.8646 1080 | 0/26 251s 31 h-m-p 1.6000 8.0000 0.0020 YC 1114.641781 1 1.0970 1136 | 0/26 251s 32 h-m-p 1.6000 8.0000 0.0003 Y 1114.641737 0 1.0701 1191 | 0/26 251s 33 h-m-p 1.6000 8.0000 0.0001 Y 1114.641736 0 0.9950 1246 | 0/26 251s 34 h-m-p 1.6000 8.0000 0.0000 Y 1114.641736 0 0.9340 1301 | 0/26 251s 35 h-m-p 1.6000 8.0000 0.0000 Y 1114.641736 0 1.0806 1356 | 0/26 251s 36 h-m-p 1.6000 8.0000 0.0000 C 1114.641736 0 1.6000 1411 | 0/26 251s 37 h-m-p 1.6000 8.0000 0.0000 -Y 1114.641736 0 0.1000 1467 251s Out.. 251s lnL = -1114.641736 251s 1468 lfun, 4404 eigenQcodon, 67528 P(t) 251s 251s Time used: 0:19 251s 251s 251s Model 2: PositiveSelection 251s 251s TREE # 1 251s (1, 2, ((3, (4, 5)), (6, (7, (8, ((((9, 11), 10), 12), 13)))))); MP score: 136 251s initial w for M2:NSpselection reset. 251s 251s 0.102872 0.071461 0.084075 0.063317 0.041263 0.098175 0.095194 0.072877 0.083516 0.087757 0.074286 0.097108 0.105118 0.100330 0.017570 0.029530 0.022315 0.077591 0.083260 0.076198 0.016888 0.069948 0.085436 2.594606 1.541646 0.488918 0.236138 2.051562 251s 251s ntime & nrate & np: 23 3 28 251s 251s Bounds (np=28): 270s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 -99.000000 -99.000000 0.000001 1.000000 270s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 99.000000 99.000000 1.000000 999.000000 270s Qfactor_NS = 4.161444 270s 270s np = 28 270s lnL0 = -1136.422387 270s 270s Iterating by ming2 270s Initial: fx= 1136.422387 270s x= 0.10287 0.07146 0.08407 0.06332 0.04126 0.09818 0.09519 0.07288 0.08352 0.08776 0.07429 0.09711 0.10512 0.10033 0.01757 0.02953 0.02231 0.07759 0.08326 0.07620 0.01689 0.06995 0.08544 2.59461 1.54165 0.48892 0.23614 2.05156 270s 270s 1 h-m-p 0.0000 0.0012 234.3198 +++YCYCCC 1118.377854 5 0.0009 44 | 0/28 270s 2 h-m-p 0.0002 0.0011 106.3298 +YYYCC 1113.476968 4 0.0008 81 | 0/28 270s 3 h-m-p 0.0003 0.0016 116.4041 YCCC 1111.543761 3 0.0006 117 | 0/28 270s 4 h-m-p 0.0002 0.0008 103.6111 YC 1110.624100 1 0.0004 149 | 0/28 270s 5 h-m-p 0.0002 0.0009 35.2377 ++ 1110.248906 m 0.0009 180 | 0/28 270s 6 h-m-p 0.0000 0.0000 22.8100 270s h-m-p: 7.88148940e-20 3.94074470e-19 2.28100417e+01 1110.248906 270s .. | 0/28 270s 7 h-m-p 0.0000 0.0020 26.6706 +++YYC 1110.040009 2 0.0006 244 | 0/28 270s 8 h-m-p 0.0008 0.0097 19.4317 CCC 1109.945439 2 0.0007 279 | 0/28 270s 9 h-m-p 0.0002 0.0011 26.3292 +YC 1109.850806 1 0.0007 312 | 0/28 270s 10 h-m-p 0.0002 0.0010 12.1321 ++ 1109.783586 m 0.0010 343 | 0/28 270s 11 h-m-p 0.0005 0.0222 23.5446 +CC 1109.648873 1 0.0019 377 | 0/28 270s 12 h-m-p 0.0019 0.0097 22.8980 CCC 1109.523890 2 0.0020 412 | 0/28 270s 13 h-m-p 0.0007 0.0259 66.0574 +CCC 1109.076620 2 0.0027 448 | 0/28 270s 14 h-m-p 0.0019 0.0114 97.2979 CCC 1108.598191 2 0.0020 483 | 0/28 270s 15 h-m-p 0.0012 0.0062 94.7866 +YCCC 1107.837097 3 0.0035 520 | 0/28 270s 16 h-m-p 0.0019 0.0093 158.6713 CYCC 1107.374672 3 0.0013 556 | 0/28 270s 17 h-m-p 0.0005 0.0023 45.9104 +YCC 1107.225719 2 0.0014 591 | 0/28 270s 18 h-m-p 0.0005 0.0024 26.5797 YC 1107.162489 1 0.0012 623 | 0/28 270s 19 h-m-p 0.0029 0.0145 10.5956 CC 1107.143850 1 0.0010 656 | 0/28 270s 20 h-m-p 0.0014 0.0071 5.5182 YC 1107.119386 1 0.0035 688 | 0/28 270s 21 h-m-p 0.0007 0.0034 6.4865 ++ 1107.094689 m 0.0034 719 | 1/28 270s 22 h-m-p 0.0013 0.0570 17.3874 +CC 1106.989719 1 0.0062 753 | 1/28 270s 23 h-m-p 0.0018 0.0282 60.7709 CCC 1106.904476 2 0.0015 788 | 1/28 270s 24 h-m-p 0.0014 0.0193 64.4058 CCC 1106.765923 2 0.0022 823 | 1/28 270s 25 h-m-p 0.0035 0.0325 41.3413 YC 1106.686904 1 0.0020 855 | 1/28 270s 26 h-m-p 0.0034 0.0169 10.0062 YC 1106.669854 1 0.0020 887 | 1/28 270s 27 h-m-p 0.0069 0.1311 2.8584 CC 1106.665142 1 0.0025 920 | 1/28 270s 28 h-m-p 0.0117 0.2210 0.6182 C 1106.664539 0 0.0026 951 | 1/28 270s 29 h-m-p 0.0024 0.5621 0.6594 +CC 1106.661644 1 0.0109 1012 | 1/28 270s 30 h-m-p 0.0025 0.5059 2.9238 +++YC 1106.540471 1 0.1007 1074 | 1/28 270s 31 h-m-p 0.0044 0.0218 28.3747 YC 1106.520025 1 0.0018 1106 | 1/28 270s 32 h-m-p 0.0215 0.4039 2.3614 CC 1106.516065 1 0.0046 1139 | 1/28 270s 33 h-m-p 0.0072 0.1414 1.5066 YC 1106.514461 1 0.0034 1171 | 1/28 270s 34 h-m-p 0.0053 1.5452 0.9569 +++YC 1106.459655 1 0.2115 1206 | 0/28 270s 35 h-m-p 0.0694 0.4338 2.9160 --C 1106.459419 0 0.0009 1266 | 0/28 270s 36 h-m-p 0.0775 4.9707 0.0345 ++CC 1106.445582 1 1.1403 1301 | 0/28 270s 37 h-m-p 1.1253 8.0000 0.0350 YC 1106.445037 1 0.7802 1361 | 0/28 270s 38 h-m-p 1.6000 8.0000 0.0027 Y 1106.445005 0 1.0087 1420 | 0/28 270s 39 h-m-p 1.6000 8.0000 0.0004 Y 1106.445004 0 1.1729 1479 | 0/28 270s 40 h-m-p 1.6000 8.0000 0.0001 Y 1106.445004 0 1.2336 1538 | 0/28 270s 41 h-m-p 1.6000 8.0000 0.0000 Y 1106.445004 0 1.0858 1597 | 0/28 270s 42 h-m-p 1.6000 8.0000 0.0000 C 1106.445004 0 0.4000 1656 | 0/28 270s 43 h-m-p 0.4916 8.0000 0.0000 Y 1106.445004 0 0.0625 1715 270s Out.. 270s lnL = -1106.445004 271s 1716 lfun, 6864 eigenQcodon, 118404 P(t) 271s 271s BEBing (dim = 4). This may take several minutes. 271s Calculating f(x_h|w): 10 categories 21 w sets. 271s Calculating f(X), the marginal likelihood. 271s log(fX) = -1112.401420 S = -1023.138909 -111.908273 271s Calculating f(w|X), posterior probabilities of site classes. 271s did 10 / 79 patterns 0:38 did 20 / 79 patterns 0:38 did 30 / 79 patterns 0:38 did 40 / 79 patterns 0:38 did 50 / 79 patterns 0:38 did 60 / 79 patterns 0:38 did 70 / 79 patterns 0:38 did 79 / 79 patterns 0:39 271s Time used: 0:39 271s Passed 271s 271s Test 2 271s 271s 15 verbose | verbose 1.00 271s 7 runmode | runmode 0.00 271s 4 seqtype | seqtype 1.00 271s 13 CodonFreq | CodonFreq 2.00 271s 9 clock | clock 0.00 271s 16 model | model 0.00 271s 20 NSsites | NSsites 2.00 271s 22 icode | icode 0.00 271s 24 fix_kappa | fix_kappa 0.00 271s 25 kappa | kappa 1.60 271s 26 fix_omega | fix_omega 0.00 271s 27 omega | omega 0.80 271s 31 ncatG | ncatG 10.00 271s 11 getSE | getSE 0.00 271s 12 RateAncestor | RateAncestor 0.00 271s 36 Small_Diff | Small_Diff 0.00 271s 6 cleandata | cleandata 0.00 271s 8 method | method 0.00 271s CODONML in paml version 4.9j, October 2019 271s 271s ---------------------------------------------- 271s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 271s TTC | TCC | TAC | TGC 271s Leu L TTA | TCA | *** * TAA | *** * TGA 271s TTG | TCG | TAG | Trp W TGG 271s ---------------------------------------------- 271s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 271s CTC | CCC | CAC | CGC 271s CTA | CCA | Gln Q CAA | CGA 271s CTG | CCG | CAG | CGG 271s ---------------------------------------------- 271s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 271s ATC | ACC | AAC | AGC 271s ATA | ACA | Lys K AAA | Arg R AGA 271s Met M ATG | ACG | AAG | AGG 271s ---------------------------------------------- 271s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 271s GTC | GCC | GAC | GGC 271s GTA | GCA | Glu E GAA | GGA 271s GTG | GCG | GAG | GGG 271s ---------------------------------------------- 271s Nice code, uuh? 271s 271s 271s Ambiguity character definition table: 271s 271s T (1): T 271s C (1): C 271s A (1): A 271s G (1): G 271s U (1): T 271s Y (2): T C 271s R (2): A G 271s M (2): C A 271s K (2): T G 271s S (2): C G 271s W (2): T A 271s H (3): T C A 271s B (3): T C G 271s V (3): C A G 271s D (3): T A G 271s - (4): T C A G 271s N (4): T C A G 271s ? (4): T C A G 271s ns = 25 ls = 405 271s Reading sequences, sequential format.. 271s Reading seq # 1: __1_H._rufescens 271s Reading seq # 2: __2_H._sorenseni 271s Reading seq # 3: __3_H._walallensis 271s Reading seq # 4: __4_H._kamtschatkana 271s Reading seq # 5: __5_H._sieboldii 271s Reading seq # 6: __6_H._discus_hannai 271s Reading seq # 7: __7_H._gigantea 271s Reading seq # 8: __8_H._corrugata 271s Reading seq # 9: __9_H._cracherodii 271s Reading seq #10: _10_H._fulgens 271s Reading seq #11: _11_H._roei 271s Reading seq #12: _12_H._scalaris 271s Reading seq #13: _13_H._laevigata 271s Reading seq #14: _14_H._cyclobates 271s Reading seq #15: _15_H._rubra 271s Reading seq #16: _16_H._conicopora 271s Reading seq #17: _17_H._pustulata 271s Reading seq #18: _18_H._midae 271s Reading seq #19: _19_H._ovina 271s Reading seq #20: _20_H._diversicolor 271s Reading seq #21: _21_H._varia 271s Reading seq #22: _22_H._australis 271s Reading seq #23: _23_H._t.tuberculata 271s Reading seq #24: _24_H._t.coccinea 271s Reading seq #25: _25_H._iris 271s 271s Sequences read.. 271s Counting site patterns.. 0:00 271s Compressing, 132 patterns at 135 / 135 sites (100.0%), 0:00 271s Collecting fpatt[] & pose[], 132 patterns at 135 / 135 sites (100.0%), 0:00 271s 1 ambiguous codons are seen in the data: 271s --- 271s Counting codons.. 271s 271s 2400 bytes for distance 271s 128832 bytes for conP 271s 3168 bytes for fhK 271s 5000000 bytes for space 271s 271s TREE # 1 271s ((10, (((4, (1, (2, 3))), (5, (6, 7))), (8, 9))), 25, ((17, (24, 23)), (22, ((18, ((11, (12, 13)), (14, (15, 16)))), ((19, 21), 20))))); MP score: -1 271s 1481568 bytes for conP, adjusted 271s 271s initial w for M2:NSpselection reset. 271s 320s 0.066922 0.025590 0.028818 0.024661 0.010989 0.039139 0.025602 0.030946 0.100992 0.034148 0.015895 0.076528 0.018204 0.031715 0.072572 0.097651 0.085395 0.032936 0.077848 0.102095 0.036575 0.027541 0.035942 0.013896 0.014379 0.043059 0.068849 0.029688 0.024767 0.020448 0.012399 0.010102 0.053746 0.077121 0.104807 0.104665 0.025785 0.093324 0.034878 0.083627 0.058621 0.032778 0.092079 0.025164 0.044132 0.083546 0.035648 1.600000 1.513844 0.349900 0.380176 2.115896 320s 320s ntime & nrate & np: 47 3 52 320s 320s Bounds (np=52): 320s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 -99.000000 -99.000000 0.000001 1.000000 320s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 99.000000 99.000000 1.000000 999.000000 320s Qfactor_NS = 6.650236 320s 320s np = 52 320s lnL0 = -5253.812000 320s 320s Iterating by ming2 320s Initial: fx= 5253.812000 320s x= 0.06692 0.02559 0.02882 0.02466 0.01099 0.03914 0.02560 0.03095 0.10099 0.03415 0.01590 0.07653 0.01820 0.03172 0.07257 0.09765 0.08539 0.03294 0.07785 0.10210 0.03658 0.02754 0.03594 0.01390 0.01438 0.04306 0.06885 0.02969 0.02477 0.02045 0.01240 0.01010 0.05375 0.07712 0.10481 0.10466 0.02579 0.09332 0.03488 0.08363 0.05862 0.03278 0.09208 0.02516 0.04413 0.08355 0.03565 1.60000 1.51384 0.34990 0.38018 2.11590 320s 320s 1 h-m-p 0.0000 0.0002 5038.9629 +++ 4618.360182 m 0.0002 58 | 1/52 320s 2 h-m-p 0.0001 0.0003 512.7431 +CYYYCCCCC 4561.512829 8 0.0003 128 | 0/52 320s 3 h-m-p 0.0000 0.0000 6705.5328 ++ 4556.066643 m 0.0000 183 | 0/52 320s 4 h-m-p 0.0000 0.0000 4533.6359 ++ 4543.901690 m 0.0000 238 | 0/52 320s 5 h-m-p 0.0000 0.0001 845.9755 ++ 4530.470158 m 0.0001 293 | 1/52 320s 6 h-m-p 0.0001 0.0004 219.9192 +CYCC 4523.925651 3 0.0003 354 | 0/52 320s 7 h-m-p 0.0002 0.0008 429.1237 YCCCC 4521.717385 4 0.0001 416 | 0/52 320s 8 h-m-p 0.0000 0.0001 161.7080 ++ 4520.300595 m 0.0001 471 | 0/52 320s 9 h-m-p 0.0001 0.0007 236.9038 +YCCC 4517.906058 3 0.0003 532 | 0/52 320s 10 h-m-p 0.0001 0.0004 91.2760 +YCCC 4517.365819 3 0.0002 593 | 0/52 320s 11 h-m-p 0.0001 0.0006 81.3052 YCCC 4516.888806 3 0.0003 653 | 0/52 320s 12 h-m-p 0.0001 0.0007 108.6418 +YC 4516.198775 1 0.0004 710 | 0/52 320s 13 h-m-p 0.0006 0.0075 74.4363 +YC 4514.455973 1 0.0018 767 | 0/52 320s 14 h-m-p 0.0006 0.0032 108.8995 YCCCC 4512.787517 4 0.0012 829 | 0/52 320s 15 h-m-p 0.0008 0.0046 164.3074 YCCC 4510.675110 3 0.0012 889 | 0/52 320s 16 h-m-p 0.0006 0.0031 114.3194 YCCC 4509.228036 3 0.0011 949 | 0/52 320s 17 h-m-p 0.0016 0.0078 72.1421 CCC 4508.256123 2 0.0014 1008 | 0/52 320s 18 h-m-p 0.0020 0.0139 51.2356 YCC 4507.532538 2 0.0016 1066 | 0/52 320s 19 h-m-p 0.0016 0.0119 53.3125 CC 4506.934577 1 0.0014 1123 | 0/52 320s 20 h-m-p 0.0015 0.0152 49.3597 CCC 4506.206290 2 0.0019 1182 | 0/52 320s 21 h-m-p 0.0015 0.0096 62.6646 CCC 4505.365655 2 0.0018 1241 | 0/52 320s 22 h-m-p 0.0012 0.0061 75.8745 CCC 4504.358224 2 0.0017 1300 | 0/52 320s 23 h-m-p 0.0022 0.0112 50.6406 CCC 4503.364039 2 0.0026 1359 | 0/52 320s 24 h-m-p 0.0024 0.0181 53.0841 YCCC 4502.742959 3 0.0015 1419 | 0/52 458s 25 h-m-p 0.0014 0.0069 51.6268 CCC 4501.894568 2 0.0020 1478 | 0/52 458s 26 h-m-p 0.0020 0.0107 50.9078 YCC 4500.432230 2 0.0034 1536 | 0/52 458s 27 h-m-p 0.0012 0.0058 88.6706 CCCC 4498.977803 3 0.0018 1597 | 0/52 458s 28 h-m-p 0.0005 0.0027 121.4859 YCCC 4497.463929 3 0.0013 1657 | 0/52 458s 29 h-m-p 0.0009 0.0045 133.2887 CCCC 4495.709044 3 0.0014 1718 | 0/52 458s 30 h-m-p 0.0006 0.0031 102.0440 YCCC 4494.645130 3 0.0011 1778 | 0/52 458s 31 h-m-p 0.0019 0.0167 59.7570 YCC 4493.834503 2 0.0015 1836 | 0/52 458s 32 h-m-p 0.0014 0.0072 28.2248 YCC 4493.533725 2 0.0012 1894 | 0/52 458s 33 h-m-p 0.0015 0.0104 21.1424 CCC 4493.098327 2 0.0022 1953 | 0/52 458s 34 h-m-p 0.0016 0.0128 28.6215 YCCC 4492.237342 3 0.0030 2013 | 0/52 458s 35 h-m-p 0.0012 0.0061 53.9875 YCCC 4490.801727 3 0.0026 2073 | 0/52 458s 36 h-m-p 0.0012 0.0096 122.1024 YCCC 4488.185550 3 0.0022 2133 | 0/52 458s 37 h-m-p 0.0023 0.0115 35.8700 YCCC 4487.643935 3 0.0016 2193 | 0/52 458s 38 h-m-p 0.0028 0.0198 20.1963 CC 4486.827631 1 0.0044 2250 | 0/52 458s 39 h-m-p 0.0017 0.0187 52.7638 +CCC 4483.358650 2 0.0073 2310 | 0/52 458s 40 h-m-p 0.0018 0.0091 127.7848 YCC 4479.540558 2 0.0035 2368 | 0/52 458s 41 h-m-p 0.0015 0.0073 125.5220 CCC 4477.391430 2 0.0020 2427 | 0/52 458s 42 h-m-p 0.0028 0.0140 45.4484 YC 4476.770180 1 0.0019 2483 | 0/52 458s 43 h-m-p 0.0029 0.0147 13.4209 YC 4476.648768 1 0.0020 2539 | 0/52 458s 44 h-m-p 0.0053 0.0490 5.0091 CC 4476.622762 1 0.0018 2596 | 0/52 458s 45 h-m-p 0.0049 0.0833 1.8719 CC 4476.580949 1 0.0059 2653 | 0/52 458s 46 h-m-p 0.0042 0.0625 2.6397 +CCC 4476.112083 2 0.0184 2713 | 0/52 458s 47 h-m-p 0.0031 0.0360 15.8356 +YCCC 4474.310897 3 0.0086 2774 | 0/52 458s 48 h-m-p 0.0034 0.0171 23.2262 YC 4473.934676 1 0.0018 2830 | 0/52 458s 49 h-m-p 0.0044 0.0270 9.3777 CC 4473.869850 1 0.0017 2887 | 0/52 458s 50 h-m-p 0.0036 0.0916 4.3110 YC 4473.846716 1 0.0026 2943 | 0/52 458s 51 h-m-p 0.0067 0.1879 1.6479 YC 4473.834850 1 0.0045 2999 | 0/52 458s 52 h-m-p 0.0047 0.3034 1.5887 YC 4473.799158 1 0.0087 3055 | 0/52 458s 53 h-m-p 0.0070 0.2433 1.9568 +YC 4473.107942 1 0.0554 3112 | 0/52 458s 54 h-m-p 0.0015 0.0074 31.5797 +C 4471.889401 0 0.0059 3168 | 0/52 458s 55 h-m-p 0.1038 0.5190 0.4946 YC 4471.880298 1 0.0138 3224 | 0/52 458s 56 h-m-p 0.0091 0.3247 0.7498 ++YC 4471.264410 1 0.2028 3334 | 0/52 458s 57 h-m-p 0.0006 0.0028 33.3782 ++ 4470.761820 m 0.0028 3441 | 0/52 458s 58 h-m-p 0.5817 2.9084 0.1447 +CCC 4469.148009 2 2.2214 3501 | 0/52 458s 59 h-m-p 0.0061 0.0304 0.0911 ++ 4469.087564 m 0.0304 3608 | 1/52 458s 60 h-m-p 0.0074 0.0370 0.2547 ++ 4468.886020 m 0.0370 3715 | 2/52 458s 61 h-m-p 0.0441 6.2459 0.2139 ++YCCC 4465.483091 3 1.4467 3828 | 2/52 458s 62 h-m-p 1.6000 8.0000 0.1169 CCC 4464.877870 2 2.5680 3937 | 2/52 458s 63 h-m-p 1.6000 8.0000 0.0636 YYC 4464.689224 2 1.3143 4044 | 1/52 458s 64 h-m-p 0.0068 0.0370 12.2023 --YC 4464.689044 1 0.0001 4152 | 1/52 458s 65 h-m-p 0.0503 8.0000 0.0171 ++YC 4464.660538 1 1.4818 4210 | 1/52 458s 66 h-m-p 1.6000 8.0000 0.0055 CC 4464.646914 1 1.8946 4318 | 1/52 458s 67 h-m-p 1.6000 8.0000 0.0046 YC 4464.634440 1 3.6059 4425 | 1/52 458s 68 h-m-p 1.6000 8.0000 0.0059 +C 4464.599247 0 6.4204 4532 | 1/52 458s 69 h-m-p 1.6000 8.0000 0.0060 YC 4464.552403 1 3.1853 4639 | 1/52 458s 70 h-m-p 1.6000 8.0000 0.0057 YC 4464.526084 1 2.5936 4746 | 1/52 458s 71 h-m-p 1.2766 8.0000 0.0116 YC 4464.513605 1 2.2526 4853 | 1/52 458s 72 h-m-p 1.3907 6.9535 0.0048 CC 4464.511672 1 1.7391 4961 | 1/52 458s 73 h-m-p 1.6000 8.0000 0.0015 C 4464.511430 0 1.5938 5067 | 1/52 458s 74 h-m-p 1.6000 8.0000 0.0005 C 4464.511389 0 1.5539 5173 | 1/52 458s 75 h-m-p 1.6000 8.0000 0.0003 C 4464.511378 0 1.6423 5279 | 1/52 458s 76 h-m-p 1.6000 8.0000 0.0001 C 4464.511376 0 1.4445 5385 | 1/52 458s 77 h-m-p 1.6000 8.0000 0.0001 C 4464.511376 0 1.5082 5491 | 1/52 458s 78 h-m-p 1.6000 8.0000 0.0000 C 4464.511376 0 1.6427 5597 | 1/52 466s 79 h-m-p 1.6000 8.0000 0.0000 C 4464.511376 0 1.6676 5703 | 1/52 466s 80 h-m-p 1.6000 8.0000 0.0000 C 4464.511376 0 1.6000 5809 | 1/52 466s 81 h-m-p 1.6000 8.0000 0.0000 ---------------Y 4464.511376 0 0.0000 5930 466s Out.. 466s lnL = -4464.511376 466s 5931 lfun, 23724 eigenQcodon, 836271 P(t) 466s 466s Collecting RasMol commands for coloring structure into RasMol.txt 466s Choose color scheme (0: 5 colors, 1: white->red, 2: rainbow) darkblue [2,2,120] mean_w < 0.62619 466s lightblue [133,57,240] mean_w < 1.25239 466s purple [186,60,200] mean_w < 1.87858 466s pinkred [200,60,160] mean_w < 2.50477 466s red [250,5,5] mean_w < 3.13097 466s 466s BEBing (dim = 4). This may take several minutes. 