Diff of the two buildlogs: -- --- b1/build.log 2021-06-13 03:36:57.887168034 +0000 +++ b2/build.log 2021-06-13 03:41:52.428089474 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 12 15:22:58 -12 2021 -I: pbuilder-time-stamp: 1623554578 +I: Current time: Sat Jul 16 23:59:57 +14 2022 +I: pbuilder-time-stamp: 1657965597 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./garli_2.1-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.pWnAbCk5/trustedkeys.kbx': General error -gpgv: Signature made Wed Nov 18 02:03:14 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.PNHA5NK9/trustedkeys.kbx': General error +gpgv: Signature made Thu Nov 19 04:03:14 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,137 +28,171 @@ dpkg-source: info: unpacking garli_2.1-4.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/17799/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/59425/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/59425/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/59425/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='bbce6133f5fa42ab89b5e9a1bbcdd5f0' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='17799' - PS1='# ' - PS2='> ' + INVOCATION_ID=dda3d90877604c198dc2e6e25a5ee8c8 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=59425 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.wAIHOIZWhz/pbuilderrc_8ihk --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wAIHOIZWhz/b1 --logfile b1/build.log garli_2.1-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.wAIHOIZWhz/pbuilderrc_7Nah --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wAIHOIZWhz/b2 --logfile b2/build.log --extrapackages usrmerge garli_2.1-4.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin - total 5792 - -rwxr-xr-x 1 root root 1367848 Feb 24 08:57 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 08:57 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 11 21:25 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/17799/tmp/hooks/D02_print_environment finished + total 5776 + -rwxr-xr-x 1 root root 1367848 Feb 25 2021 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 2021 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 17 00:00 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 15 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/59425/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -290,7 +324,7 @@ Get: 86 http://deb.debian.org/debian bullseye/main i386 openmpi-bin i386 4.1.0-10 [209 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libopenmpi-dev i386 4.1.0-10 [1142 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 ncl-tools i386 2.1.21+git20190531.feceb81-3 [214 kB] -Fetched 44.0 MB in 6s (6900 kB/s) +Fetched 44.0 MB in 1s (84.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) @@ -661,8 +695,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (5161 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 25116 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-4 dpkg-buildpackage: info: source distribution unstable @@ -719,13 +789,13 @@ checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -746,8 +816,8 @@ checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes @@ -803,7 +873,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j10 + make -j18 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' @@ -819,12 +889,22 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:26: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); @@ -848,18 +928,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp -datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': -datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': -configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 602 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); @@ -921,8 +990,13 @@ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 602 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -958,58 +1032,10 @@ model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:323:28: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] - 323 | else sprintf(temp, ".run%d", rank); - | ^~ -garlimain.cpp:323:23: note: directive argument in the range [10, 2147483647] - 323 | else sprintf(temp, ".run%d", rank); - | ^~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /usr/include/c++/10/cstdio:42, - from /usr/include/c++/10/ext/string_conversions.h:43, - from /usr/include/c++/10/bits/basic_string.h:6545, - from /usr/include/c++/10/string:55, - from /usr/include/c++/10/bits/locale_classes.h:40, - from /usr/include/c++/10/bits/ios_base.h:41, - from /usr/include/c++/10/ios:42, - from /usr/include/c++/10/ostream:38, - from /usr/include/c++/10/iostream:39, - from population.h:23, - from garlimain.cpp:40: -/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -garlimain.cpp:322:38: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~ -garlimain.cpp:322:32: note: directive argument in the range [-2147483648, 9] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /usr/include/c++/10/cstdio:42, - from /usr/include/c++/10/ext/string_conversions.h:43, - from /usr/include/c++/10/bits/basic_string.h:6545, - from /usr/include/c++/10/string:55, - from /usr/include/c++/10/bits/locale_classes.h:40, - from /usr/include/c++/10/bits/ios_base.h:41, - from /usr/include/c++/10/ios:42, - from /usr/include/c++/10/ostream:38, - from /usr/include/c++/10/iostream:39, - from population.h:23, - from garlimain.cpp:40: -/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': +datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1041,9 +1067,6 @@ population.cpp:1896:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1111,6 +1134,53 @@ tree.cpp:6881:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +garlimain.cpp: In function 'int SubGarliMain(int)': +garlimain.cpp:323:28: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] + 323 | else sprintf(temp, ".run%d", rank); + | ^~ +garlimain.cpp:323:23: note: directive argument in the range [10, 2147483647] + 323 | else sprintf(temp, ".run%d", rank); + | ^~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /usr/include/c++/10/cstdio:42, + from /usr/include/c++/10/ext/string_conversions.h:43, + from /usr/include/c++/10/bits/basic_string.h:6545, + from /usr/include/c++/10/string:55, + from /usr/include/c++/10/bits/locale_classes.h:40, + from /usr/include/c++/10/bits/ios_base.h:41, + from /usr/include/c++/10/ios:42, + from /usr/include/c++/10/ostream:38, + from /usr/include/c++/10/iostream:39, + from population.h:23, + from garlimain.cpp:40: +/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +garlimain.cpp:322:38: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] + 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); + | ^~ +garlimain.cpp:322:32: note: directive argument in the range [-2147483648, 9] + 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); + | ^~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /usr/include/c++/10/cstdio:42, + from /usr/include/c++/10/ext/string_conversions.h:43, + from /usr/include/c++/10/bits/basic_string.h:6545, + from /usr/include/c++/10/string:55, + from /usr/include/c++/10/bits/locale_classes.h:40, + from /usr/include/c++/10/bits/ios_base.h:41, + from /usr/include/c++/10/ios:42, + from /usr/include/c++/10/ostream:38, + from /usr/include/c++/10/iostream:39, + from population.h:23, + from garlimain.cpp:40: +/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:22: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); @@ -1198,13 +1268,13 @@ checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -1225,8 +1295,8 @@ checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes @@ -1280,7 +1350,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/garli-2.1' dh_auto_build - make -j10 + make -j18 make[1]: Entering directory '/build/garli-2.1' make all-recursive make[2]: Entering directory '/build/garli-2.1' @@ -1296,12 +1366,22 @@ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:26: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); @@ -1325,19 +1405,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': -configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 602 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); @@ -1399,7 +1471,13 @@ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 602 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -1435,11 +1513,6 @@ model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1471,9 +1544,6 @@ population.cpp:1896:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1575,7 +1645,7 @@ # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1/' \{\} \; dh_auto_test - make -j10 check VERBOSE=1 + make -j18 check VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' @@ -3959,7 +4029,7 @@ pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8625 +lnL after optimization: -474.8624 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** @@ -4245,7 +4315,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4542,7 +4612,7 @@ pass 10: -12956.1235 (branch= 0.0000 omega= 0.0000) Looking for minimum length branches... Final score = -12956.1235 -Time used = 0 hours, 0 minutes and 37 seconds +Time used = 0 hours, 0 minutes and 13 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4694,7 +4764,7 @@ pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 -Time used = 0 hours, 0 minutes and 22 seconds +Time used = 0 hours, 0 minutes and 8 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4898,7 +4968,7 @@ pass 78: -3350.2332 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2332 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5106,7 +5176,7 @@ pass 72: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 3 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5268,7 +5338,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5588,7 +5658,7 @@ pass 12: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 -Time used = 0 hours, 0 minutes and 13 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -5842,7 +5912,7 @@ pass 38: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0001) Looking for minimum length branches... Final score = -13306.2061 -Time used = 0 hours, 0 minutes and 9 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6692,7 +6762,7 @@ pass 19: -477.6847 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6847 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7323,7 +7393,7 @@ pass 13: -493.6676 (branch= 0.0000) Looking for minimum length branches... Final score = -493.6676 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7516,27 +7586,30 @@ pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8625 -Current score = -474.8625 +lnL after optimization: -474.8624 +Current score = -474.8624 Performing final optimizations... -pass 1 : -474.7980 (branch= 0.0575 subset rates= 0.0070) -pass 2 : -474.7014 (branch= 0.0912 subset rates= 0.0053) -pass 3 : -474.6759 (branch= 0.0227 subset rates= 0.0028) -pass 4 : -474.6617 (branch= 0.0143 subset rates= 0.0000) -pass 5 : -474.6552 (branch= 0.0064 subset rates= 0.0000) -pass 6 : -474.6521 (branch= 0.0032 subset rates= 0.0000) -pass 7 : -474.6512 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -474.6505 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -474.6503 (branch= 0.0003 subset rates= 0.0000) -pass 10: -474.6484 (branch= 0.0001 subset rates= 0.0018) -pass 11: -474.6482 (branch= 0.0002 subset rates= 0.0000) -pass 12: -474.6481 (branch= 0.0001 subset rates= 0.0000) -pass 13: -474.6480 (branch= 0.0000 subset rates= 0.0000) -pass 14: -474.6480 (branch= 0.0000 subset rates= 0.0000) -pass 15: -474.6480 (branch= 0.0000 subset rates= 0.0000) -pass 16: -474.6464 (branch= 0.0000 subset rates= 0.0017) +pass 1 : -474.7985 (branch= 0.0575 subset rates= 0.0064) +pass 2 : -474.6992 (branch= 0.0939 subset rates= 0.0054) +pass 3 : -474.6721 (branch= 0.0241 subset rates= 0.0030) +pass 4 : -474.6603 (branch= 0.0118 subset rates= 0.0000) +pass 5 : -474.6548 (branch= 0.0055 subset rates= 0.0000) +pass 6 : -474.6526 (branch= 0.0021 subset rates= 0.0000) +pass 7 : -474.6518 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -474.6510 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -474.6508 (branch= 0.0003 subset rates= 0.0000) +pass 10: -474.6507 (branch= 0.0001 subset rates= 0.0000) +pass 11: -474.6483 (branch= 0.0001 subset rates= 0.0023) +pass 12: -474.6470 (branch= 0.0013 subset rates= 0.0000) +pass 13: -474.6466 (branch= 0.0005 subset rates= 0.0000) +pass 14: -474.6463 (branch= 0.0002 subset rates= 0.0000) +pass 15: -474.6462 (branch= 0.0001 subset rates= 0.0000) +pass 16: -474.6461 (branch= 0.0001 subset rates= 0.0000) +pass 17: -474.6461 (branch= 0.0000 subset rates= 0.0000) +pass 18: -474.6461 (branch= 0.0000 subset rates= 0.0000) +pass 19: -474.6461 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -474.6463 +Final score = -474.6461 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... @@ -7544,7 +7617,7 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -474.6463 +Replicate 1 : -474.6461 Parameter estimates: @@ -7559,15 +7632,15 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.578 0.588 2.016 2.972 +rep 1: 4.588 0.585 2.011 3.027 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkvO.ssr.best.all.tre ***********TEST************** -***Score is 474.64626 +***Score is 474.64609 ***Expected is 474.6455633 -***SCORE DIFFERENCE IS .0006967 +***SCORE DIFFERENCE IS .0005267 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkvO.ssr.conf *** ************************** @@ -7693,54 +7766,54 @@ Reached termination condition! last topological improvement at gen 1215 Improvement over last 500 gen = 0.03351 -Current score = -210.5120 +Current score = -210.5119 Performing final optimizations... -pass 1 : -210.1437 (branch= 0.0000 alpha= 0.0976 pinv= 0.2247 eq freqs= 0.0000 rel rates= 0.0459) -pass 2 : -209.5319 (branch= 0.0000 alpha= 0.3292 pinv= 0.2569 eq freqs= 0.0029 rel rates= 0.0228) -pass 3 : -209.3277 (branch= 0.0357 alpha= 0.1369 pinv= 0.0172 eq freqs= 0.0073 rel rates= 0.0071) -pass 4 : -209.2552 (branch= 0.0542 alpha= 0.0095 pinv= 0.0014 eq freqs= 0.0010 rel rates= 0.0064) -pass 5 : -209.2196 (branch= 0.0206 alpha= 0.0076 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0073) -pass 6 : -209.1971 (branch= 0.0100 alpha= 0.0030 pinv= 0.0009 eq freqs= 0.0002 rel rates= 0.0083) -pass 7 : -209.1768 (branch= 0.0069 alpha= 0.0021 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0106) -pass 8 : -209.1592 (branch= 0.0041 alpha= 0.0010 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0118) -pass 9 : -209.1455 (branch= 0.0021 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0110) -pass 10: -209.1344 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0098) -pass 11: -209.1249 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0088) -pass 12: -209.1162 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0081) -pass 13: -209.1084 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) -pass 14: -209.1013 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) -pass 15: -209.0946 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) -pass 16: -209.0884 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) -pass 17: -209.0825 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) -pass 18: -209.0770 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) -pass 19: -209.0718 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) -pass 20: -209.0669 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 1 : -210.1430 (branch= 0.0000 alpha= 0.0976 pinv= 0.2252 eq freqs= 0.0000 rel rates= 0.0461) +pass 2 : -209.5364 (branch= 0.0000 alpha= 0.3283 pinv= 0.2534 eq freqs= 0.0028 rel rates= 0.0222) +pass 3 : -209.3313 (branch= 0.0350 alpha= 0.1417 pinv= 0.0149 eq freqs= 0.0067 rel rates= 0.0067) +pass 4 : -209.2603 (branch= 0.0428 alpha= 0.0189 pinv= 0.0022 eq freqs= 0.0011 rel rates= 0.0061) +pass 5 : -209.2226 (branch= 0.0234 alpha= 0.0075 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0068) +pass 6 : -209.1995 (branch= 0.0109 alpha= 0.0027 pinv= 0.0009 eq freqs= 0.0002 rel rates= 0.0084) +pass 7 : -209.1784 (branch= 0.0077 alpha= 0.0023 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0105) +pass 8 : -209.1600 (branch= 0.0046 alpha= 0.0012 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0118) +pass 9 : -209.1460 (branch= 0.0024 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0111) +pass 10: -209.1346 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) +pass 11: -209.1249 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0089) +pass 12: -209.1162 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0083) +pass 13: -209.1083 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) +pass 14: -209.1012 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) +pass 15: -209.0945 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) +pass 16: -209.0883 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) +pass 17: -209.0824 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) +pass 18: -209.0769 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) +pass 19: -209.0716 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) +pass 20: -209.0668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... -pass 30: -208.9994 (branch= 0.0076 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0584) +pass 30: -208.9992 (branch= 0.0076 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0013 rel rates= 0.0585) optimization up to ... -pass 40: -208.8385 (branch= 0.0297 alpha= 0.0000 pinv= 0.0016 eq freqs= 0.0076 rel rates= 0.1220) +pass 40: -208.8386 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1218) optimization up to ... pass 50: -208.6974 (branch= 0.0132 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1209) optimization up to ... -pass 60: -208.6232 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0721) +pass 60: -208.6232 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0722) optimization up to ... -pass 70: -208.5739 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0487) +pass 70: -208.5738 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0489) optimization up to ... -pass 80: -208.5379 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0357) +pass 80: -208.5379 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0355) optimization up to ... -pass 90: -208.5108 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) +pass 90: -208.5107 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0270) optimization up to ... -pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0211) +pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) optimization up to ... -pass 110: -208.4727 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0168) +pass 110: -208.4725 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0169) optimization up to ... -pass 120: -208.4587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0139) +pass 120: -208.4587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... -pass 130: -208.4473 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) +pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) optimization up to ... -pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) +pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) optimization up to ... -pass 150: -208.4292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) +pass 150: -208.4293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... pass 160: -208.4222 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) optimization up to ... @@ -7748,29 +7821,29 @@ optimization up to ... pass 180: -208.4107 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) optimization up to ... -pass 190: -208.4060 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 190: -208.4059 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... pass 200: -208.4018 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0041) optimization up to ... pass 210: -208.3981 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) optimization up to ... -pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) optimization up to ... -pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) +pass 230: -208.3917 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 240: -208.3889 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... -pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) +pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 260: -208.3840 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... pass 270: -208.3819 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 280: -208.3799 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3799 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 290: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... -pass 300: -208.3765 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) +pass 300: -208.3764 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... @@ -7784,7 +7857,7 @@ optimization up to ... pass 360: -208.3685 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 370: -208.3674 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 370: -208.3675 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 380: -208.3665 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... @@ -7810,16 +7883,16 @@ optimization up to ... pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... -pass 497: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 495: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... -Final score = -208.3584 -Time used = 0 hours, 0 minutes and 10 seconds +Final score = -208.3585 +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.576, AG = 189.150, AT = 6.993, CG = 205.365, CT = 195.402, GT = 1.000 + AC = 122.054, AG = 188.347, AT = 6.963, CG = 204.493, CT = 194.576, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: @@ -7843,11 +7916,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3584 +Replicate 1 : -208.3585 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122.6 189.1 6.993 205.4 195.4 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.1 188.3 6.963 204.5 194.6 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -7969,66 +8042,66 @@ 0 -231.0119 0.500 0 500 -214.6598 0.500 276 Optimization precision reduced - Optimizing parameters... improved 1.751 lnL + Optimizing parameters... improved 1.752 lnL Optimizing branchlengths... improved 0.106 lnL -1000 -212.3290 0.010 825 -1500 -212.1958 0.010 825 -2000 -211.9100 0.010 825 -2500 -211.7710 0.010 825 -3000 -211.6571 0.010 825 -3500 -211.4394 0.010 825 -4000 -211.3130 0.010 825 +1000 -212.3288 0.010 825 +1500 -212.1956 0.010 825 +2000 -211.9098 0.010 825 +2500 -211.7708 0.010 825 +3000 -211.6570 0.010 825 +3500 -211.4393 0.010 825 +4000 -211.3137 0.010 825 Reached termination condition! last topological improvement at gen 825 -Improvement over last 500 gen = 0.03748 -Current score = -211.2888 +Improvement over last 500 gen = 0.03822 +Current score = -211.2855 Performing final optimizations... -pass 1 : -209.0461 (branch= 0.0000 alpha= 0.7597 pinv= 1.3968 eq freqs= 0.0054 rel rates= 0.0808) -pass 2 : -208.5891 (branch= 0.0507 alpha= 0.3555 pinv= 0.0095 eq freqs= 0.0124 rel rates= 0.0290) -pass 3 : -208.5203 (branch= 0.0382 alpha= 0.0021 pinv= 0.0021 eq freqs= 0.0019 rel rates= 0.0245) -pass 4 : -208.4907 (branch= 0.0066 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0013 rel rates= 0.0216) -pass 5 : -208.4687 (branch= 0.0009 alpha= 0.0008 pinv= 0.0004 eq freqs= 0.0003 rel rates= 0.0195) -pass 6 : -208.4494 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0181) -pass 7 : -208.4324 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0166) -pass 8 : -208.4168 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0152) -pass 9 : -208.4025 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0141) -pass 10: -208.3893 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0130) -pass 