466s Calculating f(x_h|w): 10 categories 21 w sets. 466s S10 w log{f(x|w)}: 0.0500 -46.233224 466s S10 w log{f(x|w)}: 0.1500 -39.238122 466s S10 w log{f(x|w)}: 0.2500 -36.352917 466s S10 w log{f(x|w)}: 0.3500 -34.683528 466s S10 w log{f(x|w)}: 0.4500 -33.605538 466s S10 w log{f(x|w)}: 0.5500 -32.877305 466s S10 w log{f(x|w)}: 0.6500 -32.379594 466s S10 w log{f(x|w)}: 0.7500 -32.044720 466s S10 w log{f(x|w)}: 0.8500 -31.830536 466s S10 w log{f(x|w)}: 0.9500 -31.709002 466s S10 w log{f(x|w)}: 1.0000 -31.676620 466s S10 w log{f(x|w)}: 1.5000 -32.036253 466s S10 w log{f(x|w)}: 2.5000 -34.474326 466s S10 w log{f(x|w)}: 3.5000 -37.625642 466s S10 w log{f(x|w)}: 4.5000 -40.887850 466s S10 w log{f(x|w)}: 5.5000 -44.050751 466s S10 w log{f(x|w)}: 6.5000 -47.027389 466s S10 w log{f(x|w)}: 7.5000 -49.782038 466s S10 w log{f(x|w)}: 8.5000 -52.305219 466s S10 w log{f(x|w)}: 9.5000 -54.602289 466s S10 w log{f(x|w)}: 10.5000 -56.686719 466s Calculating f(X), the marginal likelihood. 466s log(fX) = -4474.552013 S = -4283.950698 -226.824084 466s Calculating f(w|X), posterior probabilities of site classes. 466s did 10 / 132 patterns 3:14 did 20 / 132 patterns 3:14 did 30 / 132 patterns 3:14 did 40 / 132 patterns 3:14 did 50 / 132 patterns 3:14 did 60 / 132 patterns 3:14 did 70 / 132 patterns 3:14 did 80 / 132 patterns 3:14 did 90 / 132 patterns 3:14 did 100 / 132 patterns 3:14 did 110 / 132 patterns 3:14 did 120 / 132 patterns 3:14 did 130 / 132 patterns 3:14 did 132 / 132 patterns 3:14 466s Time used: 3:14 466s Passed 466s 466s Test 3 466s 466s CODONML in paml version 4.9j, October 2019 466s 466s ---------------------------------------------- 466s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 466s TTC | TCC | TAC | TGC 466s Leu L TTA | TCA | *** * TAA | *** * TGA 466s TTG | TCG | TAG | Trp W TGG 466s ---------------------------------------------- 466s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 466s CTC | CCC | CAC | CGC 466s CTA | CCA | Gln Q CAA | CGA 466s CTG | CCG | CAG | CGG 466s ---------------------------------------------- 466s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 466s ATC | ACC | AAC | AGC 466s ATA | ACA | Lys K AAA | Arg R AGA 466s Met M ATG | ACG | AAG | AGG 466s ---------------------------------------------- 466s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 466s GTC | GCC | GAC | GGC 466s GTA | GCA | Glu E GAA | GGA 466s GTG | GCG | GAG | GGG 466s ---------------------------------------------- 466s Nice code, uuh? 466s ns = 25 ls = 402 466s Reading sequences, sequential format.. 466s Reading seq # 1: __1_H._rufescens Reading seq # 2: __2_H._sorenseni Reading seq # 3: __3_H._walallensis Reading seq # 4: __4_H._kamtschatkana Reading seq # 5: __5_H._sieboldii Reading seq # 6: __6_H._discus_hannai Reading seq # 7: __7_H._gigantea Reading seq # 8: __8_H._corrugata Reading seq # 9: __9_H._cracherodii Reading seq #10: _10_H._fulgens Reading seq #11: _11_H._roei Reading seq #12: _12_H._scalaris Reading seq #13: _13_H._laevigata Reading seq #14: _14_H._cyclobates Reading seq #15: _15_H._rubra Reading seq #16: _16_H._conicopora Reading seq #17: _17_H._pustulata Reading seq #18: _18_H._midae Reading seq #19: _19_H._ovina Reading seq #20: _20_H._diversicolor Reading seq #21: _21_H._varia Reading seq #22: _22_H._australis Reading seq #23: _23_H._t.tuberculata Reading seq #24: _24_H._t.coccinea Reading seq #25: _25_H._iris 466s Sequences read.. 466s Counting site patterns.. 0:00 466s 466s Compressing, 132 patterns at 134 / 134 sites (100.0%), 0:00 466s 466s Collecting fpatt[] & pose[], 132 patterns at 134 / 134 sites (100.0%), 0:00 466s 1 ambiguous codons are seen in the data: 466s --- 466s Counting codons.. 466s 466s 2400 bytes for distance 466s 128832 bytes for conP 466s 13609349203701813248 bytes for fhK 466s 5000000 bytes for space 466s 466s TREE # 1 466s ((10, (((4, (1, (2, 3))), (5, (6, 7))), (8, 9))), 25, ((17, (24, 23)), (22, ((18, ((11, (12, 13)), (14, (15, 16)))), ((19, 21), 20))))); MP score: -1 466s 1481568 bytes for conP, adjusted 466s 466s 0.035162 0.038498 0.068564 0.095693 0.057780 0.024295 0.063587 0.079879 0.108713 0.107900 0.082549 0.072319 0.019908 0.011463 0.091720 0.045571 0.091924 0.044744 0.056670 0.071411 0.028038 0.081619 0.043505 0.098264 0.013162 0.100553 0.107903 0.101199 0.042284 0.049977 0.064124 0.102921 0.078104 0.074499 0.101190 0.039192 0.092552 0.012900 0.088425 0.017128 0.021890 0.053836 0.087527 0.089799 0.040066 0.010201 0.063383 1.000000 1.600000 0.800000 466s 466s ntime & nrate & np: 47 2 50 466s 466s Bounds (np=50): 466s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.010000 0.000100 0.000100 498s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 99.000000 999.000000 999.000000 498s 498s np = 50 498s lnL0 = -5336.677155 498s 498s Iterating by ming2 498s Initial: fx= 5336.677155 498s x= 0.03516 0.03850 0.06856 0.09569 0.05778 0.02430 0.06359 0.07988 0.10871 0.10790 0.08255 0.07232 0.01991 0.01146 0.09172 0.04557 0.09192 0.04474 0.05667 0.07141 0.02804 0.08162 0.04351 0.09826 0.01316 0.10055 0.10790 0.10120 0.04228 0.04998 0.06412 0.10292 0.07810 0.07450 0.10119 0.03919 0.09255 0.01290 0.08842 0.01713 0.02189 0.05384 0.08753 0.08980 0.04007 0.01020 0.06338 1.00000 1.60000 0.80000 498s 498s 1 h-m-p 0.0000 0.0003 4045.2954 +++ 4725.693126 m 0.0003 56 | 0/50 498s 2 h-m-p 0.0000 0.0001 2349.9496 CYYYCCCC 4722.996745 7 0.0000 120 | 0/50 498s 3 h-m-p 0.0000 0.0001 377.1115 ++ 4713.241788 m 0.0001 173 | 1/50 498s 4 h-m-p 0.0001 0.0013 223.3162 ++ 4686.151842 m 0.0013 226 | 1/50 498s 5 h-m-p 0.0000 0.0001 772.0856 +CYC 4683.690888 2 0.0001 283 | 1/50 498s 6 h-m-p 0.0000 0.0000 2703.4561 +YYCCC 4679.850268 4 0.0000 343 | 1/50 498s 7 h-m-p 0.0000 0.0000 2029.3254 ++ 4675.030227 m 0.0000 396 | 1/50 498s 8 h-m-p 0.0003 0.0015 267.8243 YCCC 4668.776740 3 0.0005 454 | 1/50 498s 9 h-m-p 0.0004 0.0019 184.1477 +YCYCCC 4659.687086 5 0.0010 516 | 1/50 498s 10 h-m-p 0.0002 0.0008 188.0810 ++ 4652.992108 m 0.0008 569 | 2/50 498s 11 h-m-p 0.0001 0.0006 184.3427 +YYYYYCCCCC 4645.575775 9 0.0005 636 | 2/50 498s 12 h-m-p 0.0003 0.0015 108.6146 YCCC 4642.856336 3 0.0006 694 | 1/50 498s 13 h-m-p 0.0002 0.0012 213.6231 YYCC 4641.058523 3 0.0004 751 | 1/50 498s 14 h-m-p 0.0000 0.0001 302.4504 +CC 4640.200925 1 0.0001 807 | 1/50 498s 15 h-m-p 0.0002 0.0013 160.3771 +YYC 4638.532839 2 0.0006 863 | 1/50 498s 16 h-m-p 0.0003 0.0017 77.3258 YCCC 4637.939819 3 0.0006 921 | 1/50 498s 17 h-m-p 0.0007 0.0037 33.7239 CYC 4637.722132 2 0.0007 977 | 1/50 498s 18 h-m-p 0.0013 0.0152 18.3385 CCC 4637.519546 2 0.0018 1034 | 1/50 498s 19 h-m-p 0.0015 0.0133 21.7537 YC 4637.400031 1 0.0010 1088 | 1/50 498s 20 h-m-p 0.0020 0.0354 11.4768 YC 4637.324434 1 0.0015 1142 | 1/50 498s 21 h-m-p 0.0011 0.0292 15.8531 CC 4637.242748 1 0.0012 1197 | 1/50 498s 22 h-m-p 0.0017 0.0216 11.6559 C 4637.154706 0 0.0017 1250 | 1/50 498s 23 h-m-p 0.0017 0.0404 11.1940 YC 4636.909204 1 0.0036 1304 | 1/50 498s 24 h-m-p 0.0013 0.0191 31.1520 YCC 4636.417391 2 0.0023 1360 | 1/50 498s 25 h-m-p 0.0026 0.0212 27.0374 CCC 4635.886696 2 0.0022 1417 | 1/50 498s 26 h-m-p 0.0029 0.0170 20.5597 CC 4635.314224 1 0.0024 1472 | 1/50 498s 27 h-m-p 0.0028 0.0189 17.2049 CCC 4634.256548 2 0.0033 1529 | 1/50 498s 28 h-m-p 0.0018 0.0122 31.3335 YC 4631.501277 1 0.0037 1583 | 1/50 498s 29 h-m-p 0.0009 0.0044 63.5791 YCCC 4628.670118 3 0.0019 1641 | 1/50 498s 30 h-m-p 0.0010 0.0049 35.7730 CCC 4627.624436 2 0.0016 1698 | 1/50 498s 31 h-m-p 0.0010 0.0050 40.7451 CCCC 4626.713461 3 0.0015 1757 | 1/50 498s 32 h-m-p 0.0018 0.0089 30.4982 CCC 4626.040440 2 0.0021 1814 | 1/50 498s 33 h-m-p 0.0017 0.0142 36.9850 CCC 4625.457076 2 0.0019 1871 | 1/50 498s 34 h-m-p 0.0018 0.0089 24.0546 YC 4625.292334 1 0.0012 1925 | 1/50 498s 35 h-m-p 0.0020 0.0249 13.9128 YC 4625.230356 1 0.0011 1979 | 1/50 498s 36 h-m-p 0.0023 0.0617 6.4656 CC 4625.176675 1 0.0029 2034 | 1/50 498s 37 h-m-p 0.0030 0.0753 6.3596 CC 4625.090350 1 0.0042 2089 | 1/50 498s 38 h-m-p 0.0020 0.0737 12.9837 YC 4624.900952 1 0.0039 2143 | 1/50 498s 39 h-m-p 0.0047 0.0521 10.7470 YC 4624.728420 1 0.0035 2197 | 1/50 498s 40 h-m-p 0.0035 0.0292 10.4729 CC 4624.502082 1 0.0033 2252 | 1/50 498s 41 h-m-p 0.0028 0.0168 12.4297 YCCC 4623.795300 3 0.0055 2310 | 1/50 539s 42 h-m-p 0.0036 0.0178 18.9508 CYC 4622.782123 2 0.0034 2366 | 1/50 539s 43 h-m-p 0.0013 0.0063 20.2076 ++ 4619.736527 m 0.0063 2419 | 1/50 539s 44 h-m-p 0.0000 0.0000 64.7728 539s h-m-p: 1.55818872e-20 7.79094361e-20 6.47727957e+01 4619.736527 539s .. | 1/50 539s 45 h-m-p 0.0000 0.0032 162.0409 ++YYCCC 4617.363315 4 0.0003 2530 | 1/50 539s 46 h-m-p 0.0001 0.0005 351.3199 +YYYYYCCC 4606.733358 7 0.0004 2593 | 1/50 539s 47 h-m-p 0.0000 0.0001 442.7759 ++ 4604.028872 m 0.0001 2646 | 2/50 539s 48 h-m-p 0.0002 0.0009 271.1175 +YYYC 4594.253993 3 0.0006 2703 | 1/50 539s 49 h-m-p 0.0001 0.0003 932.4961 +YCCC 4588.283525 3 0.0002 2762 | 1/50 539s 50 h-m-p 0.0001 0.0003 1008.8594 YCCC 4583.810746 3 0.0001 2820 | 1/50 539s 51 h-m-p 0.0000 0.0002 338.0224 ++ 4581.473185 m 0.0002 2873 | 1/50 539s 52 h-m-p 0.0002 0.0009 234.2280 YCCC 4579.093625 3 0.0003 2931 | 1/50 539s 53 h-m-p 0.0000 0.0002 175.9863 +YCCC 4578.507472 3 0.0001 2990 | 1/50 539s 54 h-m-p 0.0001 0.0011 138.0100 YC 4577.589181 1 0.0003 3044 | 1/50 539s 55 h-m-p 0.0002 0.0011 222.9295 YCCC 4575.775974 3 0.0004 3102 | 1/50 539s 56 h-m-p 0.0002 0.0009 241.9341 YCCC 4573.493232 3 0.0005 3160 | 1/50 539s 57 h-m-p 0.0002 0.0008 267.5581 CCC 4572.606307 2 0.0002 3217 | 1/50 539s 58 h-m-p 0.0008 0.0038 64.1725 YYC 4572.068816 2 0.0006 3272 | 1/50 539s 59 h-m-p 0.0003 0.0016 40.9918 CC 4571.926162 1 0.0003 3327 | 1/50 539s 60 h-m-p 0.0002 0.0072 69.5021 CCC 4571.765980 2 0.0003 3384 | 1/50 539s 61 h-m-p 0.0005 0.0041 37.5197 CCC 4571.541241 2 0.0008 3441 | 1/50 539s 62 h-m-p 0.0014 0.0109 21.1909 YC 4571.446413 1 0.0007 3495 | 1/50 539s 63 h-m-p 0.0014 0.0145 10.9318 CYC 4571.366000 2 0.0012 3551 | 1/50 539s 64 h-m-p 0.0011 0.0336 12.1237 CYC 4571.258611 2 0.0012 3607 | 1/50 539s 65 h-m-p 0.0007 0.0065 22.2491 +YCC 4570.841923 2 0.0019 3664 | 1/50 539s 66 h-m-p 0.0007 0.0079 63.3001 YC 4569.939595 1 0.0013 3718 | 1/50 539s 67 h-m-p 0.0008 0.0040 66.6876 CCC 4569.192994 2 0.0009 3775 | 1/50 539s 68 h-m-p 0.0008 0.0039 61.0056 YC 4567.957995 1 0.0015 3829 | 1/50 539s 69 h-m-p 0.0007 0.0036 52.7668 CC 4567.281242 1 0.0008 3884 | 1/50 539s 70 h-m-p 0.0021 0.0132 21.4953 YCC 4566.650865 2 0.0016 3940 | 1/50 539s 71 h-m-p 0.0010 0.0091 33.4531 YC 4565.377529 1 0.0018 3994 | 1/50 539s 72 h-m-p 0.0006 0.0029 77.1599 YCCCC 4563.305724 4 0.0012 4054 | 1/50 539s 73 h-m-p 0.0001 0.0007 110.3783 ++ 4561.302670 m 0.0007 4107 | 1/50 539s 74 h-m-p 0.0000 0.0000 128.7484 539s h-m-p: 1.17720348e-20 5.88601738e-20 1.28748382e+02 4561.302670 539s .. | 1/50 539s 75 h-m-p 0.0000 0.0008 110.2732 ++CYC 4560.406655 2 0.0002 4215 | 1/50 539s 76 h-m-p 0.0000 0.0001 227.6426 +YCYC 4559.670125 3 0.0001 4273 | 1/50 539s 77 h-m-p 0.0000 0.0001 405.5851 YCCCC 4558.672586 4 0.0001 4333 | 1/50 539s 78 h-m-p 0.0000 0.0001 94.9742 ++ 4558.321345 m 0.0001 4386 | 1/50 539s 79 h-m-p 0.0001 0.0006 124.5115 +YYCC 4557.620087 3 0.0003 4444 | 1/50 539s 80 h-m-p 0.0001 0.0005 135.0714 +YC 4556.928745 1 0.0003 4499 | 1/50 539s 81 h-m-p 0.0002 0.0009 141.1391 CCC 4556.558417 2 0.0002 4556 | 1/50 539s 82 h-m-p 0.0002 0.0009 105.6589 CCCC 4556.209001 3 0.0002 4615 | 1/50 539s 83 h-m-p 0.0002 0.0020 146.1110 YC 4555.551310 1 0.0004 4669 | 1/50 539s 84 h-m-p 0.0002 0.0009 154.7753 CCC 4555.193787 2 0.0002 4726 | 1/50 539s 85 h-m-p 0.0003 0.0026 112.6198 YCCC 4554.430260 3 0.0006 4784 | 1/50 539s 86 h-m-p 0.0005 0.0039 148.8921 CCC 4553.899257 2 0.0004 4841 | 1/50 539s 87 h-m-p 0.0001 0.0006 281.7574 CCCC 4553.269193 3 0.0002 4900 | 1/50 539s 88 h-m-p 0.0004 0.0026 150.8114 YCCC 4552.215934 3 0.0008 4958 | 1/50 539s 89 h-m-p 0.0001 0.0007 196.8840 YCCCC 4551.659248 4 0.0003 5018 | 1/50 539s 90 h-m-p 0.0003 0.0017 189.9821 YC 4551.322034 1 0.0002 5072 | 1/50 539s 91 h-m-p 0.0004 0.0026 114.2709 CCC 4550.971261 2 0.0004 5129 | 1/50 539s 92 h-m-p 0.0007 0.0035 46.2670 YC 4550.844277 1 0.0004 5183 | 1/50 539s 93 h-m-p 0.0011 0.0075 18.4535 YC 4550.799802 1 0.0005 5237 | 1/50 539s 94 h-m-p 0.0004 0.0145 24.1222 CC 4550.747242 1 0.0006 5292 | 1/50 577s 95 h-m-p 0.0005 0.0143 29.9066 YC 4550.638371 1 0.0011 5346 | 1/50 577s 96 h-m-p 0.0005 0.0086 63.2020 YCC 4550.465981 2 0.0008 5402 | 1/50 577s 97 h-m-p 0.0008 0.0075 65.3414 YC 4550.364014 1 0.0005 5456 | 1/50 577s 98 h-m-p 0.0014 0.0152 23.7906 CC 4550.340042 1 0.0004 5511 | 1/50 577s 99 h-m-p 0.0015 0.0510 6.1457 YC 4550.330250 1 0.0009 5565 | 1/50 577s 100 h-m-p 0.0014 0.0436 3.9334 CC 4550.327549 1 0.0006 5620 | 1/50 577s 101 h-m-p 0.0008 0.0789 2.7517 YC 4550.322611 1 0.0019 5674 | 1/50 577s 102 h-m-p 0.0007 0.0846 7.4158 C 4550.317482 0 0.0008 5727 | 1/50 577s 103 h-m-p 0.0021 0.1257 2.7865 CC 4550.315716 1 0.0008 5782 | 1/50 577s 104 h-m-p 0.0014 0.1046 1.5161 YC 4550.314472 1 0.0009 5836 | 1/50 577s 105 h-m-p 0.0009 0.0666 1.4866 YC 4550.311024 1 0.0018 5890 | 1/50 577s 106 h-m-p 0.0015 0.0574 1.8261 YC 4550.301295 1 0.0023 5944 | 1/50 577s 107 h-m-p 0.0007 0.0150 6.0698 YC 4550.276022 1 0.0013 5998 | 1/50 577s 108 h-m-p 0.0010 0.0072 7.7333 CC 4550.233448 1 0.0013 6053 | 1/50 577s 109 h-m-p 0.0006 0.0028 13.8430 YC 4550.164428 1 0.0010 6107 | 1/50 577s 110 h-m-p 0.0003 0.0017 15.6482 +YC 4550.095465 1 0.0009 6162 | 1/50 577s 111 h-m-p 0.0002 0.0009 16.3119 +CC 4550.057930 1 0.0006 6218 | 1/50 577s 112 h-m-p 0.0002 0.0010 6.1022 +YC 4550.050133 1 0.0006 6273 | 1/50 577s 113 h-m-p 0.0002 0.0008 2.2260 +YC 4550.049083 1 0.0005 6328 | 1/50 577s 114 h-m-p 0.0003 0.0015 1.1970 C 4550.048816 0 0.0004 6381 | 1/50 577s 115 h-m-p 0.0021 0.6231 0.2574 YC 4550.048713 1 0.0012 6435 | 1/50 577s 116 h-m-p 0.0011 0.5680 0.2837 +Y 4550.048061 0 0.0037 6538 | 1/50 577s 117 h-m-p 0.0009 0.2985 1.1347 +YC 4550.039178 1 0.0079 6642 | 1/50 577s 118 h-m-p 0.0004 0.0331 20.8314 +YC 4550.011919 1 0.0013 6697 | 1/50 577s 119 h-m-p 0.0026 0.0357 10.4970 YC 4550.006895 1 0.0005 6751 | 1/50 577s 120 h-m-p 0.0010 0.0664 5.0573 YC 4550.004596 1 0.0006 6805 | 1/50 577s 121 h-m-p 0.0035 0.0276 0.8033 Y 4550.004428 0 0.0006 6858 | 1/50 577s 122 h-m-p 0.0043 0.7120 0.1141 C 4550.004398 0 0.0015 6960 | 1/50 577s 123 h-m-p 0.0032 1.6188 0.1670 YC 4550.004043 1 0.0062 7063 | 1/50 577s 124 h-m-p 0.0012 0.1245 0.8354 ++C 4549.996205 0 0.0187 7167 | 1/50 577s 125 h-m-p 0.0036 0.0178 3.6271 YC 4549.995193 1 0.0006 7270 | 1/50 577s 126 h-m-p 0.0130 0.2036 0.1795 -C 4549.995177 0 0.0009 7324 | 1/50 577s 127 h-m-p 0.0494 8.0000 0.0034 ++C 4549.994745 0 0.7484 7428 | 1/50 577s 128 h-m-p 1.6000 8.0000 0.0007 Y 4549.994728 0 0.7904 7530 | 1/50 577s 129 h-m-p 1.6000 8.0000 0.0001 Y 4549.994728 0 0.7474 7632 | 1/50 577s 130 h-m-p 1.6000 8.0000 0.0000 Y 4549.994728 0 0.7758 7734 | 1/50 577s 131 h-m-p 1.6000 8.0000 0.0000 Y 4549.994728 0 0.7003 7836 | 1/50 577s 132 h-m-p 1.6000 8.0000 0.0000 Y 4549.994728 0 0.4000 7938 | 1/50 577s 133 h-m-p 0.6675 8.0000 0.0000 C 4549.994728 0 0.6675 8040 | 1/50 577s 134 h-m-p 1.6000 8.0000 0.0000 ------Y 4549.994728 0 0.0001 8148 577s Out.. 577s lnL = -4549.994728 577s 8149 lfun, 8149 eigenQcodon, 766006 P(t) 577s 577s Time used: 1:52 577s Passed 577s 577s Test 4 578s 578s CODONML in paml version 4.9j, October 2019 578s 578s ---------------------------------------------- 578s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 578s TTC | TCC | TAC | TGC 578s Leu L TTA | TCA | *** * TAA | *** * TGA 578s TTG | TCG | TAG | Trp W TGG 578s ---------------------------------------------- 578s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 578s CTC | CCC | CAC | CGC 578s CTA | CCA | Gln Q CAA | CGA 578s CTG | CCG | CAG | CGG 578s ---------------------------------------------- 578s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 578s ATC | ACC | AAC | AGC 578s ATA | ACA | Lys K AAA | Arg R AGA 578s Met M ATG | ACG | AAG | AGG 578s ---------------------------------------------- 578s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 578s GTC | GCC | GAC | GGC 578s GTA | GCA | Glu E GAA | GGA 578s GTG | GCG | GAG | GGG 578s ---------------------------------------------- 578s Nice code, uuh? 578s ns = 7 ls = 390 578s Reading sequences, sequential format.. 578s Reading seq # 1: Hsa_Human Reading seq # 2: Hla_gibbon Reading seq # 3: Cgu/Can_colobus Reading seq # 4: Pne_langur Reading seq # 5: Mmu_rhesus Reading seq # 6: Ssc_squirrelM Reading seq # 7: Cja_marmoset 578s Sequences read.. 578s Counting site patterns.. 0:00 578s Compressing, 81 patterns at 130 / 130 sites (100.0%), 0:00 578s Collecting fpatt[] & pose[], 81 patterns at 130 / 130 sites (100.0%), 0:00 578s Counting codons.. 578s 578s 168 bytes for distance 578s 79056 bytes for conP 578s 4995164145716396288 bytes for fhK 578s 5000000 bytes for space 578s 578s 2 branch types are in tree. Stop if wrong. 578s TREE # 1 578s ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 578s 197640 bytes for conP, adjusted 578s 578s 0.019034 0.078896 0.021824 0.013329 0.022824 0.084138 0.044809 0.047908 0.108494 0.062061 0.026697 0.987053 1.147363 0.818198 578s 578s ntime & nrate & np: 11 3 14 578s 578s Bounds (np=14): 578s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 578s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 578s 578s np = 14 578s lnL0 = -942.004871 578s 578s Iterating by ming2 578s Initial: fx= 942.004871 578s x= 0.01903 0.07890 0.02182 0.01333 0.02282 0.08414 0.04481 0.04791 0.10849 0.06206 0.02670 0.98705 1.14736 0.81820 578s 578s 1 h-m-p 0.0000 0.0010 438.0589 ++YYCCC 930.608665 4 0.0002 27 | 0/14 578s 2 h-m-p 0.0002 0.0008 118.5975 +YCYCCC 926.700112 5 0.0005 53 | 0/14 578s 3 h-m-p 0.0003 0.0017 50.9153 CCC 926.316117 2 0.0004 74 | 0/14 578s 4 h-m-p 0.0003 0.0036 53.9674 +YCCC 925.627831 3 0.0009 97 | 0/14 578s 5 h-m-p 0.0004 0.0043 121.2464 +CYCCC 922.667607 4 0.0019 122 | 0/14 578s 6 h-m-p 0.0005 0.0037 488.2747 +YYYCC 912.570349 4 0.0019 145 | 0/14 578s 7 h-m-p 0.0003 0.0014 605.3636 CCC 909.830856 2 0.0004 166 | 0/14 578s 8 h-m-p 0.0004 0.0020 164.2954 CCCCC 908.965227 4 0.0005 191 | 0/14 578s 9 h-m-p 0.0017 0.0084 22.5573 CYC 908.891504 2 0.0005 211 | 0/14 578s 10 h-m-p 0.0006 0.0076 19.3466 CYC 908.840956 2 0.0005 231 | 0/14 578s 11 h-m-p 0.0036 0.0514 2.8271 CC 908.836338 1 0.0010 250 | 0/14 578s 12 h-m-p 0.0005 0.0597 6.4355 ++YCC 908.785974 2 0.0055 272 | 0/14 578s 13 h-m-p 0.0005 0.0273 77.6861 ++YYCC 908.209547 3 0.0052 295 | 0/14 578s 14 h-m-p 0.0325 0.7197 12.5493 +CYCCC 906.393776 4 0.1487 320 | 0/14 578s 15 h-m-p 1.6000 8.0000 0.5379 CCCC 904.871871 3 2.1950 343 | 0/14 578s 16 h-m-p 0.9662 4.8311 0.6572 CCCCC 903.950624 4 1.4463 382 | 0/14 578s 17 h-m-p 1.6000 8.0000 0.5232 CCC 903.624162 2 1.4463 417 | 0/14 578s 18 h-m-p 1.5902 8.0000 0.4759 CCC 903.502203 2 2.1302 452 | 0/14 578s 19 h-m-p 1.6000 8.0000 0.1753 CC 903.480782 1 1.8480 485 | 0/14 578s 20 h-m-p 1.6000 8.0000 0.1083 YC 903.466591 1 2.9887 517 | 0/14 581s 21 h-m-p 1.6000 8.0000 0.0831 +CC 903.448985 1 5.5497 551 | 0/14 581s 22 h-m-p 1.4151 8.0000 0.3259 ++ 903.354889 m 8.0000 582 | 0/14 581s 23 h-m-p 1.0546 8.0000 2.4721 +YCCC 903.245842 3 3.2251 619 | 0/14 581s 24 h-m-p 1.6000 8.0000 2.4396 CC 903.197638 1 2.0378 638 | 0/14 581s 25 h-m-p 1.5771 8.0000 3.1524 +YCC 903.154354 2 4.9563 659 | 0/14 581s 26 h-m-p 1.6000 8.0000 5.6583 CC 903.130118 1 2.2625 678 | 0/14 581s 27 h-m-p 1.6000 8.0000 7.3046 +YC 903.110691 1 4.5245 697 | 0/14 581s 28 h-m-p 1.6000 8.0000 12.2865 CC 903.099652 1 2.2801 716 | 0/14 581s 29 h-m-p 1.6000 8.0000 16.2347 +YC 903.090857 1 4.3448 735 | 0/14 581s 30 h-m-p 1.6000 8.0000 27.0670 CC 903.085776 1 2.2160 754 | 0/14 581s 31 h-m-p 1.6000 8.0000 35.3296 +YC 903.081767 1 4.1595 773 | 0/14 581s 32 h-m-p 1.6000 8.0000 57.7767 CC 903.079335 1 2.3250 792 | 0/14 581s 33 h-m-p 1.2488 6.2440 75.9893 +CC 903.077366 1 4.3995 812 | 0/14 581s 34 h-m-p 0.2221 1.1106 126.2100 ++ 903.076582 m 1.1106 829 | 1/14 581s 35 h-m-p 1.6000 8.0000 0.0022 YC 903.076552 1 1.0019 847 | 1/14 581s 36 h-m-p 1.6000 8.0000 0.0001 Y 903.076551 0 1.2762 877 | 1/14 581s 37 h-m-p 1.6000 8.0000 0.0000 C 903.076551 0 1.3792 907 | 1/14 581s 38 h-m-p 1.6000 8.0000 0.0000 -C 903.076551 0 0.1000 938 581s Out.. 581s lnL = -903.076551 581s 939 lfun, 1878 eigenQcodon, 10329 P(t) 581s 581s 2 branch types are in tree. Stop if wrong. 581s TREE # 2 581s ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 581s 0.044597 0.070099 0.065551 0.096406 0.017510 0.099761 0.102292 0.098162 0.061329 0.049923 0.062782 0.859499 1.152147 0.814455 581s 581s ntime & nrate & np: 11 3 14 581s 581s Bounds (np=14): 581s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 581s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 581s 581s np = 14 581s lnL0 = -952.912663 581s 581s Iterating by ming2 581s Initial: fx= 952.912663 581s x= 0.04460 0.07010 0.06555 0.09641 0.01751 0.09976 0.10229 0.09816 0.06133 0.04992 0.06278 0.85950 1.15215 0.81445 581s 581s 1 h-m-p 0.0000 0.0009 322.4709 +++YYCCC 936.224387 4 0.0005 28 | 0/14 581s 2 h-m-p 0.0001 0.0007 135.8984 +YYCCCC 931.818526 5 0.0005 54 | 0/14 581s 3 h-m-p 0.0002 0.0009 72.2621 CCC 931.381979 2 0.0002 75 | 0/14 581s 4 h-m-p 0.0003 0.0043 58.7046 +YYC 930.414047 2 0.0010 95 | 0/14 581s 5 h-m-p 0.0004 0.0049 161.5944 +CCCC 925.689930 3 0.0020 119 | 0/14 581s 6 h-m-p 0.0006 0.0032 282.3812 CCCC 922.175199 3 0.0010 142 | 0/14 581s 7 h-m-p 0.0002 0.0011 490.2301 YCYCCC 917.420707 5 0.0006 167 | 0/14 581s 8 h-m-p 0.0003 0.0017 235.0551 YCCCCC 914.931407 5 0.0007 193 | 0/14 581s 9 h-m-p 0.0003 0.0014 373.6758 CYCCC 912.082635 4 0.0005 217 | 0/14 581s 10 h-m-p 0.0010 0.0050 24.5672 YCC 912.005582 2 0.0004 237 | 0/14 581s 11 h-m-p 0.0009 0.0215 11.0435 +YCC 911.875892 2 0.0027 258 | 0/14 581s 12 h-m-p 0.0003 0.0082 91.5176 +YCYCCC 910.464086 5 0.0030 284 | 0/14 581s 13 h-m-p 0.0011 0.0056 46.0394 YC 910.384345 1 0.0004 302 | 0/14 581s 14 h-m-p 0.0060 1.7207 3.4615 +++YCCC 906.601637 3 0.6864 327 | 0/14 581s 15 h-m-p 0.7978 3.9889 0.6557 CCCC 904.276135 3 1.0990 350 | 0/14 581s 16 h-m-p 0.9697 4.8485 0.5850 CCCC 903.003420 3 1.1470 387 | 0/14 581s 17 h-m-p 1.6000 8.0000 0.3436 CYC 902.406160 2 1.6393 421 | 0/14 581s 18 h-m-p 1.4136 8.0000 0.3985 CYCC 901.929209 3 1.9314 457 | 0/14 581s 19 h-m-p 1.6000 8.0000 0.4450 CCC 901.686887 2 1.3424 492 | 0/14 581s 20 h-m-p 1.6000 8.0000 0.2522 YCC 901.641836 2 1.2535 526 | 0/14 581s 21 h-m-p 1.6000 8.0000 0.1063 YC 901.637241 1 1.0132 558 | 0/14 581s 22 h-m-p 1.6000 8.0000 0.0472 YC 901.636537 1 1.1059 590 | 0/14 581s 23 h-m-p 1.6000 8.0000 0.0202 +YC 901.635946 1 4.3627 623 | 0/14 582s 24 h-m-p 1.4717 8.0000 0.0599 ++ 901.632574 m 8.0000 654 | 0/14 582s 25 h-m-p 1.6000 8.0000 0.1144 C 901.631048 0 1.7374 685 | 0/14 582s 26 h-m-p 1.6000 8.0000 0.0440 YC 901.630901 1 1.2770 717 | 0/14 582s 27 h-m-p 1.6000 8.0000 0.0063 C 901.630891 0 1.5495 748 | 0/14 582s 28 h-m-p 1.6000 8.0000 0.0024 C 901.630891 0 1.3241 779 | 0/14 582s 29 h-m-p 1.6000 8.0000 0.0003 Y 901.630891 0 1.2219 810 | 0/14 582s 30 h-m-p 1.6000 8.0000 0.0000 Y 901.630891 0 0.8752 841 | 0/14 582s 31 h-m-p 1.6000 8.0000 0.0000 Y 901.630891 0 0.9598 872 | 0/14 582s 32 h-m-p 1.6000 8.0000 0.0000 ++ 901.630891 m 8.0000 903 | 0/14 582s 33 h-m-p 1.1163 8.0000 0.0000 --N 901.630891 0 0.0174 936 | 0/14 582s 34 h-m-p 0.0160 8.0000 0.0000 Y 901.630891 0 0.0160 967 | 0/14 582s 35 h-m-p 0.0202 8.0000 0.0000 Y 901.630891 0 0.0202 998 | 0/14 582s 36 h-m-p 0.0251 8.0000 0.0000 ---C 901.630891 0 0.0001 1032 582s Out.. 582s lnL = -901.630891 582s 1033 lfun, 2066 eigenQcodon, 11363 P(t) 582s 582s Tree comparisons (Kishino & Hasegawa 1989; Shimodaira & Hasegawa 1999) 582s Reading lnf for tree # 1 Reading lnf for tree # 2, done. 582s Calculating SEs by sitewise comparison, 0:05 582s RELL Bootstrapping.. replicate: 100 / 10000 0:05 RELL Bootstrapping.. replicate: 200 / 10000 0:05 RELL Bootstrapping.. replicate: 300 / 10000 0:05 RELL Bootstrapping.. replicate: 400 / 10000 0:05 RELL Bootstrapping.. replicate: 500 / 10000 0:05 RELL Bootstrapping.. replicate: 600 / 10000 0:05 RELL Bootstrapping.. replicate: 700 / 10000 0:05 RELL Bootstrapping.. replicate: 800 / 10000 0:05 RELL Bootstrapping.. replicate: 900 / 10000 0:05 RELL Bootstrapping.. replicate: 1000 / 10000 0:05 RELL Bootstrapping.. replicate: 1100 / 10000 0:05 RELL Bootstrapping.. replicate: 1200 / 10000 0:05 RELL Bootstrapping.. replicate: 1300 / 10000 0:05 RELL Bootstrapping.. replicate: 1400 / 10000 0:05 RELL Bootstrapping.. replicate: 1500 / 10000 0:05 RELL Bootstrapping.. replicate: 1600 / 10000 0:05 RELL Bootstrapping.. replicate: 1700 / 10000 0:05 RELL Bootstrapping.. replicate: 1800 / 10000 0:05 RELL Bootstrapping.. replicate: 1900 / 10000 0:05 RELL Bootstrapping.. replicate: 2000 / 10000 0:05 RELL Bootstrapping.. replicate: 2100 / 10000 0:05 RELL Bootstrapping.. replicate: 2200 / 10000 0:05 RELL Bootstrapping.. replicate: 2300 / 10000 0:05 RELL Bootstrapping.. replicate: 2400 / 10000 0:05 RELL Bootstrapping.. replicate: 2500 / 10000 0:05 RELL Bootstrapping.. replicate: 2600 / 10000 0:05 RELL Bootstrapping.. replicate: 2700 / 10000 0:05 RELL Bootstrapping.. replicate: 2800 / 10000 0:05 RELL Bootstrapping.. replicate: 2900 / 10000 0:05 RELL Bootstrapping.. replicate: 3000 / 10000 0:05 RELL Bootstrapping.. replicate: 3100 / 10000 0:05 RELL Bootstrapping.. replicate: 3200 / 10000 0:05 RELL Bootstrapping.. replicate: 3300 / 10000 0:05 RELL Bootstrapping.. replicate: 3400 / 10000 0:05 RELL Bootstrapping.. replicate: 3500 / 10000 0:05 RELL Bootstrapping.. replicate: 3600 / 10000 0:05 RELL Bootstrapping.. replicate: 3700 / 10000 0:05 RELL Bootstrapping.. replicate: 3800 / 10000 0:05 RELL Bootstrapping.. replicate: 3900 / 10000 0:05 RELL Bootstrapping.. replicate: 4000 / 10000 0:05 RELL Bootstrapping.. replicate: 4100 / 10000 0:05 RELL Bootstrapping.. replicate: 4200 / 10000 0:05 RELL Bootstrapping.. replicate: 4300 / 10000 0:05 RELL Bootstrapping.. replicate: 4400 / 10000 0:05 RELL Bootstrapping.. replicate: 4500 / 10000 0:05 RELL Bootstrapping.. replicate: 4600 / 10000 0:05 RELL Bootstrapping.. replicate: 4700 / 10000 0:05 RELL Bootstrapping.. replicate: 4800 / 10000 0:05 RELL Bootstrapping.. replicate: 4900 / 10000 0:05 RELL Bootstrapping.. replicate: 5000 / 10000 0:05 RELL Bootstrapping.. replicate: 5100 / 10000 0:05 RELL Bootstrapping.. replicate: 5200 / 10000 0:05 RELL Bootstrapping.. replicate: 5300 / 10000 0:05 RELL Bootstrapping.. replicate: 5400 / 10000 0:05 RELL Bootstrapping.. replicate: 5500 / 10000 0:05 RELL Bootstrapping.. replicate: 5600 / 10000 0:05 RELL Bootstrapping.. replicate: 5700 / 10000 0:05 RELL Bootstrapping.. replicate: 5800 / 10000 0:05 RELL Bootstrapping.. replicate: 5900 / 10000 0:05 RELL Bootstrapping.. replicate: 6000 / 10000 0:05 RELL Bootstrapping.. replicate: 6100 / 10000 0:05 RELL Bootstrapping.. replicate: 6200 / 10000 0:05 RELL Bootstrapping.. replicate: 6300 / 10000 0:05 RELL Bootstrapping.. replicate: 6400 / 10000 0:05 RELL Bootstrapping.. replicate: 6500 / 10000 0:05 RELL Bootstrapping.. replicate: 6600 / 10000 0:05 RELL Bootstrapping.. replicate: 6700 / 10000 0:05 RELL Bootstrapping.. replicate: 6800 / 10000 0:05 RELL Bootstrapping.. replicate: 6900 / 10000 0:05 RELL Bootstrapping.. replicate: 7000 / 10000 0:05 RELL Bootstrapping.. replicate: 7100 / 10000 0:05 RELL Bootstrapping.. replicate: 7200 / 10000 0:05 RELL Bootstrapping.. replicate: 7300 / 10000 0:05 RELL Bootstrapping.. replicate: 7400 / 10000 0:05 RELL Bootstrapping.. replicate: 7500 / 10000 0:05 RELL Bootstrapping.. replicate: 7600 / 10000 0:05 RELL Bootstrapping.. replicate: 7700 / 10000 0:05 RELL Bootstrapping.. replicate: 7800 / 10000 0:05 RELL Bootstrapping.. replicate: 7900 / 10000 0:05 RELL Bootstrapping.. replicate: 8000 / 10000 0:05 RELL Bootstrapping.. replicate: 8100 / 10000 0:05 RELL Bootstrapping.. replicate: 8200 / 10000 0:05 RELL Bootstrapping.. replicate: 8300 / 10000 0:05 RELL Bootstrapping.. replicate: 8400 / 10000 0:05 RELL Bootstrapping.. replicate: 8500 / 10000 0:05 RELL Bootstrapping.. replicate: 8600 / 10000 0:05 RELL Bootstrapping.. replicate: 8700 / 10000 0:05 RELL Bootstrapping.. replicate: 8800 / 10000 0:05 RELL Bootstrapping.. replicate: 8900 / 10000 0:05 RELL Bootstrapping.. replicate: 9000 / 10000 0:05 RELL Bootstrapping.. replicate: 9100 / 10000 0:05 RELL Bootstrapping.. replicate: 9200 / 10000 0:05 RELL Bootstrapping.. replicate: 9300 / 10000 0:05 RELL Bootstrapping.. replicate: 9400 / 10000 0:05 RELL Bootstrapping.. replicate: 9500 / 10000 0:05 RELL Bootstrapping.. replicate: 9600 / 10000 0:05 RELL Bootstrapping.. replicate: 9700 / 10000 0:05 RELL Bootstrapping.. replicate: 9800 / 10000 0:05 RELL Bootstrapping.. replicate: 9900 / 10000 0:05 RELL Bootstrapping.. replicate: 10000 / 10000 0:05 582s now doing S-H test 582s 582s Time used: 0:05 582s Passed 582s 582s Test 5 582s 582s 15 verbose | verbose 1.00 582s 7 runmode | runmode 0.00 582s 4 seqtype | seqtype 1.00 582s 13 CodonFreq | CodonFreq 2.00 582s 9 clock | clock 0.00 582s 16 model | model 2.00 582s 20 NSsites | NSsites 0.00 582s 22 icode | icode 0.00 582s 24 fix_kappa | fix_kappa 0.00 582s 25 kappa | kappa 2.00 582s 26 fix_omega | fix_omega 0.00 582s 27 omega | omega 2.00 582s 28 fix_alpha | fix_alpha 1.00 582s 29 alpha | alpha 0.00 582s 30 Malpha | Malpha 0.00 582s 31 ncatG | ncatG 4.00 582s 11 getSE | getSE 0.00 582s 12 RateAncestor | RateAncestor 0.00 582s 8 method | method 0.00 582s 37 fix_blength | fix_blength 0.00 582s CODONML in paml version 4.9j, October 2019 582s 582s ---------------------------------------------- 582s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 582s TTC | TCC | TAC | TGC 582s Leu L TTA | TCA | *** * TAA | *** * TGA 582s TTG | TCG | TAG | Trp W TGG 582s ---------------------------------------------- 582s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 582s CTC | CCC | CAC | CGC 582s CTA | CCA | Gln Q CAA | CGA 582s CTG | CCG | CAG | CGG 582s ---------------------------------------------- 582s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 582s ATC | ACC | AAC | AGC 582s ATA | ACA | Lys K AAA | Arg R AGA 582s Met M ATG | ACG | AAG | AGG 582s ---------------------------------------------- 582s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 582s GTC | GCC | GAC | GGC 582s GTA | GCA | Glu E GAA | GGA 582s GTG | GCG | GAG | GGG 582s ---------------------------------------------- 582s Nice code, uuh? 582s 582s 582s Ambiguity character definition table: 582s 582s T (1): T 582s C (1): C 582s A (1): A 582s G (1): G 582s U (1): T 582s Y (2): T C 582s R (2): A G 582s M (2): C A 582s K (2): T G 582s S (2): C G 582s W (2): T A 582s H (3): T C A 582s B (3): T C G 582s V (3): C A G 582s D (3): T A G 582s - (4): T C A G 582s N (4): T C A G 582s ? (4): T C A G 582s ns = 7 ls = 390 582s Reading sequences, sequential format.. 