11: -208.3775 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0117) -pass 12: -208.3664 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0110) -pass 13: -208.3563 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0100) -pass 14: -208.3471 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0092) -pass 15: -208.3386 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0085) -pass 16: -208.3306 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0079) -pass 17: -208.3232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) -pass 18: -208.3162 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) -pass 19: -208.3098 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) -pass 20: -208.3037 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) +pass 1 : -208.6996 (branch= 0.0000 alpha= 0.7686 pinv= 1.7145 eq freqs= 0.0072 rel rates= 0.0955) +pass 2 : -208.5457 (branch= 0.0718 alpha= 0.0438 pinv= 0.0000 eq freqs= 0.0120 rel rates= 0.0262) +pass 3 : -208.5108 (branch= 0.0105 alpha= 0.0026 pinv= 0.0023 eq freqs= 0.0014 rel rates= 0.0181) +pass 4 : -208.4858 (branch= 0.0031 alpha= 0.0008 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0204) +pass 5 : -208.4646 (branch= 0.0019 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0192) +pass 6 : -208.4458 (branch= 0.0007 alpha= 0.0006 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0174) +pass 7 : -208.4292 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0159) +pass 8 : -208.4137 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0151) +pass 9 : -208.3997 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0137) +pass 10: -208.3868 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0128) +pass 11: -208.3750 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0116) +pass 12: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) +pass 13: -208.3544 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0099) +pass 14: -208.3453 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) +pass 15: -208.3368 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0084) +pass 16: -208.3290 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) +pass 17: -208.3219 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0071) +pass 18: -208.3149 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) +pass 19: -208.3086 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) +pass 20: -208.3025 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) optimization up to ... -pass 30: -208.2585 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0450) +pass 30: -208.2578 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0445) optimization up to ... -pass 40: -208.2304 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0280) +pass 40: -208.2300 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0277) optimization up to ... -pass 50: -208.2113 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0190) +pass 50: -208.2110 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) optimization up to ... -pass 60: -208.1974 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) +pass 60: -208.1972 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... -pass 70: -208.1869 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 70: -208.1867 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... -pass 80: -208.1786 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) +pass 80: -208.1785 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... -pass 90: -208.1718 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) +pass 90: -208.1717 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... -pass 100: -208.1663 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) +pass 100: -208.1662 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... -pass 110: -208.1617 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 110: -208.1616 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) optimization up to ... -pass 120: -208.1577 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) +pass 120: -208.1576 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... -pass 130: -208.1543 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 130: -208.1542 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... -pass 140: -208.1513 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) +pass 140: -208.1512 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... -pass 150: -208.1486 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) +pass 150: -208.1485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 160: -208.1462 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... @@ -8044,9 +8117,9 @@ optimization up to ... pass 220: -208.1362 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 230: -208.1350 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 230: -208.1349 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 240: -208.1339 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 240: -208.1338 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 250: -208.1328 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... @@ -8058,9 +8131,9 @@ optimization up to ... pass 290: -208.1293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 300: -208.1286 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 300: -208.1285 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 310: -208.1279 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 310: -208.1278 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 320: -208.1272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... @@ -8077,13 +8150,13 @@ pass 372: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1244 -Time used = 0 hours, 0 minutes and 10 seconds +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 22.219, AG = 32.284, AT = 0.001, CG = 36.368, CT = 80.246, GT = 1.000 + AC = 22.228, AG = 32.297, AT = 0.001, CG = 36.383, CT = 80.278, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: @@ -8111,7 +8184,7 @@ Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 22.22 32.28 0.001 36.37 80.25 1 0.221 0.344 0.216 0.218 999.900 0.338 +rep 1: 22.23 32.3 0.001 36.38 80.28 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL @@ -8241,162 +8314,156 @@ Optimizing branchlengths... improved 0.702 lnL 2000 -210.9688 0.010 1502 2500 -210.8711 0.010 1502 -3000 -210.7511 0.010 2883 +3000 -210.7510 0.010 2883 3500 -210.7006 0.010 2883 -4000 -210.6776 0.010 2883 +4000 -210.6775 0.010 2883 4500 -210.6527 0.010 2883 5000 -210.5909 0.010 4692 5500 -210.5077 0.010 4692 -6000 -210.3155 0.010 5804 -6500 -210.2907 0.010 5804 -7000 -210.2665 0.010 5804 -7500 -210.2316 0.010 5804 -8000 -210.1487 0.010 7792 -8500 -210.0550 0.010 8414 -9000 -210.0297 0.010 8414 -9500 -210.0085 0.010 8414 -10000 -209.9708 0.010 8414 - Optimizing parameters... improved 0.535 lnL - Optimizing branchlengths... improved 0.003 lnL -10500 -209.4059 0.010 8414 +6000 -210.3810 0.010 4692 +6500 -210.3718 0.010 4692 Reached termination condition! -last topological improvement at gen 8414 -Improvement over last 500 gen = 0.01529 -Current score = -209.4046 +last topological improvement at gen 4692 +Improvement over last 500 gen = 0.02215 +Current score = -210.3565 Performing final optimizations... -pass 1 : -209.2928 (branch= 0.0000 alpha= 0.0761 pinv= 0.0171 eq freqs= 0.0000 rel rates= 0.0185) -pass 2 : -209.2265 (branch= 0.0413 alpha= 0.0162 pinv= 0.0000 eq freqs= 0.0089 rel rates= 0.0000) -pass 3 : -209.1694 (branch= 0.0378 alpha= 0.0123 pinv= 0.0017 eq freqs= 0.0014 rel rates= 0.0038) -pass 4 : -209.1272 (branch= 0.0218 alpha= 0.0116 pinv= 0.0015 eq freqs= 0.0025 rel rates= 0.0048) -pass 5 : -209.0984 (branch= 0.0125 alpha= 0.0070 pinv= 0.0000 eq freqs= 0.0022 rel rates= 0.0071) -pass 6 : -209.0811 (branch= 0.0070 alpha= 0.0014 pinv= 0.0000 eq freqs= 0.0013 rel rates= 0.0076) -pass 7 : -209.0722 (branch= 0.0018 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0066) -pass 8 : -209.0657 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0056) -pass 9 : -209.0602 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0050) -pass 10: -209.0550 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0048) -pass 11: -209.0498 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0048) -pass 12: -209.0442 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0050) -pass 13: -209.0381 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) -pass 14: -209.0314 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0058) -pass 15: -209.0238 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0063) -pass 16: -209.0151 (branch= 0.0015 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0069) -pass 17: -209.0054 (branch= 0.0018 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0076) -pass 18: -208.9945 (branch= 0.0021 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0083) -pass 19: -208.9824 (branch= 0.0025 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0005 rel rates= 0.0091) -pass 20: -208.9690 (branch= 0.0028 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0006 rel rates= 0.0099) +pass 1 : -209.8577 (branch= 0.0038 alpha= 0.1386 pinv= 0.2652 eq freqs= 0.0000 rel rates= 0.0912) +pass 2 : -209.3897 (branch= 0.0090 alpha= 0.3086 pinv= 0.1263 eq freqs= 0.0000 rel rates= 0.0240) +pass 3 : -209.2848 (branch= 0.0504 alpha= 0.0392 pinv= 0.0090 eq freqs= 0.0039 rel rates= 0.0026) +pass 4 : -209.2432 (branch= 0.0233 alpha= 0.0114 pinv= 0.0000 eq freqs= 0.0031 rel rates= 0.0037) +pass 5 : -209.1919 (branch= 0.0316 alpha= 0.0133 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0054) +pass 6 : -209.1625 (branch= 0.0150 alpha= 0.0038 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0091) +pass 7 : -209.1386 (branch= 0.0083 alpha= 0.0039 pinv= 0.0001 eq freqs= 0.0008 rel rates= 0.0109) +pass 8 : -209.1226 (branch= 0.0051 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0099) +pass 9 : -209.1116 (branch= 0.0017 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0087) +pass 10: -209.1027 (branch= 0.0007 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0077) +pass 11: -209.0952 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0068) +pass 12: -209.0887 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0061) +pass 13: -209.0828 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) +pass 14: -209.0773 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) +pass 15: -209.0721 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) +pass 16: -209.0669 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) +pass 17: -209.0614 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 18: -209.0555 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) +pass 19: -209.0490 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) +pass 20: -209.0419 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0059) optimization up to ... -pass 30: -208.7944 (branch= 0.0303 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0087 rel rates= 0.1337) +pass 30: -208.9170 (branch= 0.0252 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0048 rel rates= 0.0941) optimization up to ... -pass 40: -208.6749 (branch= 0.0077 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0039 rel rates= 0.1069) +pass 40: -208.7462 (branch= 0.0228 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0081 rel rates= 0.1381) optimization up to ... -pass 50: -208.6090 (branch= 0.0008 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0646) +pass 50: -208.6516 (branch= 0.0031 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0018 rel rates= 0.0893) optimization up to ... -pass 60: -208.5637 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0448) +pass 60: -208.5935 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0572) optimization up to ... -pass 70: -208.5303 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0332) +pass 70: -208.5525 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0406) optimization up to ... -pass 80: -208.5048 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0252) +pass 80: -208.5218 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0304) optimization up to ... -pass 90: -208.4850 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0197) +pass 90: -208.4983 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0234) optimization up to ... -pass 100: -208.4688 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0161) +pass 100: -208.4796 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0185) optimization up to ... -pass 110: -208.4557 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0130) +pass 110: -208.4646 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0150) optimization up to ... -pass 120: -208.4446 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0110) +pass 120: -208.4520 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0125) optimization up to ... -pass 130: -208.4353 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0093) +pass 130: -208.4416 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0103) optimization up to ... -pass 140: -208.4273 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0079) +pass 140: -208.4327 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) optimization up to ... -pass 150: -208.4205 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0068) +pass 150: -208.4251 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) optimization up to ... -pass 160: -208.4146 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0059) +pass 160: -208.4186 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... -pass 170: -208.4094 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) +pass 170: -208.4129 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... -pass 180: -208.4049 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) +pass 180: -208.4080 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... -pass 190: -208.4008 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0041) +pass 190: -208.4036 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... -pass 200: -208.3971 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) +pass 200: -208.3997 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... -pass 210: -208.3939 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) +pass 210: -208.3962 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... -pass 220: -208.3909 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) +pass 220: -208.3930 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... -pass 230: -208.3882 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) +pass 230: -208.3901 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... -pass 240: -208.3857 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) +pass 240: -208.3875 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 250: -208.3835 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) +pass 250: -208.3851 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... -pass 260: -208.3814 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) +pass 260: -208.3829 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... -pass 270: -208.3795 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 270: -208.3808 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 280: -208.3777 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +pass 280: -208.3790 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... -pass 290: -208.3760 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 290: -208.3772 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 300: -208.3745 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) +pass 300: -208.3756 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 310: -208.3731 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 310: -208.3741 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... -pass 320: -208.3718 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) +pass 