582s Reading seq # 1: Hsa_Human 582s Reading seq # 2: Hla_gibbon 582s Reading seq # 3: Cgu/Can_colobus 582s Reading seq # 4: Pne_langur 582s Reading seq # 5: Mmu_rhesus 582s Reading seq # 6: Ssc_squirrelM 582s Reading seq # 7: Cja_marmoset 582s 582s Sequences read.. 582s Counting site patterns.. 0:00 582s Compressing, 81 patterns at 130 / 130 sites (100.0%), 0:00 582s Collecting fpatt[] & pose[], 81 patterns at 130 / 130 sites (100.0%), 0:00 582s Counting codons.. 582s 582s 168 bytes for distance 582s 79056 bytes for conP 582s 2778373841848603904 bytes for fhK 582s 5000000 bytes for space 582s 582s 2 branch types are in tree. Stop if wrong. 582s TREE # 1 582s ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 582s 197640 bytes for conP, adjusted 582s 582s 0.094545 0.024527 0.096767 0.031792 0.027668 0.108147 0.105725 0.021084 0.084375 0.015115 0.101653 2.087568 2.202991 1.605487 582s 582s ntime & nrate & np: 11 3 14 582s 582s Bounds (np=14): 582s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 582s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 582s 582s np = 14 582s lnL0 = -937.147034 582s 582s Iterating by ming2 582s Initial: fx= 937.147034 582s x= 0.09454 0.02453 0.09677 0.03179 0.02767 0.10815 0.10572 0.02108 0.08437 0.01512 0.10165 2.08757 2.20299 1.60549 582s 582s 1 h-m-p 0.0000 0.0012 283.6710 +++YCCCC 926.086787 4 0.0004 29 | 0/14 582s 2 h-m-p 0.0001 0.0006 158.8040 +YYCCCC 920.746341 5 0.0004 55 | 0/14 582s 3 h-m-p 0.0004 0.0022 50.6992 YCCC 920.483011 3 0.0003 77 | 0/14 584s 4 h-m-p 0.0006 0.0062 21.7148 CCC 920.380026 2 0.0005 98 | 0/14 584s 5 h-m-p 0.0005 0.0074 24.1973 YCC 920.249024 2 0.0009 118 | 0/14 584s 6 h-m-p 0.0008 0.0078 24.8862 YCCC 920.055063 3 0.0015 140 | 0/14 584s 7 h-m-p 0.0004 0.0146 99.3711 ++CCCCC 916.965848 4 0.0065 167 | 0/14 584s 8 h-m-p 0.0005 0.0023 1134.1328 YCYCCC 909.232180 5 0.0013 193 | 0/14 584s 9 h-m-p 0.0003 0.0016 681.1624 CYCCCC 907.474473 5 0.0005 219 | 0/14 584s 10 h-m-p 0.0002 0.0010 125.9862 CCCCC 907.317105 4 0.0003 244 | 0/14 584s 11 h-m-p 0.0038 0.0693 8.3876 +YYYC 906.881647 3 0.0146 265 | 0/14 584s 12 h-m-p 0.0005 0.0057 226.6949 +YCCC 905.727930 3 0.0015 288 | 0/14 584s 13 h-m-p 0.0020 0.0098 75.8845 YCC 905.394485 2 0.0013 308 | 0/14 584s 14 h-m-p 0.1514 5.5428 0.6750 ++YYCCC 904.034414 4 1.8003 333 | 0/14 584s 15 h-m-p 1.6000 8.0000 0.4212 YCC 903.836672 2 1.1468 367 | 0/14 584s 16 h-m-p 1.5385 8.0000 0.3140 YC 903.725742 1 2.5934 399 | 0/14 584s 17 h-m-p 1.0973 8.0000 0.7420 YCCC 903.561562 3 2.3889 435 | 0/14 584s 18 h-m-p 1.2647 8.0000 1.4017 CCC 903.457995 2 1.0820 470 | 0/14 584s 19 h-m-p 0.9634 8.0000 1.5741 CCC 903.375807 2 1.3339 491 | 0/14 584s 20 h-m-p 1.0630 8.0000 1.9752 YCC 903.298605 2 1.7348 511 | 0/14 584s 21 h-m-p 1.4961 8.0000 2.2904 YCCC 903.232896 3 2.4683 533 | 0/14 584s 22 h-m-p 1.6000 8.0000 3.0936 YCC 903.186482 2 2.5183 553 | 0/14 584s 23 h-m-p 1.6000 8.0000 4.4043 YCC 903.152722 2 2.5849 573 | 0/14 584s 24 h-m-p 1.6000 8.0000 5.9385 YCC 903.127768 2 2.9726 593 | 0/14 584s 25 h-m-p 1.6000 8.0000 8.3589 YCC 903.110541 2 3.0866 613 | 0/14 584s 26 h-m-p 1.6000 8.0000 11.9529 YCC 903.099302 2 3.1192 633 | 0/14 584s 27 h-m-p 1.6000 8.0000 16.9800 YC 903.091511 1 3.3175 651 | 0/14 584s 28 h-m-p 1.6000 8.0000 25.3250 YC 903.085870 1 3.0802 669 | 0/14 584s 29 h-m-p 1.6000 8.0000 38.5929 YC 903.082002 1 2.9135 687 | 0/14 584s 30 h-m-p 1.6000 8.0000 51.9940 YC 903.079824 1 2.5079 705 | 0/14 584s 31 h-m-p 1.6000 8.0000 60.5425 YC 903.078440 1 3.1773 723 | 0/14 584s 32 h-m-p 0.7721 3.8603 80.4868 ++ 903.077003 m 3.8603 740 | 1/14 584s 33 h-m-p 0.8779 8.0000 0.0089 CC 903.076628 1 1.3081 759 | 1/14 584s 34 h-m-p 1.5074 8.0000 0.0077 C 903.076552 0 1.8533 789 | 1/14 584s 35 h-m-p 1.6000 8.0000 0.0001 C 903.076551 0 1.4835 819 | 1/14 584s 36 h-m-p 1.6000 8.0000 0.0000 Y 903.076551 0 1.1993 849 | 1/14 584s 37 h-m-p 1.6000 8.0000 0.0000 ----Y 903.076551 0 0.0016 883 584s Out.. 584s lnL = -903.076551 584s 884 lfun, 1768 eigenQcodon, 9724 P(t) 584s 584s d123[*] = 0.03093 0.03339 0.00627 average 0.02353 584s [B] = 0.00003 0.00003 0.00003 average 0.00003 584s accept =982.57114999.00000191.44792 584s 584s w =999.00000 dN = 0.03251 dS = 0.00003 d4 = 0.00003 (55.6 four-fold sites) 584s dN*= 0.03053 dS*= 0.00004 S* = 89.52 N* = 300.48 584s 584s d123[*] = 0.00729 0.00768 0.01045 average 0.00848 584s [B] = 0.01072 0.01138 0.01114 average 0.01108 584s accept = 0.68069 0.67535 0.93805 584s 584s w = 0.67535 dN = 0.00748 dS = 0.01108 d4 = 0.00940 (55.6 four-fold sites) 584s dN*= 0.00702 dS*= 0.01335 S* = 89.52 N* = 300.48 584s 584s d123[*] = 0.01118 0.01178 0.01602 average 0.01300 584s [B] = 0.01643 0.01744 0.01708 average 0.01699 584s accept = 0.68069 0.67535 0.93805 584s 584s w = 0.67535 dN = 0.01147 dS = 0.01699 d4 = 0.01442 (55.6 four-fold sites) 584s dN*= 0.01077 dS*= 0.02047 S* = 89.52 N* = 300.48 584s 584s d123[*] = 0.01222 0.01288 0.01751 average 0.01420 584s [B] = 0.01796 0.01907 0.01867 average 0.01856 584s accept = 0.68069 0.67535 0.93805 584s 584s w = 0.67535 dN = 0.01254 dS = 0.01856 d4 = 0.01576 (55.6 four-fold sites) 584s dN*= 0.01177 dS*= 0.02237 S* = 89.52 N* = 300.48 584s 584s d123[*] = 0.02257 0.02378 0.03234 average 0.02623 584s [B] = 0.03316 0.03521 0.03447 average 0.03428 584s accept = 0.68069 0.67535 0.93805 584s 584s w = 0.67535 dN = 0.02315 dS = 0.03428 d4 = 0.02910 (55.6 four-fold sites) 584s dN*= 0.02174 dS*= 0.04130 S* = 89.52 N* = 300.48 584s 585s d123[*] = 0.01258 0.01326 0.01803 average 0.01462 585s [B] = 0.01849 0.01963 0.01922 average 0.01911 585s accept = 0.68069 0.67535 0.93805 585s 585s w = 0.67535 dN = 0.01291 dS = 0.01911 d4 = 0.01622 (55.6 four-fold sites) 585s dN*= 0.01212 dS*= 0.02303 S* = 89.52 N* = 300.48 585s 585s d123[*] = 0.01506 0.01587 0.02158 average 0.01750 585s [B] = 0.02213 0.02350 0.02301 average 0.02288 585s accept = 0.68069 0.67535 0.93805 585s 585s w = 0.67535 dN = 0.01545 dS = 0.02288 d4 = 0.01942 (55.6 four-fold sites) 585s dN*= 0.01451 dS*= 0.02756 S* = 89.52 N* = 300.48 585s 585s d123[*] = 0.00561 0.00591 0.00803 average 0.00652 585s [B] = 0.00824 0.00875 0.00856 average 0.00852 585s accept = 0.68069 0.67535 0.93805 585s 585s w = 0.67535 dN = 0.00575 dS = 0.00852 d4 = 0.00723 (55.6 four-fold sites) 585s dN*= 0.00540 dS*= 0.01026 S* = 89.52 N* = 300.48 585s 585s d123[*] = 0.03473 0.03658 0.04976 average 0.04036 585s [B] = 0.05102 0.05417 0.05304 average 0.05274 585s accept = 0.68069 0.67535 0.93805 585s 585s w = 0.67535 dN = 0.03562 dS = 0.05274 d4 = 0.04477 (55.6 four-fold sites) 585s dN*= 0.03345 dS*= 0.06355 S* = 89.52 N* = 300.48 585s 585s d123[*] = 0.01191 0.01254 0.01706 average 0.01384 585s [B] = 0.01749 0.01857 0.01819 average 0.01808 585s accept = 0.68069 0.67535 0.93805 585s 585s w = 0.67535 dN = 0.01221 dS = 0.01808 d4 = 0.01535 (55.6 four-fold sites) 585s dN*= 0.01147 dS*= 0.02179 S* = 89.52 N* = 300.48 585s 585s d123[*] = 0.00669 0.00705 0.00958 average 0.00777 585s [B] = 0.00983 0.01043 0.01022 average 0.01016 585s accept = 0.68069 0.67535 0.93805 585s 585s w = 0.67535 dN = 0.00686 dS = 0.01016 d4 = 0.00862 (55.6 four-fold sites) 585s dN*= 0.00644 dS*= 0.01224 S* = 89.52 N* = 300.48 585s 585s 2 branch types are in tree. Stop if wrong. 585s TREE # 2 585s ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 585s 0.086512 0.100488 0.050418 0.064434 0.103029 0.031957 0.045885 0.039457 0.088476 0.088674 0.017799 2.109366 2.174928 1.669317 585s 585s ntime & nrate & np: 11 3 14 585s 585s Bounds (np=14): 585s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 585s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 585s 585s np = 14 585s lnL0 = -928.323578 585s 585s Iterating by ming2 585s Initial: fx= 928.323578 585s x= 0.08651 0.10049 0.05042 0.06443 0.10303 0.03196 0.04588 0.03946 0.08848 0.08867 0.01780 2.10937 2.17493 1.66932 585s 585s 1 h-m-p 0.0000 0.0007 154.2934 +++YYCCCC 920.915346 5 0.0005 30 | 0/14 585s 2 h-m-p 0.0001 0.0005 161.3551 YCYCCC 918.948557 5 0.0002 55 | 0/14 585s 3 h-m-p 0.0002 0.0012 48.0403 YYYC 918.711689 3 0.0002 75 | 0/14 585s 4 h-m-p 0.0006 0.0092 18.3907 CC 918.591698 1 0.0008 94 | 0/14 585s 5 h-m-p 0.0008 0.0110 20.2542 CYC 918.496185 2 0.0009 114 | 0/14 585s 6 h-m-p 0.0004 0.0145 43.7870 +CCCC 918.016565 3 0.0024 138 | 0/14 585s 7 h-m-p 0.0007 0.0084 156.5636 +CCCCC 915.477620 4 0.0033 164 | 0/14 585s 8 h-m-p 0.0006 0.0031 807.0073 +YYCYCCC 904.882346 6 0.0021 191 | 0/14 585s 9 h-m-p 0.0001 0.0006 1377.5419 CCCCC 903.948876 4 0.0001 216 | 0/14 585s 10 h-m-p 0.0010 0.0052 24.4204 YC 903.905375 1 0.0004 234 | 0/14 585s 11 h-m-p 0.0012 0.0677 8.6499 +CCC 903.786911 2 0.0045 256 | 0/14 585s 12 h-m-p 0.0008 0.0130 49.4820 +YYC 903.380150 2 0.0027 276 | 0/14 585s 13 h-m-p 0.0006 0.0060 224.6980 YCCC 902.635436 3 0.0011 298 | 0/14 585s 14 h-m-p 0.2791 8.0000 0.9056 +YYCCC 901.957860 4 1.7616 322 | 0/14 585s 15 h-m-p 1.6000 8.0000 0.5425 YCCC 901.791122 3 0.9241 358 | 0/14 585s 16 h-m-p 1.3801 8.0000 0.3632 YCC 901.711483 2 2.3264 392 | 0/14 585s 17 h-m-p 1.6000 8.0000 0.4816 CYC 901.660343 2 1.8203 426 | 0/14 585s 18 h-m-p 1.6000 8.0000 0.4748 CC 901.638489 1 1.4052 459 | 0/14 585s 19 h-m-p 1.6000 8.0000 0.3201 C 901.632071 0 1.7684 490 | 0/14 586s 20 h-m-p 1.6000 8.0000 0.1112 C 901.631185 0 1.6000 521 | 0/14 586s 21 h-m-p 1.6000 8.0000 0.0437 C 901.630949 0 1.8755 552 | 0/14 586s 22 h-m-p 1.6000 8.0000 0.0138 C 901.630899 0 1.6628 583 | 0/14 586s 23 h-m-p 1.6000 8.0000 0.0135 C 901.630891 0 1.4877 614 | 0/14 586s 24 h-m-p 1.6000 8.0000 0.0013 C 901.630891 0 1.2916 645 | 0/14 586s 25 h-m-p 1.6000 8.0000 0.0006 Y 901.630891 0 0.9481 676 | 0/14 586s 26 h-m-p 1.6000 8.0000 0.0000 C 901.630891 0 1.3432 707 | 0/14 586s 27 h-m-p 1.6000 8.0000 0.0000 Y 901.630891 0 0.2146 738 | 0/14 586s 28 h-m-p 0.2558 8.0000 0.0000 Y 901.630891 0 0.0639 769 | 0/14 586s 29 h-m-p 0.0633 8.0000 0.0000 Y 901.630891 0 0.0158 800 | 0/14 586s 30 h-m-p 0.0215 8.0000 0.0000 ---Y 901.630891 0 0.0001 834 586s Out.. 586s lnL = -901.630891 586s 835 lfun, 1670 eigenQcodon, 9185 P(t) 586s 586s d123[*] = 0.03023 0.03255 0.00961 average 0.02413 586s [B] = 0.00422 0.00448 0.00439 average 0.00436 586s accept = 7.16054 7.26349 2.18932 586s 586s w = 7.26349 dN = 0.03170 dS = 0.00436 d4 = 0.00370 (55.6 four-fold sites) 586s dN*= 0.02975 dS*= 0.00526 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.00673 0.00705 0.01167 average 0.00848 586s [B] = 0.01230 0.01306 0.01279 average 0.01272 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.00686 dS = 0.01272 d4 = 0.01079 (55.6 four-fold sites) 586s dN*= 0.00644 dS*= 0.01534 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.01033 0.01081 0.01791 average 0.01302 586s [B] = 0.01888 0.02004 0.01962 average 0.01951 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.01053 dS = 0.01951 d4 = 0.01656 (55.6 four-fold sites) 586s dN*= 0.00988 dS*= 0.02353 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.01145 0.01199 0.01985 average 0.01443 586s [B] = 0.02093 0.02221 0.02175 average 0.02163 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.01167 dS = 0.02163 d4 = 0.01835 (55.6 four-fold sites) 586s dN*= 0.01096 dS*= 0.02608 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.03422 0.03684 0.01087 average 0.02731 586s [B] = 0.00478 0.00507 0.00497 average 0.00494 586s accept = 7.16054 7.26349 2.18932 586s 586s w = 7.26349 dN = 0.03588 dS = 0.00494 d4 = 0.00419 (55.6 four-fold sites) 586s dN*= 0.03367 dS*= 0.00596 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.01165 0.01220 0.02020 average 0.01468 586s [B] = 0.02130 0.02261 0.02213 average 0.02201 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.01188 dS = 0.02201 d4 = 0.01868 (55.6 four-fold sites) 586s dN*= 0.01115 dS*= 0.02655 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.01377 0.01441 0.02386 average 0.01735 586s [B] = 0.02516 0.02671 0.02615 average 0.02601 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.01403 dS = 0.02601 d4 = 0.02207 (55.6 four-fold sites) 586s dN*= 0.01317 dS*= 0.03136 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.00457 0.00478 0.00792 average 0.00576 586s [B] = 0.00835 0.00886 0.00868 average 0.00863 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.00466 dS = 0.00863 d4 = 0.00732 (55.6 four-fold sites) 586s dN*= 0.00437 dS*= 0.01041 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.03179 0.03327 0.05509 average 0.04005 586s [B] = 0.05809 0.06166 0.06037 average 0.06004 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.03240 dS = 0.06004 d4 = 0.05095 (55.6 four-fold sites) 586s dN*= 0.03041 dS*= 0.07241 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.01108 0.01160 0.01920 average 0.01396 586s [B] = 0.02025 0.02149 0.02104 average 0.02093 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.01129 dS = 0.02093 d4 = 0.01776 (55.6 four-fold sites) 586s dN*= 0.01060 dS*= 0.02524 S* = 89.52 N* = 300.48 586s 586s d123[*] = 0.00611 0.00639 0.01059 average 0.00770 586s [B] = 0.01116 0.01185 0.01160 average 0.01154 586s accept = 0.54721 0.53964 0.91259 586s 586s w = 0.53964 dN = 0.00623 dS = 0.01154 d4 = 0.00979 (55.6 four-fold sites) 586s dN*= 0.00584 dS*= 0.01392 S* = 89.52 N* = 300.48 586s 586s Tree comparisons (Kishino & Hasegawa 1989; Shimodaira & Hasegawa 1999) 586s Reading lnf for tree # 1 Reading lnf for tree # 2, done. 586s Calculating SEs by sitewise comparison, 0:04 586s RELL Bootstrapping.. replicate: 100 / 10000 0:04 RELL Bootstrapping.. replicate: 200 / 10000 0:04 RELL Bootstrapping.. replicate: 300 / 10000 0:04 RELL Bootstrapping.. replicate: 400 / 10000 0:04 RELL Bootstrapping.. replicate: 500 / 10000 0:04 RELL Bootstrapping.. replicate: 600 / 10000 0:04 RELL Bootstrapping.. replicate: 700 / 10000 0:04 RELL Bootstrapping.. replicate: 800 / 10000 0:04 RELL Bootstrapping.. replicate: 900 / 10000 0:04 RELL