320: -208.3727 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 330: -208.3705 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 330: -208.3714 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 340: -208.3693 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 340: -208.3702 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 350: -208.3682 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 350: -208.3690 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 360: -208.3672 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 360: -208.3679 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 370: -208.3662 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 370: -208.3669 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 380: -208.3653 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 380: -208.3659 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 390: -208.3644 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 390: -208.3650 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 400: -208.3636 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 400: -208.3642 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 410: -208.3628 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 410: -208.3634 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) + optimization up to ... +pass 420: -208.3626 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) + optimization up to ... +pass 430: -208.3619 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 420: -208.3621 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 440: -208.3612 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 430: -208.3614 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 450: -208.3605 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 440: -208.3607 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 460: -208.3599 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 450: -208.3600 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 470: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 460: -208.3594 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 480: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 470: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 490: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 480: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 500: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 483: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 504: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... -Final score = -208.3585 -Time used = 0 hours, 0 minutes and 17 seconds +Final score = -208.3583 +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.195, AG = 188.563, AT = 6.971, CG = 204.730, CT = 194.797, GT = 1.000 + AC = 122.898, AG = 190.128, AT = 7.015, CG = 206.090, CT = 195.971, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2035 0.2835 + (ACGT) 0.2225 0.2906 0.2034 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated - 0.2780 + 0.2781 Substitution rate categories under this model: rate proportion - 0.0000 0.2780 + 0.0000 0.2781 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 @@ -8415,11 +8482,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3585 +Replicate 1 : -208.3583 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122.2 188.6 6.971 204.7 194.8 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.9 190.1 7.015 206.1 196 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -8546,91 +8613,91 @@ Optimization precision reduced Optimizing parameters... improved 1.494 lnL Optimizing branchlengths... improved 0.350 lnL -1500 -210.9425 0.010 1230 +1500 -210.9424 0.010 1230 2000 -210.7769 0.010 1230 2500 -210.6534 0.010 1230 3000 -210.6127 0.010 1230 Reached termination condition! last topological improvement at gen 1230 -Improvement over last 500 gen = 0.03867 +Improvement over last 500 gen = 0.03866 Current score = -210.5967 Performing final optimizations... -pass 1 : -210.1950 (branch= 0.0000 alpha= 0.1301 pinv= 0.2108 eq freqs= 0.0000 rel rates= 0.0609) -pass 2 : -209.5821 (branch= 0.0039 alpha= 0.3411 pinv= 0.2322 eq freqs= 0.0033 rel rates= 0.0325) -pass 3 : -209.3373 (branch= 0.0519 alpha= 0.1500 pinv= 0.0232 eq freqs= 0.0089 rel rates= 0.0110) -pass 4 : -209.2546 (branch= 0.0532 alpha= 0.0216 pinv= 0.0016 eq freqs= 0.0022 rel rates= 0.0040) -pass 5 : -209.2044 (branch= 0.0347 alpha= 0.0094 pinv= 0.0011 eq freqs= 0.0004 rel rates= 0.0047) -pass 6 : -209.1736 (branch= 0.0174 alpha= 0.0054 pinv= 0.0004 eq freqs= 0.0006 rel rates= 0.0070) -pass 7 : -209.1476 (branch= 0.0102 alpha= 0.0034 pinv= 0.0002 eq freqs= 0.0012 rel rates= 0.0111) -pass 8 : -209.1255 (branch= 0.0071 alpha= 0.0022 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0117) -pass 9 : -209.1111 (branch= 0.0033 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0099) -pass 10: -209.1008 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0084) -pass 11: -209.0924 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0075) -pass 12: -209.0852 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) -pass 13: -209.0790 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) -pass 14: -209.0734 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) -pass 15: -209.0681 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) -pass 16: -209.0633 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 17: -209.0584 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 18: -209.0535 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 19: -209.0482 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) -pass 20: -209.0425 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) +pass 1 : -210.1946 (branch= 0.0000 alpha= 0.1301 pinv= 0.2112 eq freqs= 0.0000 rel rates= 0.0609) +pass 2 : -209.5773 (branch= 0.0039 alpha= 0.3415 pinv= 0.2360 eq freqs= 0.0033 rel rates= 0.0326) +pass 3 : -209.3399 (branch= 0.0528 alpha= 0.1450 pinv= 0.0206 eq freqs= 0.0087 rel rates= 0.0104) +pass 4 : -209.2596 (branch= 0.0471 alpha= 0.0256 pinv= 0.0017 eq freqs= 0.0022 rel rates= 0.0037) +pass 5 : -209.2096 (branch= 0.0339 alpha= 0.0096 pinv= 0.0012 eq freqs= 0.0003 rel rates= 0.0049) +pass 6 : -209.1738 (branch= 0.0211 alpha= 0.0064 pinv= 0.0004 eq freqs= 0.0011 rel rates= 0.0069) +pass 7 : -209.1472 (branch= 0.0110 alpha= 0.0042 pinv= 0.0002 eq freqs= 0.0006 rel rates= 0.0107) +pass 8 : -209.1255 (branch= 0.0077 alpha= 0.0019 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0112) +pass 9 : -209.1115 (branch= 0.0033 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0098) +pass 10: -209.1013 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0085) +pass 11: -209.0930 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0073) +pass 12: -209.0859 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) +pass 13: -209.0797 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) +pass 14: -209.0740 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) +pass 15: -209.0687 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) +pass 16: -209.0639 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) +pass 17: -209.0590 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 18: -209.0542 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 19: -209.0489 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) +pass 20: -209.0433 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) optimization up to ... -pass 30: -208.9336 (branch= 0.0198 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0039 rel rates= 0.0845) +pass 30: -208.9356 (branch= 0.0194 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0038 rel rates= 0.0837) optimization up to ... -pass 40: -208.7581 (branch= 0.0266 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1383) +pass 40: -208.7597 (branch= 0.0269 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1383) optimization up to ... -pass 50: -208.6574 (branch= 0.0042 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0023 rel rates= 0.0936) +pass 50: -208.6583 (branch= 0.0043 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0024 rel rates= 0.0941) optimization up to ... -pass 60: -208.5974 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0591) +pass 60: -208.5980 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0593) optimization up to ... -pass 70: -208.5553 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0416) +pass 70: -208.5558 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0418) optimization up to ... -pass 80: -208.5240 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0310) +pass 80: -208.5244 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0311) optimization up to ... -pass 90: -208.5000 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0239) +pass 90: -208.5003 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0240) optimization up to ... -pass 100: -208.4810 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0189) +pass 100: -208.4813 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) optimization up to ... -pass 110: -208.4657 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0153) +pass 110: -208.4658 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0153) optimization up to ... -pass 120: -208.4529 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0126) +pass 120: -208.4531 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0127) optimization up to ... -pass 130: -208.4424 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 130: -208.4425 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... -pass 140: -208.4334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) +pass 140: -208.4336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) optimization up to ... -pass 150: -208.4257 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) +pass 150: -208.4258 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) optimization up to ... -pass 160: -208.4191 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 160: -208.4192 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) optimization up to ... pass 170: -208.4134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... pass 180: -208.4084 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... -pass 190: -208.4039 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) +pass 190: -208.4040 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) optimization up to ... pass 200: -208.4000 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... -pass 210: -208.3965 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) +pass 210: -208.3964 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3932 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... -pass 230: -208.3904 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) +pass 230: -208.3903 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3877 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 250: -208.3853 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 250: -208.3852 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... -pass 260: -208.3831 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) +pass 260: -208.3830 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3810 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3791 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... -pass 290: -208.3774 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) +pass 290: -208.3773 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 300: -208.3758 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 300: -208.3757 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3742 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... @@ -8650,7 +8717,7 @@ optimization up to ... pass 390: -208.3651 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 400: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 400: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 410: -208.3634 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... @@ -8668,16 +8735,16 @@ optimization up to ... pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 490: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) +pass 488: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) Looking for minimum length branches... -Final score = -208.3583 -Time used = 0 hours, 0 minutes and 9 seconds +Final score = -208.3585 +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.663, AG = 189.753, AT = 6.984, CG = 205.688, CT = 195.619, GT = 1.000 + AC = 122.151, AG = 188.970, AT = 6.955, CG = 204.834, CT = 194.810, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2834 Rate Heterogeneity Model: @@ -8706,11 +8773,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3583 +Replicate 1 : -208.3585 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122.7 189.8 6.984 205.7 195.6 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.2 189 6.955 204.8 194.8 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -10714,9 +10781,9 @@ pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8625 +lnL after optimization: -474.8624 gen current_lnL precision last_tree_imp -0 -474.8625 0.010 0 +0 -474.8624 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT @@ -10758,7 +10825,7 @@ Completed 1 replicate search(es) (of 5). Results: -Replicate 1 : -474.8617 (best) +Replicate 1 : -474.8616 (best) Parameter estimates across search replicates: @@ -10865,7 +10932,7 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -474.8617 +Replicate 1 : -474.8616 Replicate 2 : -474.8506 (best) Parameter estimates across search replicates: @@ -10976,7 +11043,7 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -474.8617 +Replicate 1 : -474.8616 Replicate 2 : -474.8506 (best) Replicate 3 : -474.8836 @@ -11089,7 +11156,7 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -474.8617 +Replicate 1 : -474.8616 Replicate 2 : -474.8506 Replicate 3 : -474.8836 Replicate 4 : -474.8493 (best) @@ -11204,7 +11271,7 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -474.8617 +Replicate 1 : -474.8616 Replicate 2 : -474.8506 Replicate 3 : -474.8836 Replicate 4 : -474.8493 (best) @@ -11381,6 +11448,14 @@ 400 -100.3300 0.500 183 500 -100.0135 0.500 183 600 -99.2983 0.500 549 +700 -99.1955 0.500 549 +800 -99.0437 0.500 783 +900 -99.0045 0.500 783 +1000 -98.8740 0.500 949 +1100 -98.8107 0.500 1029 +1200 -98.8004 0.500 1029 +1300 -98.7501 0.500 1029 +1400 -98.6926 0.500 1029 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11477,16 +11552,11 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 676, seed 1492100964, best lnL -99.238 +Bootstrap rep 1 (of 1) generation 1429, seed 760181010, best lnL -98.692 gen current_lnL precision last_tree_imp -676 -99.2377 0.500 549 -700 -99.1955 0.500 549 -800 -99.0437 0.500 783 -900 -99.0045 0.500 783 -1000 -98.8740 0.500 949 -NOTE: ****Specified generation limit (1000) reached... +1429 -98.6923 0.500 1029 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -11498,41 +11568,37 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.6652 + 0.8003 with an invariant (invariable) site category, proportion estimated - 0.0626 + 0.0530 Substitution rate categories under this model: rate proportion - 0.0000 0.0626 - 0.1054 0.3125 - 0.5916 0.3125 - 2.3030 0.3125 + 0.0000 0.0530 + 0.1411 0.3157 + 0.6503 0.3157 + 2.2087 0.3157 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -98.8740 +Replicate 1 : -98.6923 Parameter estimates: alpha pinv -rep 1: 0.665 0.063 +rep 1: 0.800 0.053 Treelengths: TL -rep 1: 1.521 +rep 1: 1.677 Saving best tree to bootstrap file ch.a.G3.