Bootstrapping.. replicate: 1000 / 10000 0:04 RELL Bootstrapping.. replicate: 1100 / 10000 0:04 RELL Bootstrapping.. replicate: 1200 / 10000 0:04 RELL Bootstrapping.. replicate: 1300 / 10000 0:04 RELL Bootstrapping.. replicate: 1400 / 10000 0:04 RELL Bootstrapping.. replicate: 1500 / 10000 0:04 RELL Bootstrapping.. replicate: 1600 / 10000 0:04 RELL Bootstrapping.. replicate: 1700 / 10000 0:04 RELL Bootstrapping.. replicate: 1800 / 10000 0:04 RELL Bootstrapping.. replicate: 1900 / 10000 0:04 RELL Bootstrapping.. replicate: 2000 / 10000 0:04 RELL Bootstrapping.. replicate: 2100 / 10000 0:04 RELL Bootstrapping.. replicate: 2200 / 10000 0:04 RELL Bootstrapping.. replicate: 2300 / 10000 0:04 RELL Bootstrapping.. replicate: 2400 / 10000 0:04 RELL Bootstrapping.. replicate: 2500 / 10000 0:04 RELL Bootstrapping.. replicate: 2600 / 10000 0:04 RELL Bootstrapping.. replicate: 2700 / 10000 0:04 RELL Bootstrapping.. replicate: 2800 / 10000 0:04 RELL Bootstrapping.. replicate: 2900 / 10000 0:04 RELL Bootstrapping.. replicate: 3000 / 10000 0:04 RELL Bootstrapping.. replicate: 3100 / 10000 0:04 RELL Bootstrapping.. replicate: 3200 / 10000 0:04 RELL Bootstrapping.. replicate: 3300 / 10000 0:04 RELL Bootstrapping.. replicate: 3400 / 10000 0:04 RELL Bootstrapping.. replicate: 3500 / 10000 0:04 RELL Bootstrapping.. replicate: 3600 / 10000 0:04 RELL Bootstrapping.. replicate: 3700 / 10000 0:04 RELL Bootstrapping.. replicate: 3800 / 10000 0:04 RELL Bootstrapping.. replicate: 3900 / 10000 0:04 RELL Bootstrapping.. replicate: 4000 / 10000 0:04 RELL Bootstrapping.. replicate: 4100 / 10000 0:04 RELL Bootstrapping.. replicate: 4200 / 10000 0:04 RELL Bootstrapping.. replicate: 4300 / 10000 0:04 RELL Bootstrapping.. replicate: 4400 / 10000 0:04 RELL Bootstrapping.. replicate: 4500 / 10000 0:04 RELL Bootstrapping.. replicate: 4600 / 10000 0:04 RELL Bootstrapping.. replicate: 4700 / 10000 0:04 RELL Bootstrapping.. replicate: 4800 / 10000 0:04 RELL Bootstrapping.. replicate: 4900 / 10000 0:04 RELL Bootstrapping.. replicate: 5000 / 10000 0:04 RELL Bootstrapping.. replicate: 5100 / 10000 0:04 RELL Bootstrapping.. replicate: 5200 / 10000 0:04 RELL Bootstrapping.. replicate: 5300 / 10000 0:04 RELL Bootstrapping.. replicate: 5400 / 10000 0:04 RELL Bootstrapping.. replicate: 5500 / 10000 0:04 RELL Bootstrapping.. replicate: 5600 / 10000 0:04 RELL Bootstrapping.. replicate: 5700 / 10000 0:04 RELL Bootstrapping.. replicate: 5800 / 10000 0:04 RELL Bootstrapping.. replicate: 5900 / 10000 0:04 RELL Bootstrapping.. replicate: 6000 / 10000 0:04 RELL Bootstrapping.. replicate: 6100 / 10000 0:04 RELL Bootstrapping.. replicate: 6200 / 10000 0:04 RELL Bootstrapping.. replicate: 6300 / 10000 0:04 RELL Bootstrapping.. replicate: 6400 / 10000 0:04 RELL Bootstrapping.. replicate: 6500 / 10000 0:04 RELL Bootstrapping.. replicate: 6600 / 10000 0:04 RELL Bootstrapping.. replicate: 6700 / 10000 0:04 RELL Bootstrapping.. replicate: 6800 / 10000 0:04 RELL Bootstrapping.. replicate: 6900 / 10000 0:04 RELL Bootstrapping.. replicate: 7000 / 10000 0:04 RELL Bootstrapping.. replicate: 7100 / 10000 0:04 RELL Bootstrapping.. replicate: 7200 / 10000 0:04 RELL Bootstrapping.. replicate: 7300 / 10000 0:04 RELL Bootstrapping.. replicate: 7400 / 10000 0:04 RELL Bootstrapping.. replicate: 7500 / 10000 0:04 RELL Bootstrapping.. replicate: 7600 / 10000 0:04 RELL Bootstrapping.. replicate: 7700 / 10000 0:04 RELL Bootstrapping.. replicate: 7800 / 10000 0:04 RELL Bootstrapping.. replicate: 7900 / 10000 0:04 RELL Bootstrapping.. replicate: 8000 / 10000 0:04 RELL Bootstrapping.. replicate: 8100 / 10000 0:04 RELL Bootstrapping.. replicate: 8200 / 10000 0:04 RELL Bootstrapping.. replicate: 8300 / 10000 0:04 RELL Bootstrapping.. replicate: 8400 / 10000 0:04 RELL Bootstrapping.. replicate: 8500 / 10000 0:04 RELL Bootstrapping.. replicate: 8600 / 10000 0:04 RELL Bootstrapping.. replicate: 8700 / 10000 0:04 RELL Bootstrapping.. replicate: 8800 / 10000 0:04 RELL Bootstrapping.. replicate: 8900 / 10000 0:04 RELL Bootstrapping.. replicate: 9000 / 10000 0:04 RELL Bootstrapping.. replicate: 9100 / 10000 0:04 RELL Bootstrapping.. replicate: 9200 / 10000 0:04 RELL Bootstrapping.. replicate: 9300 / 10000 0:04 RELL Bootstrapping.. replicate: 9400 / 10000 0:04 RELL Bootstrapping.. replicate: 9500 / 10000 0:04 RELL Bootstrapping.. replicate: 9600 / 10000 0:04 RELL Bootstrapping.. replicate: 9700 / 10000 0:04 RELL Bootstrapping.. replicate: 9800 / 10000 0:04 RELL Bootstrapping.. replicate: 9900 / 10000 0:04 RELL Bootstrapping.. replicate: 10000 / 10000 0:04 586s now doing S-H test 586s 586s Time used: 0:04 586s Passed 586s 586s Test 6 586s 586s CODONML in paml version 4.9j, October 2019 586s 586s ---------------------------------------------- 586s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 586s TTC | TCC | TAC | TGC 586s Leu L TTA | TCA | *** * TAA | *** * TGA 586s TTG | TCG | TAG | Trp W TGG 586s ---------------------------------------------- 586s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 586s CTC | CCC | CAC | CGC 586s CTA | CCA | Gln Q CAA | CGA 586s CTG | CCG | CAG | CGG 586s ---------------------------------------------- 586s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 586s ATC | ACC | AAC | AGC 586s ATA | ACA | Lys K AAA | Arg R AGA 586s Met M ATG | ACG | AAG | AGG 586s ---------------------------------------------- 586s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 586s GTC | GCC | GAC | GGC 586s GTA | GCA | Glu E GAA | GGA 586s GTG | GCG | GAG | GGG 586s ---------------------------------------------- 586s Nice code, uuh? 586s ns = 19 ls = 390 586s Reading sequences, sequential format.. 586s Reading seq # 1: 1.human Reading seq # 2: 2.chimp_bonobo_gorilla Reading seq # 3: 3.orangutan_Ppy Reading seq # 4: 4.gibbon_Ggo Reading seq # 5: 5.colobus_Cgu&Can Reading seq # 6: 6.langur_Sen&Sve Reading seq # 7: 7.langur_Tob&Tfr Reading seq # 8: 8.Douc_langur_Pne Reading seq # 9: 9.probiscis_Nla Reading seq #10: 10.baboon_Pcy Reading seq #11: 11.mangabey_Cat Reading seq #12: 12.rhesus_Mmu Reading seq #13: 13.Allen_Ani Reading seq #14: 14.talapoin_Mta Reading seq #15: 15.patas_Epa Reading seq #16: 16.vervet_Cae Reading seq #17: 17.squirrel_m Reading seq #18: 18.tamarin_Soe Reading seq #19: 19.Marmoset_Cja 586s Sequences read.. 586s Counting site patterns.. 0:00 586s Compressing, 86 patterns at 130 / 130 sites (100.0%), 0:00 586s Collecting fpatt[] & pose[], 86 patterns at 130 / 130 sites (100.0%), 0:00 586s Counting codons.. 586s 586s 1368 bytes for distance 586s 83936 bytes for conP 586s 2752 bytes for fhK 586s 5000000 bytes for space 586s 586s 2 branch types are in tree. Stop if wrong. 586s TREE # 1 586s (((((6, 7, 8), 9), 5), (((10, 11), 12), 13, (14, (15, 16)))), (((1, 2), 3), 4), (17, (18, 19))); MP score: 83 586s 629520 bytes for conP, adjusted 586s 586s 0.099332 0.081411 0.017505 0.059984 0.041937 0.083929 0.091795 0.082884 0.031720 0.102232 0.101024 0.013031 0.031985 0.068435 0.035192 0.089077 0.077779 0.064447 0.096350 0.095504 0.089002 0.019286 0.088995 0.042888 0.054891 0.015662 0.087331 0.078539 0.019590 0.091777 0.096559 0.050947 0.073474 3.000000 1.446401 0.180823 0.216477 2.199271 586s 586s ntime & nrate & np: 33 3 38 586s 586s Bounds (np=38): 586s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 -99.000000 -99.000000 0.000001 1.000000 586s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 99.000000 99.000000 1.000000 999.000000 586s branch=0 freq=0.779985 w0 = 0.216477 586s branch=0 freq=0.220015 w1 = 1.000000 586s Qfactor for branch 0 = 6.526921 586s branch=1 freq=0.658982 w0 = 0.216477 586s branch=1 freq=0.185883 w1 = 1.000000 586s branch=1 freq=0.155135 w2 = 2.199271 586s Qfactor for branch 1 = 4.732311 586s w[0] = 0.216477 586s w[1] = 1.000000 586s w[2] = 2.199271 586s 586s np = 38 586s lnL0 = -1185.750475 586s 586s Iterating by ming2 638s Initial: fx= 1185.750475 638s x= 0.09933 0.08141 0.01750 0.05998 0.04194 0.08393 0.09179 0.08288 0.03172 0.10223 0.10102 0.01303 0.03198 0.06843 0.03519 0.08908 0.07778 0.06445 0.09635 0.09550 0.08900 0.01929 0.08900 0.04289 0.05489 0.01566 0.08733 0.07854 0.01959 0.09178 0.09656 0.05095 0.07347 3.00000 1.44640 0.18082 0.21648 2.19927 638s 638s 1 h-m-p 0.0000 0.0001 751.3993 ++ 1144.006538 m 0.0001 43 | 1/38 638s 2 h-m-p 0.0000 0.0000 639.8182 ++ 1139.869961 m 0.0000 84 | 2/38 638s 3 h-m-p 0.0000 0.0000 4852.3267 ++ 1071.439019 m 0.0000 125 | 3/38 638s 4 h-m-p 0.0000 0.0000 3255.7414 ++ 1057.725663 m 0.0000 166 | 4/38 638s 5 h-m-p 0.0000 0.0000 1047.9212 ++ 1054.129997 m 0.0000 207 | 5/38 638s 6 h-m-p 0.0000 0.0000 602.4127 ++ 1049.728880 m 0.0000 248 | 6/38 638s 7 h-m-p 0.0000 0.0001 339.1243 ++ 1047.517261 m 0.0001 289 | 7/38 638s 8 h-m-p 0.0001 0.0008 158.8244 +YYCCCC 1045.720839 5 0.0003 339 | 7/38 638s 9 h-m-p 0.0002 0.0010 68.5117 CCCC 1045.125460 3 0.0003 386 | 7/38 638s 10 h-m-p 0.0002 0.0012 47.4566 YCCCC 1044.593311 4 0.0005 434 | 7/38 638s 11 h-m-p 0.0002 0.0009 41.4714 CYCCC 1044.292048 4 0.0003 482 | 7/38 638s 12 h-m-p 0.0001 0.0004 34.9310 CCCC 1044.217461 3 0.0001 529 | 7/38 638s 13 h-m-p 0.0002 0.0015 17.4367 CCCC 1044.132204 3 0.0003 576 | 7/38 638s 14 h-m-p 0.0003 0.0023 18.3262 YCCC 1043.983760 3 0.0005 622 | 7/38 638s 15 h-m-p 0.0002 0.0012 44.3619 YCCC 1043.491071 3 0.0006 668 | 7/38 638s 16 h-m-p 0.0001 0.0005 114.9871 YCYCCC 1042.762965 5 0.0003 717 | 7/38 638s 17 h-m-p 0.0002 0.0008 126.4178 YCCCCC 1041.866557 5 0.0003 767 | 7/38 638s 18 h-m-p 0.0001 0.0004 132.3098 YCYCCC 1041.375871 5 0.0002 816 | 7/38 638s 19 h-m-p 0.0001 0.0005 85.0292 CYC 1041.253923 2 0.0001 860 | 7/38 638s 20 h-m-p 0.0003 0.0022 30.6419 CCC 1041.142589 2 0.0003 905 | 7/38 638s 21 h-m-p 0.0004 0.0022 23.8443 CCC 1041.113838 2 0.0002 950 | 7/38 638s 22 h-m-p 0.0005 0.0102 7.8450 C 1041.093775 0 0.0005 991 | 7/38 638s 23 h-m-p 0.0003 0.0046 13.2539 CC 1041.061732 1 0.0004 1034 | 7/38 638s 24 h-m-p 0.0002 0.0053 24.6577 +YYC 1040.932126 2 0.0008 1078 | 7/38 638s 25 h-m-p 0.0004 0.0037 43.9248 YCCC 1040.641609 3 0.0009 1124 | 7/38 638s 26 h-m-p 0.0003 0.0015 99.4204 CCCC 1040.318041 3 0.0004 1171 | 7/38 638s 27 h-m-p 0.0005 0.0026 39.8665 YCC 1040.227761 2 0.0004 1215 | 7/38 638s 28 h-m-p 0.0003 0.0013 21.4035 YC 1040.213296 1 0.0001 1257 | 7/38 638s 29 h-m-p 0.0004 0.0158 7.6824 YC 1040.197665 1 0.0007 1299 | 7/38 638s 30 h-m-p 0.0005 0.0595 10.8012 +++YYCCC 1039.531009 4 0.0221 1349 | 7/38 638s 31 h-m-p 0.0002 0.0009 603.6901 ++ 1037.798779 m 0.0009 1390 | 8/38 638s 32 h-m-p 0.2679 1.3396 0.9902 CCCC 1037.155256 3 0.4672 1437 | 8/38 638s 33 h-m-p 0.1670 0.8349 2.6971 CCC 1036.668054 2 0.1515 1512 | 7/38 638s 34 h-m-p 0.0993 0.4966 3.1838 -CC 1036.650558 1 0.0061 1556 | 7/38 638s 35 h-m-p 0.0182 0.1631 1.0672 ++ 1036.357799 m 0.1631 1597 | 8/38 638s 36 h-m-p 0.1655 4.8553 1.0493 +CYC 1035.843653 2 0.7447 1642 | 8/38 638s 37 h-m-p 1.1834 5.9169 0.6313 YCC 1035.652594 2 0.6475 1686 | 8/38 638s 38 h-m-p 0.5489 2.7446 0.6086 YCC 1035.584521 2 0.3130 1760 | 8/38 638s 39 h-m-p 1.0534 6.0514 0.1808 YCC 1035.562844 2 0.6838 1834 | 8/38 638s 40 h-m-p 1.0900 8.0000 0.1134 CC 1035.553327 1 0.9974 1907 | 8/38 638s 41 h-m-p 1.2377 8.0000 0.0914 YC 1035.549024 1 0.9568 1979 | 8/38 638s 42 h-m-p 1.2718 8.0000 0.0688 CC 1035.544686 1 2.0106 2052 | 8/38 638s 43 h-m-p 1.6000 8.0000 0.0521 CC 1035.542285 1 2.0979 2125 | 8/38 638s 44 h-m-p 1.1789 8.0000 0.0927 CC 1035.540297 1 1.3062 2198 | 8/38 638s 45 h-m-p 1.5194 8.0000 0.0797 CC 1035.539129 1 1.2689 2271 | 8/38 638s 46 h-m-p 1.4258 8.0000 0.0709 C 1035.538200 0 1.4572 2342 | 8/38 638s 47 h-m-p 1.4584 8.0000 0.0708 YC 1035.536679 1 2.6866 2414 | 8/38 638s 48 h-m-p 1.6000 8.0000 0.0940 YC 1035.534650 1 2.8658 2486 | 8/38 638s 49 h-m-p 1.6000 8.0000 0.0714 CC 1035.534005 1 1.3286 2559 | 8/38 650s 50 h-m-p 1.6000 8.0000 0.0215 YC 1035.533922 1 1.1660 2631 | 8/38 650s 51 h-m-p 1.6000 8.0000 0.0088 Y 1035.533916 0 1.0989 2702 | 8/38 650s 52 h-m-p 1.6000 8.0000 0.0010 Y 1035.533916 0 1.1457 2773 | 8/38 650s 53 h-m-p 1.6000 8.0000 0.0003 Y 1035.533916 0 1.0880 2844 | 8/38 650s 54 h-m-p 1.6000 8.0000 0.0001 C 1035.533916 0 1.3158 2915 | 8/38 650s 55 h-m-p 1.6000 8.0000 0.0000 C 1035.533916 0 1.3860 2986 | 8/38 650s 56 h-m-p 1.1090 8.0000 0.0000 --Y 1035.533916 0 0.0173 3059 | 8/38 650s 57 h-m-p 0.1596 8.0000 0.0000 ---N 1035.533916 0 0.0006 3133 650s Out.. 650s lnL = -1035.533916 650s 3134 lfun, 15670 eigenQcodon, 413688 P(t) 650s 650s BEBing (dim = 4). This may take many minutes. 650s Trying to get 0.6M memory in lfunNSsites_ACD 650s 650s Calculating f(x_h|w) for 121 w's 650s 10 / 121 sets. w for branches: 0.9500 0.9500 lnfX = -1058.2047 20 / 121 sets. w for branches: 0.0500 9.5000 lnfX = -1109.1660 30 / 121 sets. w for branches: 0.1500 9.5000 lnfX = -1072.3726 40 / 121 sets. w for branches: 0.2500 9.5000 lnfX = -1060.2343 50 / 121 sets. w for branches: 0.3500 9.5000 lnfX = -1055.3914 60 / 121 sets. w for branches: 0.4500 9.5000 lnfX = -1054.1056 70 / 121 sets. w for branches: 0.5500 9.5000 lnfX = -1054.9337 80 / 121 sets. w for branches: 0.6500 9.5000 lnfX = -1057.1653 90 / 121 sets. w for branches: 0.7500 9.5000 lnfX = -1060.3967 100 / 121 sets. w for branches: 0.8500 9.5000 lnfX = -1064.3760 110 / 121 sets. w for branches: 0.9500 9.5000 lnfX = -1068.9351 120 / 121 sets. w for branches: 1.0000 9.5000 lnfX = -1071.3937 121 / 121 sets. w for branches: 1.0000 10.5000 lnfX = -1073.7802 650s Time: 1:04 650s Calculating the marginal likelihood f(X). 650s 1000 / 10000 grid points, 1:04 2000 / 10000 grid points, 1:04 3000 / 10000 grid points, 1:04 4000 / 10000 grid points, 1:04 5000 / 10000 grid points, 1:04 6000 / 10000 grid points, 1:04 7000 / 10000 grid points, 1:04 8000 / 10000 grid points, 1:04 9000 / 10000 grid points, 1:04 10000 / 10000 grid points, 1:04 log(fX) = -1040.172966 S = -972.039021 -64.399173 650s Calculating f(w_k|X), posterior for site classes for each site. Slow! 650s did 10 / 86 site patterns 1:04 did 20 / 86 site patterns 1:04 did 30 / 86 site patterns 1:04 did 40 / 86 site patterns 1:04 did 50 / 86 site patterns 1:04 did 60 / 86 site patterns 1:04 did 70 / 86 site patterns 1:04 did 80 / 86 site patterns 1:04 did 86 / 86 site patterns 1:04 650s Time used: 1:04 650s Passed 650s 650s Test 7 650s BASEML in paml version 4.9j, October 2019 650s ns = 35 ls = 1812 650s Reading sequences, sequential format.. 650s Reading seq # 1: Equus Reading seq # 2: Rhinoceros Reading seq # 3: Balaenoptera Reading seq # 4: Physeter Reading seq # 5: Hippopotamus Reading seq # 6: Bos Reading seq # 7: Canis Reading seq # 8: Ursus Reading seq # 9: Felis Reading seq #10: Homo Reading seq #11: Pan Reading seq #12: Gorilla Reading seq #13: Pongo Reading seq #14: Macaca Reading seq #15: Callithrix Reading seq #16: Galago Reading seq #17: Loris Reading seq #18: Daubentonia Reading seq #19: Lepilemur Reading seq #20: Propithecus Reading seq #21: Varecia Reading seq #22: Hapalemur Reading seq #23: Lemur Reading seq #24: Eulemur Reading seq #25: Cheirogaleus Reading seq #26: Mirza Reading seq #27: M.ravelobensis Reading seq #28: M.sambiranensis Reading seq #29: M.myoxinus Reading seq #30: M.tavaratra Reading seq #31: M.griseorufus Reading seq #32: M.berthae Reading seq #33: M.murinus Reading seq #34: M.rufus1 Reading seq #35: M.rufus2 650s Sequences read.. 650s Counting site patterns.. 0:00 650s 650s 650s Compressing, 1023 patterns at 1812 / 1812 sites (100.0%), 0:00 650s 650s 650s Collecting fpatt[] & pose[], 1023 patterns at 1812 / 1812 sites (100.0%), 0:00 650s Counting frequencies.. 650s 650s 7140 bytes for distance 650s 1113024 bytes for conP 650s 40920 bytes for fhK 650s 8000000 bytes for space 650s 650s 3 branch types are in tree. Stop if wrong. 650s TREE # 1: (((((((((((27, (28, (35, (30, (34, (32, 29)))))), (31, 33)), 26), 25), 19), 20), (((22, 23), 24), 21)), 18), (16, 17)), (15, (14, (13, (12, (11, 10)))))), ((9, (7, 8)), ((((4, 3), 5), 6), (2, 1)))); MP score: -1.00 650s 650s found 3 branch rates in tree. 650s 0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 650s 650s ntime & nrate & np: 40 1 44 650s 36..37 37..38 38..39 39..40 40..41 41..42 42..43 43..44 44..45 45..46 46..27 46..47 47..28 47..48 48..35 48..49 49..30 49..50 50..34 50..51 51..32 51..29 45..52 52..31 52..33 44..26 43..25 42..19 41..20 40..53 53..54 54..55 55..22 55..23 54..24 53..21 39..18 38..56 56..16 56..17 37..57 57..15 57..58 58..14 58..59 59..13 59..60 60..12 60..61 61..11 61..10 36..62 62..63 63..9 63..64 64..7 64..8 62..65 65..66 66..67 67..68 68..4 68..3 67..5 66..6 65..69 69..2 69..1 650s 650s 0.105457 0.793379 0.673640 0.460138 0.571462 0.591309 0.420229 0.568105 0.736722 0.467419 0.494115 0.818063 0.591527 0.485836 0.506775 0.766725 0.745040 0.470143 0.611715 0.832238 0.624317 0.731625 0.879802 0.855184 0.503693 0.898579 0.769821 0.553633 0.687984 0.651397 0.655172 0.864417 0.747922 0.543087 0.118533 0.077566 0.086258 0.061987 0.088869 0.115584 1.000000 1.000000 1.948625 0.510400 650s 650s lnL0 = -37863.548283 650s 650s Bounds (np=44): 650s 0.000004 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000100 0.000100 0.000100 0.000100 0.000100 0.000100 0.000100 0.000100 0.000010 0.005000 658s 50.000000 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 999.000000 999.000000 999.000000 999.000000 658s 658s Iterating by ming2 658s Initial: fx= 37863.548283 658s x= 0.10546 0.79338 0.67364 0.46014 0.57146 0.59131 0.42023 0.56810 0.73672 0.46742 0.49411 0.81806 0.59153 0.48584 0.50678 0.76673 0.74504 0.47014 0.61171 0.83224 0.62432 0.73162 0.87980 0.85518 0.50369 0.89858 0.76982 0.55363 0.68798 0.65140 0.65517 0.86442 0.74792 0.54309 0.11853 0.07757 0.08626 0.06199 0.08887 0.11558 1.00000 1.00000 1.94862 0.51040 658s 658s 1 h-m-p 0.0000 0.0000 45450.0479 ++ 28972.475009 m 0.0000 49 | 1/44 658s 2 h-m-p 0.0000 0.0002 4193.5136 +YYCYCCC 27537.622657 6 0.0002 106 | 1/44 658s 3 h-m-p 0.0001 0.0003 2000.8674 YCCC 27378.129633 3 0.0001 158 | 1/44 658s 4 h-m-p 0.0001 0.0005 1794.3843 +YCCC 27123.743521 3 0.0003 211 | 1/44 658s 5 h-m-p 0.0003 0.0014 1084.1956 +YCCC 26828.910485 3 0.0009 264 | 1/44 658s 6 h-m-p 0.0002 0.0010 752.2007 YCYCCC 26740.512323 5 0.0005 319 | 1/44 658s 7 h-m-p 0.0001 0.0003 1383.9635 +YCYCCC 26680.596863 5 0.0002 376 | 1/44 658s 8 h-m-p 0.0002 0.0009 592.1569 ++ 26582.843483 m 0.0009 423 | 1/44 658s 9 h-m-p 0.0000 0.0001 1377.4515 ++ 26549.181141 m 0.0001 470 | 1/44 658s 10 h-m-p 0.0001 0.0005 1193.3458 YCYCCC 26510.180004 5 0.0002 525 | 1/44 658s 11 h-m-p 0.0000 0.0002 1157.5732 ++ 26471.492537 m 0.0002 572 | 1/44 658s 12 h-m-p 0.0003 0.0014 502.8646 +YYYCC 26416.523399 4 0.0010 625 | 1/44 658s 13 h-m-p 0.0002 0.0009 452.3895 CYCCC 26407.795158 4 0.0003 679 | 1/44 658s 14 h-m-p 0.0002 0.0020 762.8522 +CCC 26373.955969 2 0.0008 731 | 1/44 658s 15 h-m-p 0.0003 0.0017 427.7418 +YCCC 26349.071478 3 0.0010 784 | 1/44 658s 16 h-m-p 0.0008 0.0039 162.9150 YCC 26341.716904 2 0.0012 834 | 1/44 658s 17 h-m-p 0.0015 0.0075 120.9990 YYC 26337.102597 2 0.0013 883 | 1/44 658s 18 h-m-p 0.0006 0.0031 67.6636 +YCC 26334.682079 2 0.0018 934 | 0/44 658s 19 h-m-p 0.0021 0.0109 55.4225 YC 26333.152769 1 0.0017 982 | 0/44 658s 20 h-m-p 0.0020 0.0102 45.6656 C 26332.094845 0 0.0020 1029 | 0/44 658s 21 h-m-p 0.0008 0.0039 25.4887 YC 26331.829608 1 0.0012 1077 | 0/44 658s 22 h-m-p 0.0020 0.0328 16.0261 CC 26331.518733 1 0.0024 1126 | 0/44 658s 23 h-m-p 0.0037 0.0278 10.4190 YC 26330.858650 1 0.0061 1174 | 0/44 658s 24 h-m-p 0.0039 0.0195 15.3996 CC 26329.335837 1 0.0059 1223 | 0/44 658s 25 h-m-p 0.0011 0.0056 19.8690 ++ 26325.618094 m 0.0056 1270 | 1/44 658s 26 h-m-p 0.0023 0.0117 28.9074 +YC 26313.488559 1 0.0074 1319 | 1/44 658s 27 h-m-p 0.0020 0.0099 55.8187 YC 26300.615564 1 0.0049 1367 | 1/44 658s 28 h-m-p 0.0030 0.0151 51.0729 YC 26297.598666 1 0.0024 1415 | 1/44 658s 29 h-m-p 0.0046 0.0229 20.6729 YC 26296.887812 1 0.0028 1463 | 1/44 658s 30 h-m-p 0.0037 0.0186 11.1989 CC 26296.243670 1 0.0050 1512 | 1/44 658s 31 h-m-p 0.0028 0.0341 20.2358 CC 26295.064493 1 0.0040 1561 | 1/44 658s 32 h-m-p 0.0053 0.0274 15.2936 CC 26292.142958 1 0.0076 1610 | 1/44 658s 33 h-m-p 0.0033 0.0167 32.6614 CC 26288.442097 1 0.0042 1659 | 1/44 658s 34 h-m-p 0.0044 0.0218 28.6441 YC 26287.340657 1 0.0027 1707 | 1/44 658s 35 h-m-p 0.0108 0.0590 7.0503 C 26287.241858 0 0.0031 1754 | 1/44 658s 36 h-m-p 0.0068 0.2039 3.2081 C 26287.142484 0 0.0071 1801 | 1/44 658s 37 h-m-p 0.0085 0.3427 2.6676 +YC 26286.299061 1 0.0258 1850 | 1/44 658s 38 h-m-p 0.0052 0.0405 13.2003 +CYC 26279.643562 2 0.0200 1901 | 1/44 658s 39 h-m-p 0.0058 0.0318 45.4712 CYC 26274.706906 2 0.0050 1951 | 1/44 658s 40 h-m-p 0.0028 0.0140 28.1454 CCC 26273.342378 2 0.0037 2002 | 1/44 658s 41 h-m-p 0.0040 0.0199 8.6378 C 26273.158945 0 0.0040 2049 | 1/44 658s 42 h-m-p 0.0230 0.1794 1.4990 C 26272.889948 0 0.0236 2096 | 1/44 658s 43 h-m-p 0.0068 0.1966 5.1805 +YC 26268.105430 1 0.0484 2145 | 1/44 658s 44 h-m-p 0.0042 0.0209 54.6040 CCC 26261.547807 2 0.0057 2196 | 1/44 658s 45 h-m-p 0.0101 0.0506 13.8304 C 26261.304408 0 0.0026 2243 | 1/44 673s 46 h-m-p 0.0196 0.2342 1.8436 C 26261.133849 0 0.0186 2290 | 1/44 673s 47 h-m-p 0.0148 0.3493 2.3132 ++C 26249.894376 0 0.2312 2339 | 1/44 673s 48 h-m-p 0.0017 0.0083 128.4904 +YC 26236.716637 1 0.0056 2388 | 1/44 673s 49 h-m-p 0.0322 0.1611 3.5690 CC 26236.421604 1 0.0117 2437 | 0/44 673s 50 h-m-p 0.0014 0.0361 29.7058 YC 26235.853570 1 0.0012 2485 | 0/44 673s 51 h-m-p 0.0037 0.3203 9.4074 ++++ 26176.799422 m 0.3203 2534 | 0/44 673s 52 h-m-p 0.1577 0.7884 3.8815 YYYYCCCC 26167.105026 7 0.1659 2591 | 0/44 673s 53 h-m-p 0.0489 0.2443 0.6179 ++ 26147.112251 m 0.2443 2638 | 1/44 673s 54 h-m-p 0.1592 1.4402 0.9333 +YCCCC 26105.669705 4 0.9305 2737 | 1/44 673s 55 h-m-p 0.2810 1.4048 1.7923 CYC 26080.834431 2 0.3495 2830 | 1/44 673s 56 h-m-p 0.3523 1.7614 0.4605 ++ 26045.723893 m 1.7614 2877 | 1/44 673s 57 h-m-p 0.8622 4.3112 0.7519 CYCCC 26018.521692 4 1.2546 2974 | 1/44 673s 58 h-m-p 0.7408 3.7040 0.3326 CCC 26007.884253 2 0.7016 3068 | 1/44 673s 59 h-m-p 0.8253 4.4349 0.2828 CCCC 25995.254954 3 1.3036 3164 | 1/44 673s 60 h-m-p 0.4127 2.0635 0.1607 +YC 25986.683659 1 1.3844 3256 | 1/44 673s 61 h-m-p 1.1697 5.8483 0.1241 CC 25981.772507 1 1.4928 3348 | 1/44 673s 62 h-m-p 1.3610 6.8050 0.0911 C 25980.116402 0 1.3726 3438 | 1/44 673s 63 h-m-p 1.2088 8.0000 0.1035 CC 25979.169809 1 1.0689 3530 | 1/44 673s 64 h-m-p 1.1412 8.0000 0.0969 YC 25977.098756 1 2.7220 3621 | 1/44 673s 65 h-m-p 1.6000 8.0000 0.1353 YCC 25973.160310 2 3.0751 3714 | 1/44 673s 66 h-m-p 0.9390 4.6952 0.1928 YC 25970.459852 1 1.6500 3805 | 1/44 673s 67 h-m-p 1.6000 8.0000 0.1260 CC 25969.548595 1 1.4484 3897 | 1/44 673s 68 h-m-p 1.6000 8.0000 0.0886 YC 25968.575990 1 2.7625 3988 | 1/44 673s 69 h-m-p 1.6000 8.0000 0.0855 CC 25967.256422 1 2.5504 4080 | 1/44 673s 70 h-m-p 1.5224 7.6122 0.1149 CCC 25966.191420 2 1.7142 4174 | 1/44 673s 71 h-m-p 1.6000 8.0000 0.0453 C 25965.723201 0 1.7357 4264 | 1/44 673s 72 h-m-p 0.9357 8.0000 0.0840 +YC 25964.981943 1 2.5004 4356 | 1/44 673s 73 h-m-p 1.6000 8.0000 0.1173 YC 25963.352641 1 3.3229 4447 | 1/44 673s 74 h-m-p 1.6000 8.0000 0.1869 +YC 25960.256588 1 4.1478 4539 | 1/44 673s 75 h-m-p 1.3677 6.8383 0.3824 YC 25956.297534 1 2.6672 4630 | 1/44 673s 76 h-m-p 1.6000 8.0000 0.3272 CC 25954.177175 1 2.0523 4722 | 1/44 673s 77 h-m-p 1.6000 8.0000 0.1505 CC 25953.607918 1 1.3924 4814 | 1/44 673s 78 h-m-p 1.6000 8.0000 0.1243 CC 25953.262331 1 2.5019 4906 | 1/44 673s 79 h-m-p 1.6000 8.0000 0.0814 YC 25952.484676 1 3.5176 4997 | 1/44 673s 80 h-m-p 1.3235 8.0000 0.2164 +CC 25949.764485 1 5.4710 5090 | 1/44 673s 81 h-m-p 1.6000 8.0000 0.3073 YC 25946.279504 1 2.7883 5181 | 1/44 673s 82 h-m-p 1.6000 8.0000 0.3474 YCC 25945.625660 2 1.2448 5274 | 1/44 673s 83 h-m-p 1.6000 8.0000 0.0836 YC 25945.524844 1 1.2182 5365 | 1/44 673s 84 h-m-p 1.6000 8.0000 0.0312 CC 25945.481798 1 2.1615 5457 | 1/44 673s 85 h-m-p 1.6000 8.0000 0.0347 +CC 25945.363753 1 5.5004 5550 | 1/44 673s 86 h-m-p 1.6000 8.0000 0.0337 +YC 25944.978747 1 5.4253 5642 | 1/44 673s 87 h-m-p 0.9857 8.0000 0.1856 +CC 25944.256320 1 3.6007 5735 | 1/44 673s 88 h-m-p 1.6000 8.0000 0.2235 CC 25944.086674 1 1.2747 5827 | 1/44 673s 89 h-m-p 1.6000 8.0000 0.0810 C 25944.062840 0 2.1525 5917 | 1/44 673s 90 h-m-p 1.6000 8.0000 0.0534 +YC 25944.007835 1 4.8509 6009 | 1/44 673s 91 h-m-p 1.6000 8.0000 0.0516 ++ 25943.724705 m 8.0000 6099 | 1/44 673s 92 h-m-p 1.6000 8.0000 0.2009 +YC 25942.821097 1 4.8806 6191 | 1/44 673s 93 h-m-p 1.6000 8.0000 0.3903 YC 25941.506674 1 3.3655 6282 | 1/44 673s 94 h-m-p 1.6000 8.0000 0.4345 C 25941.073369 0 1.6000 6372 | 1/44 673s 95 h-m-p 1.6000 8.0000 0.2380 C 25941.021762 0 1.4426 6462 | 1/44 673s 96 h-m-p 1.6000 8.0000 0.0979 C 25941.012630 0 1.4382 6552 | 1/44 673s 97 h-m-p 1.2094 8.0000 0.1164 Y 25941.011066 0 0.7258 6642 | 1/44 673s 98 h-m-p 1.6000 8.0000 0.0162 Y 25941.010708 0 1.1829 6732 | 1/44 676s 99 h-m-p 1.6000 8.0000 0.0032 C 25941.010622 0 2.1882 6822 | 1/44 676s 100 h-m-p 1.6000 8.0000 0.0021 Y 25941.010549 0 3.4443 6912 | 1/44 676s 101 h-m-p 1.6000 8.0000 0.0006 ++ 25941.010141 m 8.0000 7002 | 1/44 676s 102 h-m-p 1.6000 8.0000 0.0026 C 25941.009345 0 1.9492 7092 | 1/44 676s 103 h-m-p 1.5969 8.0000 0.0032 C 25941.009093 0 1.6503 7182 | 1/44 676s 104 h-m-p 1.6000 8.0000 0.0005 Y 25941.009092 0 0.9252 7272 | 1/44 676s 105 h-m-p 1.6000 8.0000 0.0000 Y 25941.009092 0 1.0572 7362 | 1/44 676s 106 h-m-p 1.6000 8.0000 0.0000 Y 25941.009092 0 0.8995 7452 | 1/44 676s 107 h-m-p 1.6000 8.0000 0.0000 C 25941.009092 0 1.6000 7542 | 1/44 676s 108 h-m-p 1.6000 8.0000 0.0000 --Y 25941.009092 0 0.0250 7634 676s Out... 676s lnL = -25941.009092 676s Calculating SE's 676s 676s Time used: 0:26 676s Passed 676s 676s Test 8 679s 679s AAML in paml version 4.9j, October 2019 679s 679s ---------------------------------------------- 679s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 679s TTC | TCC | TAC | TGC 679s Leu L TTA | TCA | *** * TAA | Trp W TGA 679s TTG | TCG | TAG | TGG 679s ---------------------------------------------- 679s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 679s CTC | CCC | CAC | CGC 679s CTA | CCA | Gln Q CAA | CGA 679s CTG | CCG | CAG | CGG 679s ---------------------------------------------- 679s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 679s ATC | ACC | AAC | AGC 679s Met M ATA | ACA | Lys K AAA | *** * AGA 679s ATG | ACG | AAG | AGG 679s ---------------------------------------------- 679s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 679s GTC | GCC | GAC | GGC 679s GTA | GCA | Glu E GAA | GGA 679s GTG | GCG | GAG | GGG 679s ---------------------------------------------- 679s Nice code, uuh? 679s ns = 7 ls = 3331 679s Reading sequences, sequential format.. 679s Reading seq # 1: human Reading seq # 2: chimpanzee Reading seq # 3: bonobo Reading seq # 4: gorilla Reading seq # 5: orangutan Reading seq # 6: Sumatran Reading seq # 7: gibbon 679s Sequences read.. 679s Counting site patterns.. 0:00 679s Compressing, 469 patterns at 3331 / 3331 sites (100.0%), 0:00 679s Collecting fpatt[] & pose[], 469 patterns at 3331 / 3331 sites (100.0%), 0:00 679s Counting frequencies.. 679s 679s 168 bytes for distance 679s 450240 bytes for conP 679s 4695622480405476096 bytes for fhK 679s 5000000 bytes for space 679s 679s TREE # 1 679s (((1, (2, 3)), 4), (5, 6), 7); MP score: -1 679s 1125600 bytes for conP, adjusted 679s 679s 0.078878 0.041806 0.027631 0.035361 0.051694 0.071631 0.102811 0.053560 0.047768 0.104080 0.051935 3.000000 1.500000 679s 679s ntime & nrate & np: 11 2 13 679s 679s Bounds (np=13): 679s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 679s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 679s 679s np = 13 679s lnL0 = -15203.909342 679s 679s Iterating by ming2 679s Initial: fx= 15203.909342 679s x= 0.07888 0.04181 0.02763 0.03536 0.05169 0.07163 0.10281 0.05356 0.04777 0.10408 0.05193 3.00000 1.50000 679s 679s 1 h-m-p 0.0000 0.0000 4395.8381 +CCYCCC 14902.145937 5 0.0000 28 | 0/13 679s 2 h-m-p 0.0000 0.0000 3987.9941 +YYCCCC 14857.556776 5 0.0000 53 | 0/13 679s 3 h-m-p 0.0000 0.0000 2425.7683 CCCCC 14837.141177 4 0.0000 77 | 0/13 679s 4 h-m-p 0.0000 0.0001 709.8099 CYC 14834.540173 2 0.0000 96 | 0/13 679s 5 h-m-p 0.0000 0.0002 243.4434 YCC 14834.152980 2 0.0000 115 | 0/13 679s 6 h-m-p 0.0000 0.0009 115.8644 CC 14833.936653 1 0.0000 133 | 0/13 679s 7 h-m-p 0.0000 0.0004 256.1146 YC 14833.574235 1 0.0000 150 | 0/13 679s 8 h-m-p 0.0000 0.0015 772.6582 +++YYCCC 14816.237892 4 0.0006 175 | 0/13 679s 9 h-m-p 0.0000 0.0006 25357.2971 +CCYC 14761.725498 3 0.0001 197 | 0/13 679s 10 h-m-p 0.0000 0.0002 8491.7951 CCCCC 14740.905801 4 0.0001 221 | 0/13 679s 11 h-m-p 0.0001 0.0006 1315.0166 YCCC 14740.014963 3 0.0000 242 | 0/13 679s 12 h-m-p 0.0002 0.0012 65.3437 -CC 14739.981614 1 0.0000 261 | 0/13 679s 13 h-m-p 0.0009 0.4396 4.7891 +++CCCC 14738.451364 3 0.0800 286 | 0/13 679s 14 h-m-p 0.4656 3.2361 0.8230 YCYCCC 14725.736515 5 1.2960 310 | 0/13 679s 15 h-m-p 0.4874 2.4369 1.6997 YCYC 14723.208501 3 0.3166 343 | 0/13 679s 16 h-m-p 0.6720 8.0000 0.8008 YCCC 14719.207083 3 1.5336 364 | 0/13 679s 17 h-m-p 1.6000 8.0000 0.1612 CCC 14718.395790 2 1.7205 397 | 0/13 679s 18 h-m-p 1.6000 8.0000 0.1122 YCC 14718.252325 2 0.8976 429 | 0/13 679s 19 h-m-p 0.5469 8.0000 0.1841 +YCC 14718.087243 2 1.5006 462 | 0/13 679s 20 h-m-p 1.6000 8.0000 0.0300 +CYC 14717.769609 2 6.0308 495 | 0/13 679s 21 h-m-p 1.2764 8.0000 0.1416 CYC 14717.411913 2 1.5695 527 | 0/13 689s 22 h-m-p 0.6101 3.0505 0.2857 YCYC 14717.157845 3 0.3815 560 | 0/13 689s 23 h-m-p 1.1513 8.0000 0.0947 YCCCC 14716.824655 4 1.3356 596 | 0/13 689s 24 h-m-p 0.8647 8.0000 0.1462 YC 14716.492300 1 0.5028 626 | 0/13 689s 25 h-m-p 1.4586 8.0000 0.0504 YYCCCCC 14716.182286 6 1.7461 665 | 0/13 689s 26 h-m-p 0.9408 8.0000 0.0936 +YCYC 14715.589472 3 2.8327 699 | 0/13 689s 27 h-m-p 1.2463 8.0000 0.2127 CC 14715.369007 1 0.2957 730 | 0/13 689s 28 h-m-p 0.6035 8.0000 0.1042 YCYC 14714.893477 3 1.5719 763 | 0/13 689s 29 h-m-p 1.1092 8.0000 0.1476 CYCCC 14714.454169 4 1.9296 799 | 0/13 689s 30 h-m-p 0.7984 8.0000 0.3568 CC 14714.194050 1 0.3161 830 | 0/13 689s 31 h-m-p 0.6260 8.0000 0.1802 CYC 14713.650951 2 1.3280 863 | 0/13 689s 32 h-m-p 1.0549 8.0000 0.2268 YCCC 14713.253178 3 2.1039 897 | 0/13 689s 33 h-m-p 1.6000 8.0000 0.0712 CC 14713.146138 1 0.5407 928 | 0/13 689s 34 h-m-p 0.0898 6.1741 0.4287 +YCYCC 14712.650405 4 0.8851 964 | 0/13 689s 35 h-m-p 1.6000 8.0000 0.0845 CYCCC 14712.255499 4 2.6912 1000 | 0/13 689s 36 h-m-p 1.6000 8.0000 0.1412 CCC 14711.992573 2 0.3788 1033 | 0/13 689s 37 h-m-p 0.1665 6.0353 0.3212 +YCCCCC 14711.471837 5 0.8395 1072 | 0/13 689s 38 h-m-p 1.3163 8.0000 0.2049 YCCC 14711.149120 3 2.2656 1106 | 0/13 689s 39 h-m-p 1.6000 8.0000 0.1317 CCC 14710.933599 2 1.4616 1139 | 0/13 689s 40 h-m-p 0.1880 2.4242 1.0244 CYCCC 14710.595390 4 0.2713 1175 | 0/13 689s 41 h-m-p 1.6000 8.0000 0.0454 YCYC 14710.503061 3 0.9337 1195 | 0/13 689s 42 h-m-p 0.3357 8.0000 0.1261 +YCYCCC 14709.976249 5 2.9945 1233 | 0/13 689s 43 h-m-p 1.6000 8.0000 0.0984 CC 14709.884436 1 0.3791 1264 | 0/13 689s 44 h-m-p 0.1297 8.0000 0.2876 +YCYC 14709.627341 3 1.1452 1298 | 0/13 689s 45 h-m-p 1.6000 8.0000 0.0517 YYYY 14709.477275 3 1.6000 1330 | 0/13 689s 46 h-m-p 0.4555 8.0000 0.1817 +YCCYC 14708.822849 4 2.8572 1366 | 0/13 689s 47 h-m-p 1.6000 8.0000 0.2339 YC 14708.711902 1 0.8960 1396 | 0/13 689s 48 h-m-p 0.1608 2.7821 1.3036 YYC 14708.596873 2 0.1608 1427 | 0/13 689s 49 h-m-p 1.6000 8.0000 0.0656 YYC 14708.519257 2 1.2930 1445 | 0/13 689s 50 h-m-p 0.6296 8.0000 0.1346 +YCCC 14708.319319 3 2.6249 1480 | 0/13 689s 51 h-m-p 1.6000 8.0000 0.0898 YC 14708.258800 1 0.7838 1510 | 0/13 689s 52 h-m-p 0.2367 8.0000 0.2972 +YYC 14708.152430 2 0.7258 1542 | 0/13 689s 53 h-m-p 1.6000 8.0000 0.0647 YYY 14708.102203 2 1.6000 1573 | 0/13 689s 54 h-m-p 0.8863 8.0000 0.1168 YYCC 14708.001941 3 1.5737 1606 | 0/13 689s 55 h-m-p 1.0843 8.0000 0.1695 CYC 14707.968649 2 0.4540 1638 | 0/13 689s 56 h-m-p 1.0312 8.0000 0.0746 CCC 14707.948186 2 1.5567 1671 | 0/13 689s 57 h-m-p 1.6000 8.0000 0.0357 YC 14707.933361 1 1.0375 1701 | 0/13 689s 58 h-m-p 0.4667 8.0000 0.0794 +YCCCC 14707.890006 4 2.1808 1738 | 0/13 689s 59 h-m-p 1.6000 8.0000 0.0412 YYC 14707.861950 2 2.2396 1769 | 0/13 689s 60 h-m-p 0.5637 8.0000 0.1636 YYY 14707.843932 2 0.5637 1800 | 0/13 689s 61 h-m-p 1.4414 8.0000 0.0640 CC 14707.822983 1 2.0326 1831 | 0/13 689s 62 h-m-p 1.6000 8.0000 0.0336 +YC 14707.791430 1 4.7109 1862 | 0/13 689s 63 h-m-p 1.6000 8.0000 0.0493 YC 14707.785270 1 0.7833 1892 | 0/13 689s 64 h-m-p 0.3879 8.0000 0.0997 +YC 14707.764637 1 1.1342 1923 | 0/13 689s 65 h-m-p 1.6000 8.0000 0.0295 +YCC 14707.696876 2 5.2411 1956 | 0/13 689s 66 h-m-p 1.6000 8.0000 0.0537 YC 14707.693405 1 0.7942 1986 | 0/13 689s 67 h-m-p 1.6000 8.0000 0.0143 C 14707.691199 0 1.3515 2015 | 0/13 689s 68 h-m-p 1.5858 8.0000 0.0122 C 14707.689667 0 2.2013 2044 | 0/13 689s 69 h-m-p 1.6000 8.0000 0.0032 +C 14707.687742 0 6.2373 2074 | 0/13 689s 70 h-m-p 1.6000 8.0000 0.0026 ++ 14707.672866 m 8.0000 2103 | 0/13 689s 71 h-m-p 0.2956 8.0000 0.0707 +Y 14707.666260 0 1.1822 2133 | 0/13 689s 72 h-m-p 1.6000 8.0000 0.0091 YC 14707.665347 1 0.8584 2163 | 0/13 689s 73 h-m-p 0.6872 8.0000 0.0113 Y 14707.665123 0 1.4811 2192 | 0/13 689s 74 h-m-p 1.6000 8.0000 0.0021 C 14707.665102 0 2.0837 2221 | 0/13 689s 75 h-m-p 1.6000 8.0000 0.0003 ++ 14707.664953 m 8.0000 2250 | 0/13 696s 76 h-m-p 0.0988 8.0000 0.0225 ++YC 14707.663821 1 1.1076 2282 | 0/13 696s 77 h-m-p 1.6000 8.0000 0.0028 Y 14707.663804 0 1.2779 2311 | 0/13 696s 78 h-m-p 1.6000 8.0000 0.0001 Y 14707.663802 0 1.0127 2340 | 0/13 696s 79 h-m-p 0.5052 8.0000 0.0002 +C 14707.663802 0 3.1432 2370 | 0/13 696s 80 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663798 m 8.0000 2399 | 0/13 696s 81 h-m-p 0.1532 8.0000 0.0018 +Y 14707.663780 0 1.0952 2429 | 0/13 696s 82 h-m-p 1.6000 8.0000 0.0004 C 14707.663779 0 1.3623 2458 | 0/13 696s 83 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663779 m 8.0000 2487 | 0/13 696s 84 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663779 m 8.0000 2516 | 0/13 696s 85 h-m-p 1.5795 8.0000 0.0001 Y 14707.663779 0 3.1643 2545 | 0/13 696s 86 h-m-p 1.6000 8.0000 0.0000 Y 14707.663779 0 1.0656 2574 | 0/13 696s 87 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663779 m 8.0000 2603 | 0/13 696s 88 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663779 m 8.0000 2632 | 0/13 696s 89 h-m-p 0.1876 8.0000 0.0000 +Y 14707.663779 0 1.2652 2662 | 0/13 696s 90 h-m-p 1.6000 8.0000 0.0000 C 14707.663779 0 1.6000 2691 | 0/13 696s 91 h-m-p 1.6000 8.0000 0.0000 C 14707.663779 0 1.6000 2720 | 0/13 696s 92 h-m-p 1.4621 8.0000 0.0000 Y 14707.663779 0 0.3655 2749 | 0/13 696s 93 h-m-p 0.2626 8.0000 0.0000 C 14707.663779 0 0.2626 2778 | 0/13 696s 94 h-m-p 0.0696 8.0000 0.0000 ----C 14707.663779 0 0.0001 2811 696s Out.. 696s lnL = -14707.663779 696s 2812 lfun, 2812 eigenQcodon, 30932 P(t) 696s Calculating SE's 696s 696s Reconstructed ancestral states go into file rst. 696s 696s lnL = -14707.663779 from ProbSitePattern. 696s Marginal reconstruction. 696s Node 8: lnL = -14707.663779 696s Node 9: lnL = -14707.663779 696s Node 10: lnL = -14707.663779 696s Node 11: lnL = -14707.663779 696s Node 12: lnL = -14707.663779 696s 696s lnL = -14707.663779 from ProbSitePattern. 696s Joint reconstruction. 696s 696s 4502400 bytes for conP, adjusted 696s 696s Time used: 0:20 696s Passed 696s 696s Test 9 696s 696s CODONML in paml version 4.9j, October 2019 696s 696s ---------------------------------------------- 696s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 696s TTC | TCC | TAC | TGC 696s Leu L TTA | TCA | *** * TAA | Trp W TGA 696s TTG | TCG | TAG | TGG 696s ---------------------------------------------- 696s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 696s CTC | CCC | CAC | CGC 696s CTA | CCA | Gln Q CAA | CGA 696s CTG | CCG | CAG | CGG 696s ---------------------------------------------- 696s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 696s ATC | ACC | AAC | AGC 696s Met M ATA | ACA | Lys K AAA | *** * AGA 696s ATG | ACG | AAG | AGG 696s ---------------------------------------------- 696s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 696s GTC | GCC | GAC | GGC 696s GTA | GCA | Glu E GAA | GGA 696s GTG | GCG | GAG | GGG 696s ---------------------------------------------- 696s Nice code, uuh? 696s 696s 696s 70 one-step aa pairs. 696s Reading omega class from OmegaAA.dat. 696s 2 dN/dS ratios estimated from data. 696s 696s Class #1: RH RK DE AG AP AS AT AV NI NS NT NY CG CF CS CW CY QL QP GS GW GV IL IM IF IS IT IV LM LF LP LS LW LV MT MV FS FY FV PS PT ST SW SY 696s 696s 696s pair 1: |RH| |HR ( 8, 1)| in class 1 696s pair 2: |RK| |KR (11, 1)| 696s This pair cannot change in one step and is ignored! 696s 696s pair 3: |DE| |ED ( 6, 3)| in class 1 696s pair 4: |AG| |GA ( 7, 0)| in class 1 696s pair 5: |AP| |PA (14, 0)| in class 1 696s pair 6: |AS| |SA (15, 0)| in class 1 696s pair 7: |AT| |TA (16, 0)| in class 1 696s pair 8: |AV| |VA (19, 0)| in class 1 696s pair 9: |NI| |IN ( 9, 2)| in class 1 696s pair 10: |NS| |SN (15, 2)| in class 1 696s pair 11: |NT| |TN (16, 2)| in class 1 696s pair 12: |NY| |YN (18, 2)| in class 1 696s pair 13: |CG| |GC ( 7, 4)| in class 1 696s pair 14: |CF| |FC (13, 4)| in class 1 696s pair 15: |CS| |SC (15, 4)| in class 1 696s pair 16: |CW| |WC (17, 4)| in class 1 696s pair 17: |CY| |YC (18, 4)| in class 1 696s pair 18: |QL| |LQ (10, 5)| in class 1 696s pair 19: |QP| |PQ (14, 5)| in class 1 696s pair 20: |GS| |SG (15, 7)| in class 1 696s pair 21: |GW| |WG (17, 7)| in class 1 696s pair 22: |GV| |VG (19, 7)| in class 1 696s pair 23: |IL| |LI (10, 9)| in class 1 696s pair 24: |IM| |MI (12, 9)| in class 1 696s pair 25: |IF| |FI (13, 9)| in class 1 696s pair 26: |IS| |SI (15, 9)| in class 1 696s pair 27: |IT| |TI (16, 9)| in class 1 696s pair 28: |IV| |VI (19, 9)| in class 1 696s pair 29: |LM| |ML (12,10)| in class 1 696s pair 30: |LF| |FL (13,10)| in class 1 696s pair 31: |LP| |PL (14,10)| in class 1 696s pair 32: |LS| |SL (15,10)| in class 1 696s pair 33: |LW| |WL (17,10)| in class 1 696s pair 34: |LV| |VL (19,10)| in class 1 696s pair 35: |MT| |TM (16,12)| in class 1 696s pair 36: |MV| |VM (19,12)| in class 1 696s pair 37: |FS| |SF (15,13)| in class 1 696s pair 38: |FY| |YF (18,13)| in class 1 696s pair 39: |FV| |VF (19,13)| in class 1 696s pair 40: |PS| |SP (15,14)| in class 1 696s pair 41: |PT| |TP (16,14)| in class 1 696s pair 42: |ST| |TS (16,15)| in class 1 696s pair 43: |SW| |WS (17,15)| in class 1 696s pair 44: |SY| |YS (18,15)| in class 1 ns = 6 ls = 10707 696s Reading sequences, sequential format.. 696s Reading seq # 1: 1.Human_Horai Reading seq # 2: 2.Human_Arnason Reading seq # 3: 3.Chimp_Horai Reading seq # 4: 4.Chimp_Arnason Reading seq # 5: 5.Gorilla_Horai Reading seq # 6: 6.Gorilla_Arnason 696s Sequences read.. 696s Counting site patterns.. 0:00 696s Compressing, 607 patterns at 3569 / 3569 sites (100.0%), 0:00 696s Collecting fpatt[] & pose[], 607 patterns at 3569 / 3569 sites (100.0%), 0:00 696s Counting codons.. 696s 696s 120 bytes for distance 696s 582720 bytes for conP 696s 9014070827248422656 bytes for fhK 696s 5000000 bytes for space 696s 696s 2 branch types are in tree. Stop if wrong. 696s TREE # 1 696s ((1, 2), (3, 4), (5, 6)); MP score: 1801 696s 1165440 bytes for conP, adjusted 696s 696s 0.017269 0.085978 0.041611 0.024368 0.078336 0.041560 0.028146 0.106395 0.013351 1.312221 1.466627 1.193442 1.562857 1.368466 696s 696s ntime & nrate & np: 9 5 14 696s 696s Bounds (np=14): 703s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 0.000100 0.000100 703s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 999.000000 999.000000 703s 703s np = 14 703s lnL0 = -26610.061782 703s 703s Iterating by ming2 703s Initial: fx= 26610.061782 703s x= 0.01727 0.08598 0.04161 0.02437 0.07834 0.04156 0.02815 0.10639 0.01335 1.31222 1.46663 1.19344 1.56286 1.36847 703s 703s 1 h-m-p 0.0000 0.0000 39439.9712 ++ 24286.968538 m 0.0000 19 | 0/14 703s 2 h-m-p 0.0000 0.0000 19419.6325 +YCYCC 24216.551223 4 0.0000 43 | 0/14 703s 3 h-m-p 0.0000 0.0000 7512.0160 ++ 24183.699666 m 0.0000 60 | 1/14 703s 4 h-m-p 0.0000 0.0000 18561.1527 +CYCYYYC 23907.273289 6 0.0000 86 | 0/14 703s 5 h-m-p 0.0000 0.0000 227897.3801 CCCC 23904.866002 3 0.0000 109 | 0/14 703s 6 h-m-p 0.0000 0.0000 9990.7061 +YYCCC 23864.223395 4 0.0000 133 | 0/14 703s 7 h-m-p 0.0000 0.0000 4773.0025 +YYCCC 23853.263388 4 0.0000 157 | 0/14 703s 8 h-m-p 0.0000 0.0004 1479.7273 ++YYCCCCC 23700.010858 6 0.0002 186 | 0/14 703s 9 h-m-p 0.0001 0.0005 3686.3605 +CYYCYCYCCC 22099.936291 9 0.0004 219 | 0/14 703s 10 h-m-p 0.0000 0.0000 4820.6485 CYCCC 22077.275717 4 0.0000 243 | 0/14 703s 11 h-m-p 0.0000 0.0019 1657.5342 +++YYYCCCC 21213.154875 6 0.0016 272 | 0/14 703s 12 h-m-p 0.0000 0.0001 1775.6031 +YYYYCYCCC 21139.642842 8 0.0001 301 | 0/14 703s 13 h-m-p 0.0048 0.0238 20.4629 +CYYCCCCC 21038.595682 7 0.0216 331 | 0/14 703s 14 h-m-p 0.0065 0.0326 26.1095 +YYCYCCC 21016.897125 6 0.0214 358 | 0/14 703s 15 h-m-p 0.0029 0.0143 60.4135 +YCYYYC 20974.943684 5 0.0135 383 | 0/14 703s 16 h-m-p 0.0461 0.2307 3.5514 +CCC 20766.068962 2 0.1845 405 | 0/14 703s 17 h-m-p 0.0368 0.1840 2.9589 YCCC 20702.439309 3 0.0725 427 | 0/14 703s 18 h-m-p 0.1036 0.5182 0.4899 +YYCCC 20685.799212 4 0.3118 451 | 0/14 703s 19 h-m-p 0.2525 2.3404 0.6048 ++ 20625.890654 m 2.3404 482 | 0/14 703s 20 h-m-p 0.0089 0.0443 18.7522 YYCC 20613.667370 3 0.0120 517 | 0/14 703s 21 h-m-p 0.0975 0.4875 1.6137 CCCC 20603.856230 3 0.1584 540 | 0/14 703s 22 h-m-p 0.0837 0.4187 2.9789 +YCYCCC 20581.146555 5 0.2458 566 | 0/14 703s 23 h-m-p 0.0595 0.2976 3.3952 +YYCCC 20566.941701 4 0.1832 590 | 0/14 703s 24 h-m-p 0.1598 1.8035 3.8926 +CYC 20526.428752 2 0.6152 611 | 0/14 703s 25 h-m-p 1.1579 8.0000 2.0683 YCCC 20505.577076 3 0.5148 633 | 0/14 703s 26 h-m-p 0.7647 3.8237 0.9020 +YCCCC 20465.313945 4 2.2463 658 | 0/14 703s 27 h-m-p 0.7531 3.7655 0.8848 YC 20458.499032 1 1.5397 690 | 0/14 703s 28 h-m-p 1.6000 8.0000 0.6328 CCC 20455.365978 2 2.5282 725 | 0/14 703s 29 h-m-p 1.6000 8.0000 0.1233 CCC 20454.588924 2 2.6372 760 | 0/14 703s 30 h-m-p 1.6000 8.0000 0.0131 +YC 20453.067700 1 5.3941 793 | 0/14 703s 31 h-m-p 0.6556 8.0000 0.1074 +YCCC 20450.356277 3 3.8837 830 | 0/14 703s 32 h-m-p 0.9562 8.0000 0.4362 +YCC 20448.854924 2 2.4982 865 | 0/14 703s 33 h-m-p 1.6000 8.0000 0.5409 YCCC 20446.458577 3 3.7042 901 | 0/14 703s 34 h-m-p 1.6000 8.0000 0.3011 CCC 20445.480175 2 2.5317 936 | 0/14 703s 35 h-m-p 1.6000 8.0000 0.0903 YC 20444.688287 1 2.7536 968 | 0/14 703s 36 h-m-p 1.6000 8.0000 0.0119 CC 20444.426514 1 1.6925 1001 | 0/14 703s 37 h-m-p 1.6000 8.0000 0.0077 CC 20444.374023 1 1.4715 1034 | 0/14 703s 38 h-m-p 0.2168 8.0000 0.0524 ++C 20444.350967 0 3.3659 1067 | 0/14 703s 39 h-m-p 1.6000 8.0000 0.0141 ++ 20444.290946 m 8.0000 1098 | 0/14 703s 40 h-m-p 1.6000 8.0000 0.0385 ++ 20443.859564 m 8.0000 1129 | 0/14 703s 41 h-m-p 0.8006 4.0032 0.0970 CCC 20443.615683 2 1.4454 1164 | 0/14 703s 42 h-m-p 0.9797 8.0000 0.1432 YC 20443.497958 1 2.0034 1196 | 0/14 703s 43 h-m-p 1.6000 8.0000 0.0127 YC 20443.356868 1 3.7899 1228 | 0/14 703s 44 h-m-p 0.7674 8.0000 0.0629 ++ 20442.545205 m 8.0000 1259 | 0/14 703s 45 h-m-p 1.6000 8.0000 0.2565 YCCC 20441.227237 3 3.6808 1295 | 0/14 703s 46 h-m-p 1.6000 8.0000 0.5771 CCC 20440.753417 2 1.7828 1330 | 0/14 705s 47 h-m-p 1.6000 8.0000 0.0665 YC 20440.475191 1 3.7281 1362 | 0/14 705s 48 h-m-p 1.6000 8.0000 0.0972 CC 20440.388976 1 1.7908 1395 | 0/14 705s 49 h-m-p 1.6000 8.0000 0.0775 C 20440.382867 0 1.3891 1426 | 0/14 705s 50 h-m-p 1.6000 8.0000 0.0008 Y 20440.382781 0 1.2491 1457 | 0/14 705s 51 h-m-p 1.6000 8.0000 0.0005 Y 20440.382774 0 1.1278 1488 | 0/14 705s 52 h-m-p 1.6000 8.0000 0.0003 C 20440.382774 0 0.4000 1519 | 0/14 705s 53 h-m-p 0.4982 8.0000 0.0003 C 20440.382774 0 0.1004 1550 | 0/14 705s 54 h-m-p 0.0856 8.0000 0.0003 -Y 20440.382774 0 0.0054 1582 | 0/14 705s 55 h-m-p 0.0160 8.0000 0.0011 +Y 20440.382774 0 0.0429 1614 | 0/14 705s 56 h-m-p 0.3431 8.0000 0.0001 -----Y 20440.382774 0 0.0001 1650 | 0/14 705s 57 h-m-p 0.0160 8.0000 0.0006 ----C 20440.382774 0 0.0000 1685 705s Out.. 705s lnL = -20440.382774 705s 1686 lfun, 3372 eigenQcodon, 15174 P(t) 705s 705s Time used: 0:09 705s Passed 705s 705s Test 10 705s 705s CODONML in paml version 4.9j, October 2019 705s 705s ---------------------------------------------- 705s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 705s TTC | TCC | TAC | TGC 705s Leu L TTA | TCA | *** * TAA | Trp W TGA 705s TTG | TCG | TAG | TGG 705s ---------------------------------------------- 705s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 705s CTC | CCC | CAC | CGC 705s CTA | CCA | Gln Q CAA | CGA 705s CTG | CCG | CAG | CGG 705s ---------------------------------------------- 705s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 705s ATC | ACC | AAC | AGC 705s Met M ATA | ACA | Lys K AAA | *** * AGA 705s ATG | ACG | AAG | AGG 705s ---------------------------------------------- 705s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 705s GTC | GCC | GAC | GGC 705s GTA | GCA | Glu E GAA | GGA 705s GTG | GCG | GAG | GGG 705s ---------------------------------------------- 705s Nice code, uuh? 705s ns = 2 ls = 10707 705s Reading sequences, sequential format.. 705s Reading seq # 1: Human_Horai Reading seq # 2: Chimp_Horai 705s Sequences read.. 705s Counting site patterns.. 0:00 705s Compressing, 243 patterns at 3569 / 3569 sites (100.0%), 0:00 705s Collecting fpatt[] & pose[], 243 patterns at 3569 / 3569 sites (100.0%), 0:00 705s Counting codons.. 705s 705s 8 bytes for distance 705s 233280 bytes for conP 705s 11795692574813266176 bytes for fhK 705s 5000000 bytes for space 705s 705s TREE # 1 705s (1, 2); MP score: 1008 705s 0.522344 1.234567 1.919032 2.477190 2.435064 1.260400 1.903828 1.433761 -0.662932 0.613276 1.474206 1.548287 -0.576504 0.785908 1.672125 -1.118396 -0.013974 1.718286 -0.721910 1.236105 2.008885 2.560137 0.865474 0.601260 1.749711 0.876841 -0.682882 -0.026085 1.338310 1.402277 -0.589980 -0.745268 0.296390 0.610410 -1.501455 1.680762 2.240942 2.246383 0.564679 1.229881 1.962432 1.798824 -0.727489 0.719643 1.942545 1.538661 -0.515701 -0.383161 0.968305 0.433407 0.803269 1.159754 -0.743308 0.598476 1.977615 1.429437 -0.610660 -0.155464 1.032154 1.318261 -0.261195 0.170093 1.431799 1.188062 1.414000 705s 705s ntime & nrate & np: 1 64 65 705s 705s Bounds (np=65): 705s 0.000004 0.000100 0.000100 0.000100 0.000100 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 0.000100 705s 50.000000 999.000000 999.000000 999.000000 999.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 999.000000 705s 705s np = 65 705s lnL0 = -19230.475941 705s 705s Iterating by ming2 705s Initial: fx= 19230.475941 707s x= 0.52234 1.23457 1.91903 2.47719 2.43506 1.26040 1.90383 1.43376 -0.66293 0.61328 1.47421 1.54829 -0.57650 0.78591 1.67213 -1.11840 -0.01397 1.71829 -0.72191 1.23611 2.00889 2.56014 0.86547 0.60126 1.74971 0.87684 -0.68288 -0.02608 1.33831 1.40228 -0.58998 -0.74527 0.29639 0.61041 -1.50146 1.68076 2.24094 2.24638 0.56468 1.22988 1.96243 1.79882 -0.72749 0.71964 1.94255 1.53866 -0.51570 -0.38316 0.96831 0.43341 0.80327 1.15975 -0.74331 0.59848 1.97761 1.42944 -0.61066 -0.15546 1.03215 1.31826 -0.26119 0.17009 1.43180 1.18806 1.41400 707s 707s 1 h-m-p 0.0000 0.0001 4017.4259 +YCCYCCC 18116.509277 6 0.0001 82 | 0/65 707s 2 h-m-p 0.0005 0.0027 787.2594 +CYCYYYCYCY 16710.271432 10 0.0026 165 | 0/65 707s 3 h-m-p 0.0001 0.0003 516.0358 CCCCC 16701.664014 4 0.0001 241 | 0/65 707s 4 h-m-p 0.0000 0.0041 1137.9569 ++YCCCCC 16433.086541 5 0.0013 320 | 0/65 707s 5 h-m-p 0.0029 0.0145 196.1636 CCCC 16415.014839 3 0.0012 394 | 0/65 707s 6 h-m-p 0.0015 0.0262 146.3841 YCCC 16388.516417 3 0.0035 467 | 0/65 707s 7 h-m-p 0.0089 1.1679 58.0849 CCC 16374.483387 2 0.0095 539 | 0/65 707s 8 h-m-p 0.0117 1.7420 46.9211 CCC 16364.437615 2 0.0113 611 | 0/65 707s 9 h-m-p 0.0105 0.5544 50.5782 CCC 16349.912253 2 0.0164 683 | 0/65 707s 10 h-m-p 0.0187 0.7911 44.3461 CCC 16334.577154 2 0.0205 755 | 0/65 707s 11 h-m-p 0.0219 0.4727 41.5379 CC 16321.284179 1 0.0190 825 | 0/65 707s 12 h-m-p 0.0158 0.1658 49.9003 CCCC 16304.251483 3 0.0200 899 | 0/65 707s 13 h-m-p 0.0161 0.0998 61.9088 YYC 16290.766232 2 0.0132 969 | 0/65 707s 14 h-m-p 0.0189 0.4533 43.1826 CCC 16277.297025 2 0.0211 1041 | 0/65 707s 15 h-m-p 0.0226 0.2485 40.2146 CCC 16263.407954 2 0.0267 1113 | 0/65 707s 16 h-m-p 0.0237 0.1837 45.3062 YYC 16252.918873 2 0.0199 1183 | 0/65 707s 17 h-m-p 0.0257 0.2356 35.1301 YCCC 16247.900443 3 0.0142 1256 | 0/65 707s 18 h-m-p 0.0168 0.2179 29.6071 CCCC 16241.967019 3 0.0222 1330 | 0/65 707s 19 h-m-p 0.0236 0.3176 27.8691 CYC 16236.917412 2 0.0210 1401 | 0/65 707s 20 h-m-p 0.0171 0.2730 34.2951 CYC 16232.399249 2 0.0166 1472 | 0/65 707s 21 h-m-p 0.0190 0.3073 29.9243 CCC 16228.019479 2 0.0194 1544 | 0/65 707s 22 h-m-p 0.0259 0.3825 22.4543 CYC 16224.381777 2 0.0236 1615 | 0/65 707s 23 h-m-p 0.0234 0.6399 22.7064 YC 16222.047623 1 0.0153 1684 | 0/65 707s 24 h-m-p 0.0198 0.4082 17.5242 CCCC 16218.457336 3 0.0302 1758 | 0/65 707s 25 h-m-p 0.0407 5.0007 13.0106 CCC 16213.566403 2 0.0439 1830 | 0/65 707s 26 h-m-p 0.0216 0.3057 26.4531 CYC 16208.377908 2 0.0212 1901 | 0/65 707s 27 h-m-p 0.0254 0.6108 22.0698 CCC 16200.045202 2 0.0394 1973 | 0/65 707s 28 h-m-p 0.0280 2.5105 31.1304 YC 16194.825934 1 0.0198 2042 | 0/65 707s 29 h-m-p 0.0434 0.4040 14.1690 YCCC 16193.136570 3 0.0192 2115 | 0/65 707s 30 h-m-p 0.0130 2.5489 20.9830 CCC 16190.798043 2 0.0203 2187 | 0/65 707s 31 h-m-p 0.0160 0.9051 26.6515 CCC 16187.913287 2 0.0217 2259 | 0/65 707s 32 h-m-p 0.0276 0.8458 20.8966 CC 16185.480810 1 0.0252 2329 | 0/65 707s 33 h-m-p 0.0301 2.5366 17.4937 CC 16183.478838 1 0.0261 2399 | 0/65 707s 34 h-m-p 0.0240 2.3940 19.0111 CC 16180.735085 1 0.0334 2469 | 0/65 707s 35 h-m-p 0.0261 0.7928 24.3072 CCC 16177.630017 2 0.0297 2541 | 0/65 707s 36 h-m-p 0.0394 1.0949 18.3035 CCC 16174.331787 2 0.0398 2613 | 0/65 707s 37 h-m-p 0.0307 1.0668 23.7486 YCCC 16167.799802 3 0.0586 2686 | 0/65 707s 38 h-m-p 0.0406 0.9954 34.2500 CC 16162.365296 1 0.0345 2756 | 0/65 707s 39 h-m-p 0.0365 0.7155 32.3751 CCC 16156.316526 2 0.0425 2828 | 0/65 707s 40 h-m-p 0.0255 0.3280 53.9241 CCCC 16147.669567 3 0.0376 2902 | 0/65 707s 41 h-m-p 0.0962 0.7894 21.0697 CC 16146.079939 1 0.0206 2972 | 0/65 707s 42 h-m-p 0.0273 2.3853 15.9210 CCC 16144.450045 2 0.0311 3044 | 0/65 707s 43 h-m-p 0.0259 2.5676 19.0694 CCC 16142.368128 2 0.0349 3116 | 0/65 707s 44 h-m-p 0.0415 1.5015 16.0454 YC 16141.163342 1 0.0255 3185 | 0/65 707s 45 h-m-p 0.0380 2.6802 10.7622 YC 16138.614395 1 0.0790 3254 | 0/65 707s 46 h-m-p 0.0294 0.6326 28.9397 CCC 16134.833780 2 0.0433 3326 | 0/65 707s 47 h-m-p 0.0362 0.8421 34.6749 CC 16130.961114 1 0.0381 3396 | 0/65 707s 48 h-m-p 0.0341 0.4677 38.7434 YCC 16128.318019 2 0.0240 3467 | 0/65 711s 49 h-m-p 0.0736 1.7585 12.6171 YC 16126.957753 1 0.0408 3536 | 0/65 711s 50 h-m-p 0.0251 2.0547 20.5301 YCC 16124.883704 2 0.0407 3607 | 0/65 711s 51 h-m-p 0.0655 1.3071 12.7658 YCC 16123.711331 2 0.0434 3678 | 0/65 711s 52 h-m-p 0.0258 0.8835 21.4937 YC 16121.363117 1 0.0540 3747 | 0/65 711s 53 h-m-p 0.0727 0.8600 15.9546 YCC 16120.058325 2 0.0431 3818 | 0/65 711s 54 h-m-p 0.0523 1.2518 13.1475 YCC 16119.209823 2 0.0371 3889 | 0/65 711s 55 h-m-p 0.0402 1.3961 12.1311 CC 16118.141382 1 0.0533 3959 | 0/65 711s 56 h-m-p 0.0252 0.6300 25.7106 YCCC 16115.420938 3 0.0613 4032 | 0/65 711s 57 h-m-p 0.0829 0.8205 18.9935 YCCC 16113.840101 3 0.0474 4105 | 0/65 711s 58 h-m-p 0.0899 3.0007 10.0059 YC 16112.913255 1 0.0497 4174 | 0/65 711s 59 h-m-p 0.0475 1.5476 10.4825 CCC 16111.944468 2 0.0514 4246 | 0/65 711s 60 h-m-p 0.0805 8.0000 6.6927 YC 16111.239198 1 0.0541 4315 | 0/65 711s 61 h-m-p 0.0527 2.9239 6.8788 CC 16110.535337 1 0.0606 4385 | 0/65 711s 62 h-m-p 0.0413 2.8673 10.0902 YC 16109.342436 1 0.0754 4454 | 0/65 711s 63 h-m-p 0.0917 2.4235 8.2968 CYC 16108.459290 2 0.0885 4525 | 0/65 711s 64 h-m-p 0.0522 1.0608 14.0749 CCC 16107.477409 2 0.0624 4597 | 0/65 711s 65 h-m-p 0.0474 0.7952 18.5265 CCC 16106.462153 2 0.0522 4669 | 0/65 711s 66 h-m-p 0.0690 1.0523 14.0106 CCC 16105.416096 2 0.0700 4741 | 0/65 711s 67 h-m-p 0.2157 7.5181 4.5463 YC 16104.889650 1 0.1282 4810 | 0/65 711s 68 h-m-p 0.1255 3.5447 4.6428 YC 16104.031317 1 0.3119 4879 | 0/65 711s 69 h-m-p 0.1308 1.9394 11.0717 CYC 16103.202914 2 0.1262 4950 | 0/65 711s 70 h-m-p 0.6478 8.0000 2.1572 YC 16102.568494 1 0.3838 5019 | 0/65 711s 71 h-m-p 0.1933 5.3503 4.2848 CC 16102.096485 1 0.1523 5089 | 0/65 711s 72 h-m-p 0.3250 8.0000 2.0076 YC 16101.710195 1 0.6021 5158 | 0/65 711s 73 h-m-p 0.1441 1.7320 8.3860 YCCC 16101.528023 3 0.0846 5231 | 0/65 711s 74 h-m-p 0.4328 8.0000 1.6395 YC 16101.407545 1 0.2128 5300 | 0/65 711s 75 h-m-p 0.1372 8.0000 2.5431 YC 16101.170072 1 0.3018 5369 | 0/65 711s 76 h-m-p 0.8783 8.0000 0.8738 YC 16101.070297 1 0.4778 5438 | 0/65 711s 77 h-m-p 0.2697 8.0000 1.5484 YC 16101.032824 1 0.1444 5572 | 0/65 711s 78 h-m-p 0.2392 8.0000 0.9348 +CC 16100.929841 1 0.9729 5643 | 0/65 711s 79 h-m-p 1.6000 8.0000 0.0667 C 16100.854879 0 1.5430 5776 | 0/65 711s 80 h-m-p 0.2749 8.0000 0.3744 +CCC 16100.730815 2 1.7796 5914 | 0/65 711s 81 h-m-p 1.4287 8.0000 0.4663 YC 16100.568748 1 0.7038 6048 | 0/65 711s 82 h-m-p 0.2201 8.0000 1.4910 +CYCCC 16100.123880 4 1.4326 6189 | 0/65 711s 83 h-m-p 1.6000 8.0000 0.9923 YYC 16099.912747 2 1.2584 6259 | 0/65 711s 84 h-m-p 1.6000 8.0000 0.4290 YC 16099.818617 1 0.7747 6393 | 0/65 711s 85 h-m-p 0.6102 8.0000 0.5446 +YYC 16099.647547 2 2.2585 6529 | 0/65 711s 86 h-m-p 1.6000 8.0000 0.2864 YC 16099.474012 1 3.8021 6663 | 0/65 711s 87 h-m-p 1.3339 8.0000 0.8164 YCCC 16099.333273 3 1.4338 6801 | 0/65 711s 88 h-m-p 1.6000 8.0000 0.6450 C 16098.969766 0 1.7256 6934 | 0/65 711s 89 h-m-p 0.4135 8.0000 2.6916 CCCC 16098.686523 3 0.5498 7073 | 0/65 711s 90 h-m-p 0.9725 8.0000 1.5217 CCCC 16097.844640 3 1.1392 7147 | 0/65 711s 91 h-m-p 1.6000 8.0000 1.0756 YC 16097.285080 1 0.8662 7216 | 0/65 711s 92 h-m-p 0.8497 8.0000 1.0965 CYC 16096.711388 2 0.9730 7287 | 0/65 711s 93 h-m-p 0.1916 8.0000 5.5670 CYCCC 16096.125631 4 0.3051 7362 | 0/65 711s 94 h-m-p 1.3055 8.0000 1.3011 CYC 16095.658806 2 1.2587 7433 | 0/65 711s 95 h-m-p 1.6000 8.0000 0.4212 YC 16095.528011 1 0.7788 7502 | 0/65 711s 96 h-m-p 0.4109 8.0000 0.7983 +YC 16095.425756 1 1.2227 7637 | 0/65 711s 97 h-m-p 1.6000 8.0000 0.1778 CC 16095.400810 1 1.7425 7772 | 0/65 711s 98 h-m-p 1.6000 8.0000 0.0682 +CC 16095.347225 1 5.8258 7908 | 0/65 711s 99 h-m-p 1.6000 8.0000 0.2024 YC 16095.252460 1 2.7241 8042 | 0/65 711s 100 h-m-p 1.6000 8.0000 0.0841 CC 16095.240382 1 1.3300 8177 | 0/65 711s 101 h-m-p 1.6000 8.0000 0.0256 +YC 16095.224980 1 4.2898 8312 | 0/65 711s 102 h-m-p 0.5649 8.0000 0.1945 +CC 16095.176197 1 3.4198 8448 | 0/65 714s 103 h-m-p 1.5835 8.0000 0.4201 CYCC 16095.039331 3 2.7752 8586 | 0/65 714s 104 h-m-p 1.6000 8.0000 0.5066 CCC 16094.872931 2 2.1560 8723 | 0/65 714s 105 h-m-p 1.6000 8.0000 0.3608 CYC 16094.761466 2 1.7103 8859 | 0/65 714s 106 h-m-p 0.5036 8.0000 1.2251 CCC 16094.703246 2 0.5776 8996 | 0/65 714s 107 h-m-p 1.6000 8.0000 0.4376 YY 16094.589722 1 1.4999 9065 | 0/65 714s 108 h-m-p 1.6000 8.0000 0.1063 YC 16094.533227 1 1.1178 9199 | 0/65 714s 109 h-m-p 0.1381 8.0000 0.8609 +YCCC 16094.467981 3 1.1140 9338 | 0/65 714s 110 h-m-p 1.6000 8.0000 0.5002 C 16094.410855 0 1.6121 9471 | 0/65 714s 111 h-m-p 1.6000 8.0000 0.3801 YCC 16094.371568 2 1.0659 9607 | 0/65 714s 112 h-m-p 0.3609 8.0000 1.1224 CYC 16094.341033 2 0.6698 9743 | 0/65 714s 113 h-m-p 1.6000 8.0000 0.2934 YY 16094.321330 1 1.4588 9812 | 0/65 714s 114 h-m-p 1.6000 8.0000 0.0551 YC 16094.305846 1 1.1851 9946 | 0/65 714s 115 h-m-p 0.1000 8.0000 0.6530 ++YC 16094.289635 1 1.0070 10082 | 0/65 714s 116 h-m-p 1.6000 8.0000 0.3988 Y 16094.277144 0 1.6000 10215 | 0/65 714s 117 h-m-p 1.6000 8.0000 0.1123 YC 16094.270702 1 0.7732 10349 | 0/65 714s 118 h-m-p 0.3159 8.0000 0.2748 +CCC 16094.261347 2 1.7920 10487 | 0/65 714s 119 h-m-p 1.6000 8.0000 0.2819 YY 16094.254974 1 1.6000 10621 | 0/65 714s 120 h-m-p 1.6000 8.0000 0.1143 CC 16094.249251 1 1.3068 10756 | 0/65 714s 121 h-m-p 0.2518 8.0000 0.5932 +CCC 16094.241015 2 1.1952 10894 | 0/65 714s 122 h-m-p 1.6000 8.0000 0.3120 CC 16094.231838 1 2.0716 11029 | 0/65 714s 123 h-m-p 1.6000 8.0000 0.1961 YC 16094.219230 1 2.6404 11163 | 0/65 714s 124 h-m-p 0.9460 8.0000 0.5473 Y 16094.215466 0 0.5977 11296 | 0/65 714s 125 h-m-p 0.2671 8.0000 1.2246 +YYC 16094.196862 2 0.8533 11432 | 0/65 714s 126 h-m-p 1.6000 8.0000 0.1492 +YC 16094.148480 1 5.1398 11502 | 0/65 714s 127 h-m-p 0.1610 8.0000 4.7642 YYC 16094.123690 2 0.1610 11637 | 0/65 714s 128 h-m-p 0.6999 8.0000 1.0960 CC 16094.094465 1 0.7213 11707 | 0/65 714s 129 h-m-p 1.6000 8.0000 0.0798 YC 16094.061435 1 0.8827 11776 | 0/65 714s 130 h-m-p 0.1181 8.0000 0.5967 ++YYY 16094.005180 2 1.8126 11913 | 0/65 714s 131 h-m-p 1.6000 8.0000 0.2708 CC 16093.946044 1 1.5795 12048 | 0/65 714s 132 h-m-p 0.3777 8.0000 1.1326 CCC 16093.919252 2 0.6028 12185 | 0/65 714s 133 h-m-p 1.5482 8.0000 0.4410 YC 16093.882489 1 1.0736 12254 | 0/65 714s 134 h-m-p 1.0948 8.0000 0.4324 CYC 16093.839131 2 1.9109 12390 | 0/65 714s 135 h-m-p 1.6000 8.0000 0.1737 CYC 16093.787282 2 1.2094 12526 | 0/65 714s 136 h-m-p 0.1431 8.0000 1.4679 +YCCC 16093.733012 3 0.6495 12665 | 0/65 714s 137 h-m-p 1.0190 8.0000 0.9357 CCC 16093.674025 2 1.0847 12737 | 0/65 714s 138 h-m-p 1.6000 8.0000 0.1455 YC 16093.636730 1 0.6451 12871 | 0/65 714s 139 h-m-p 0.1447 8.0000 0.6488 ++YYC 16093.543488 2 1.9783 13008 | 0/65 714s 140 h-m-p 1.6000 8.0000 0.3070 CC 16093.493647 1 1.5881 13143 | 0/65 714s 141 h-m-p 0.2820 8.0000 1.7288 CYC 16093.449264 2 0.4754 13279 | 0/65 714s 142 h-m-p 1.6000 8.0000 0.3017 YC 16093.430120 1 0.8804 13348 | 0/65 714s 143 h-m-p 0.3263 8.0000 0.8140 YC 16093.415047 1 0.5867 13482 | 0/65 714s 144 h-m-p 1.6000 8.0000 0.1015 YC 16093.399833 1 0.9642 13616 | 0/65 714s 145 h-m-p 0.1830 8.0000 0.5346 +CYC 16093.378463 2 1.3375 13753 | 0/65 714s 146 h-m-p 1.6000 8.0000 0.2361 C 16093.361914 0 2.0126 13886 | 0/65 714s 147 h-m-p 0.9848 8.0000 0.4825 YC 16093.352119 1 0.9848 14020 | 0/65 714s 148 h-m-p 1.6000 8.0000 0.1722 CC 16093.344992 1 0.6375 14155 | 0/65 714s 149 h-m-p 0.3612 8.0000 0.3039 +CC 16093.338223 1 1.5659 14291 | 0/65 714s 150 h-m-p 1.6000 8.0000 0.1053 C 16093.333088 0 1.6000 14424 | 0/65 714s 151 h-m-p 0.6093 8.0000 0.2764 C 16093.331319 0 0.7164 14557 | 0/65 714s 152 h-m-p 1.6000 8.0000 0.0341 C 16093.330660 0 1.2939 14690 | 0/65 714s 153 h-m-p 1.6000 8.0000 0.0215 YC 16093.329697 1 3.6846 14824 | 0/65 714s 154 h-m-p 0.6864 8.0000 0.1152 +C 16093.327690 0 3.4752 14958 | 0/65 714s 155 h-m-p 1.6000 8.0000 0.1275 YC 16093.326884 1 1.0668 15092 | 0/65 714s 156 h-m-p 1.6000 8.0000 0.0637 Y 16093.326673 0 1.1509 15225 | 0/65 716s 157 h-m-p 1.6000 8.0000 0.0026 ++ 16093.326214 m 8.0000 15358 | 0/65 716s 158 h-m-p 1.6000 8.0000 0.0075 ++ 16093.321581 m 8.0000 15491 | 0/65 716s 159 h-m-p 0.1078 8.0000 0.5593 ++YYC 16093.287472 2 1.7326 15628 | 0/65 716s 160 h-m-p 0.7538 8.0000 1.2854 YC 16093.275493 1 0.3901 15762 | 0/65 716s 161 h-m-p 0.9504 8.0000 0.5277 CC 16093.267243 1 0.3386 15832 | 0/65 716s 162 h-m-p 0.3364 8.0000 0.5311 YC 16093.254312 1 0.7619 15966 | 0/65 716s 163 h-m-p 1.6000 8.0000 0.1006 YC 16093.249848 1 1.1036 16100 | 0/65 716s 164 h-m-p 0.2507 8.0000 0.4427 +Y 16093.246182 0 0.7168 16234 | 0/65 716s 165 h-m-p 1.3736 8.0000 0.2310 CCC 16093.242104 2 1.9886 16371 | 0/65 716s 166 h-m-p 1.6000 8.0000 0.0982 C 16093.238717 0 1.4430 16504 | 0/65 716s 167 h-m-p 0.4245 8.0000 0.3338 +YC 16093.235770 1 1.2022 16639 | 0/65 716s 168 h-m-p 1.6000 8.0000 0.1959 Y 16093.234148 0 1.2012 16772 | 0/65 716s 169 h-m-p 0.8096 8.0000 0.2907 Y 16093.232738 0 0.5395 16905 | 0/65 716s 170 h-m-p 0.7632 8.0000 0.2055 YC 16093.230783 1 1.9066 17039 | 0/65 716s 171 h-m-p 1.6000 8.0000 0.0588 C 16093.230544 0 0.4301 17172 | 0/65 716s 172 h-m-p 0.1610 8.0000 0.1569 +C 16093.230246 0 0.7188 17306 | 0/65 716s 173 h-m-p 1.6000 8.0000 0.0389 C 16093.230180 0 1.4132 17439 | 0/65 716s 174 h-m-p 1.6000 8.0000 0.0140 C 16093.230165 0 2.0428 17572 | 0/65 716s 175 h-m-p 1.6000 8.0000 0.0135 C 16093.230155 0 1.4111 17705 | 0/65 716s 176 h-m-p 1.6000 8.0000 0.0106 Y 16093.230152 0 0.9114 17838 | 0/65 716s 177 h-m-p 1.6000 8.0000 0.0025 Y 16093.230152 0 1.0423 17971 | 0/65 716s 178 h-m-p 1.6000 8.0000 0.0002 Y 16093.230152 0 1.1809 18104 | 0/65 716s 179 h-m-p 1.6000 8.0000 0.0000 C 16093.230152 0 1.6064 18237 | 0/65 716s 180 h-m-p 1.6000 8.0000 0.0000 ---Y 16093.230152 0 0.0063 18373 716s Out.. 716s lnL = -16093.230152 716s 18374 lfun, 18374 eigenQcodon, 36748 P(t) 716s 716s Time used: 0:11 716s Passed 716s 716s autopkgtest [21:53:27]: test run-unit-test: -----------------------] 716s run-unit-test PASS 716s autopkgtest [21:53:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 717s autopkgtest [21:53:28]: @@@@@@@@@@@@@@@@@@@@ summary 717s run-unit-test PASS 734s nova [W] Skipping flock for amd64 734s Creating nova instance adt-plucky-amd64-paml-20250315-210524-juju-7f2275-prod-proposed-migration-environment-20-12c2ac69-6de5-4f38-891b-72d554451989 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 734s nova [W] Timed out waiting for f696ebfa-c6e3-4725-b959-f92194e7dd72 to get deleted.