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf @@ -11654,6 +11720,13 @@ 200 -112.4964 0.500 84 300 -112.3224 0.500 84 400 -112.1061 0.500 84 +500 -111.8129 0.500 84 +600 -111.7788 0.500 84 +Optimization precision reduced + Optimizing parameters... improved 0.386 lnL + Optimizing branchlengths... improved 0.390 lnL +700 -110.8142 0.010 615 +800 -110.5642 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11740,16 +11813,9 @@ STARTING RUN Restarting from checkpoint... - generation 445, seed 537557747, best lnL -111.953 + generation 863, seed 2112122269, best lnL -110.559 gen current_lnL precision last_tree_imp -445 -111.9532 0.500 84 -500 -111.8129 0.500 84 -600 -111.7788 0.500 84 -Optimization precision reduced - Optimizing parameters... improved 0.386 lnL - Optimizing branchlengths... improved 0.390 lnL -700 -110.8142 0.010 615 -800 -110.5642 0.010 707 +863 -110.5588 0.010 707 900 -110.5555 0.010 707 1000 -110.5065 0.010 707 NOTE: ****Specified generation limit (1000) reached... @@ -11930,6 +11996,23 @@ Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.000 lnL 1200 -111.6824 0.010 563 +1300 -111.6822 0.010 563 +1400 -111.6821 0.010 563 +1500 -111.6819 0.010 563 +1600 -111.6818 0.010 563 +1700 -111.6818 0.010 563 +1800 -111.6818 0.010 563 +1900 -111.6818 0.010 563 +2000 -111.6817 0.010 563 +2100 -111.6817 0.010 563 +2200 -111.6817 0.010 563 +2300 -111.6817 0.010 563 +2400 -111.6817 0.010 563 +2500 -111.6817 0.010 563 +2600 -111.6816 0.010 563 +2700 -111.6816 0.010 563 +2800 -111.6816 0.010 563 +2900 -111.6815 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12015,9 +12098,9 @@ STARTING RUN Restarting from checkpoint... - generation 1238, seed 1780602363, best lnL -111.682 + generation 2931, seed 2029578049, best lnL -111.682 gen current_lnL precision last_tree_imp -1238 -111.6822 0.010 563 +2931 -111.6815 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -12041,14 +12124,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6822 +Replicate 1 : -111.6815 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.605 +rep 1: 2.606 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log @@ -12180,6 +12263,13 @@ 30 -205.6499 0.500 18 40 -205.6371 0.500 18 50 -205.6175 0.500 18 +60 -205.5990 0.500 53 +70 -205.5741 0.500 53 +80 -205.4022 0.500 76 +90 -205.3871 0.500 76 +100 -205.3829 0.500 76 +110 -205.3431 0.500 106 +120 -205.3431 0.500 106 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12266,17 +12356,11 @@ STARTING RUN Restarting from checkpoint... - generation 53, seed 606061956, best lnL -205.599 + generation 129, seed 1946584308, best lnL -205.250 gen current_lnL precision last_tree_imp -53 -205.5990 0.500 53 -60 -205.5990 0.500 53 -70 -205.5741 0.500 53 -80 -205.4022 0.500 76 -90 -205.3871 0.500 76 -100 -205.3829 0.500 76 -NOTE: ****Specified generation limit (100) reached... +129 -205.2505 0.500 121 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates @@ -12301,38 +12385,31 @@ 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion - 0.0490 0.5211 + 0.0473 0.5211 0.4995 0.4789 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file ch.c.M3x2.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -205.3829 +Replicate 1 : -205.2505 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.049 0.521 0.499 0.479 1.586 3.999 0.04 2.453 3.968 1 +rep 1: 0.047 0.521 0.499 0.479 1.586 3.999 0.04 2.453 3.968 1 Treelengths: TL -rep 1: 7.371 +rep 1: 7.702 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/c.conf @@ -12463,6 +12540,14 @@ 30 -199.1219 0.500 20 40 -198.6459 0.500 33 50 -198.5841 0.500 33 +60 -197.5337 0.500 55 +70 -197.4975 0.500 55 +80 -197.3837 0.500 55 +90 -197.3176 0.500 55 +100 -197.3150 0.500 55 +110 -197.3052 0.500 55 +120 -197.2873 0.500 55 +130 -197.2746 0.500 121 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12550,22 +12635,16 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 54, seed 227725811, best lnL -198.584 +Bootstrap rep 1 (of 1) generation 131, seed 135423804, best lnL -197.275 gen current_lnL precision last_tree_imp -54 -198.5840 0.500 33 -60 -197.5337 0.500 55 -70 -197.4975 0.500 55 -80 -197.3837 0.500 55 -90 -197.3176 0.500 55 -100 -197.3150 0.500 55 -NOTE: ****Specified generation limit (100) reached... +131 -197.2746 0.500 121 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.150419 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 2.462, AG = 3.999, AT = 0.008, CG = 2.703, CT = 2.137, GT = 1.000 + AC = 2.462, AG = 4.049, AT = 0.008, CG = 2.703, CT = 2.137, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -12589,27 +12668,23 @@ No branches were short enough to be collapsed. -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -197.3150 +Replicate 1 : -197.2746 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.150 1.000 2.462 3.999 0.007962 2.703 2.137 1 +rep 1: 0.150 1.000 2.462 4.049 0.007962 2.703 2.137 1 Treelengths: TL -rep 1: 7.698 +rep 1: 7.660 Saving best tree to bootstrap file ch.c.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -12772,6 +12847,22 @@ Optimizing branchlengths... improved 0.085 lnL 1100 -3352.7145 0.010 0 1200 -3352.6335 0.010 0 +1300 -3352.5109 0.010 0 +1400 -3352.4007 0.010 0 +1500 -3352.3958 0.010 0 +1600 -3352.2886 0.010 0 +1700 -3352.2809 0.010 0 +1800 -3352.2008 0.010 0 +1900 -3351.8457 0.010 0 +2000 -3351.7672 0.010 0 +2100 -3351.6171 0.010 0 +2200 -3351.3728 0.010 0 +2300 -3351.3480 0.010 0 +2400 -3351.3405 0.010 0 +2500 -3351.2378 0.010 0 +2600 -3351.1720 0.010 0 +2700 -3351.1717 0.010 0 +2800 -3351.1180 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12875,76 +12966,89 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1200, seed 431100195, best lnL -3352.634 +Search rep 1 (of 2) generation 2814, seed 1956236688, best lnL -3351.118 gen current_lnL precision last_tree_imp -1200 -3352.6335 0.010 0 -1300 -3352.5109 0.010 0 -1400 -3352.4007 0.010 0 -1500 -3352.3958 0.010 0 -1600 -3352.2886 0.010 0 -1700 -3352.2809 0.010 0 -1800 -3352.2008 0.010 0 -1900 -3351.8457 0.010 0 -2000 -3351.7672 0.010 0 -2100 -3351.6171 0.010 0 +2814 -3351.1180 0.010 0 +2900 -3351.1167 0.010 0 +3000 -3351.1126 0.010 0 +3100 -3351.1001 0.010 0 +3200 -3351.0885 0.010 0 +3300 -3351.0866 0.010 0 +3400 -3351.0847 0.010 0 +3500 -3351.0836 0.010 0 +3600 -3351.0811 0.010 0 +3700 -3351.0480 0.010 0 +3800 -3351.0358 0.010 0 +3900 -3350.9815 0.010 0 +4000 -3350.9815 0.010 0 +4100 -3350.9746 0.010 0 +4200 -3350.9681 0.010 0 +4300 -3350.9675 0.010 0 +4400 -3350.9635 0.010 0 +4500 -3350.9635 0.010 0 +4600 -3350.9230 0.010 0 +4700 -3350.9227 0.010 0 +4800 -3350.9217 0.010 0 +4900 -3350.9217 0.010 0 +5000 -3350.9207 0.010 0 +5100 -3350.8980 0.010 0 +5200 -3350.8798 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.5730 +Current score = -3350.8784 Performing final optimizations... -pass 1 : -3351.3686 (branch= 0.0160 alpha= 0.0000 pinv= 0.0160 eq freqs= 0.0225 rel rates= 0.1329 subset rates= 0.0169) -pass 2 : -3351.2136 (branch= 0.0178 alpha= 0.0169 pinv= 0.0177 eq freqs= 0.0000 rel rates= 0.0982 subset rates= 0.0042) -pass 3 : -3351.0818 (branch= 0.0117 alpha= 0.0145 pinv= 0.0169 eq freqs= 0.0035 rel rates= 0.0840 subset rates= 0.0014) -pass 4 : -3350.9716 (branch= 0.0085 alpha= 0.0145 pinv= 0.0157 eq freqs= 0.0000 rel rates= 0.0693 subset rates= 0.0021) -pass 5 : -3350.8763 (branch= 0.0067 alpha= 0.0132 pinv= 0.0148 eq freqs= 0.0007 rel rates= 0.0581 subset rates= 0.0019) -pass 6 : -3350.7944 (branch= 0.0049 alpha= 0.0121 pinv= 0.0137 eq freqs= 0.0000 rel rates= 0.0499 subset rates= 0.0012) -pass 7 : -3350.7218 (branch= 0.0030 alpha= 0.0119 pinv= 0.0126 eq freqs= 0.0004 rel rates= 0.0433 subset rates= 0.0012) -pass 8 : -3350.6608 (branch= 0.0025 alpha= 0.0108 pinv= 0.0116 eq freqs= 0.0001 rel rates= 0.0361 subset rates= 0.0000) -pass 9 : -3350.6054 (branch= 0.0005 alpha= 0.0106 pinv= 0.0105 eq freqs= 0.0000 rel rates= 0.0326 subset rates= 0.0011) -pass 10: -3350.5573 (branch= 0.0012 alpha= 0.0100 pinv= 0.0102 eq freqs= 0.0001 rel rates= 0.0266 subset rates= 0.0000) -pass 11: -3350.5159 (branch= 0.0003 alpha= 0.0090 pinv= 0.0087 eq freqs= 0.0000 rel rates= 0.0234 subset rates= 0.0000) -pass 12: -3350.4783 (branch= 0.0001 alpha= 0.0085 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0203 subset rates= 0.0009) -pass 13: -3350.4468 (branch= 0.0007 alpha= 0.0074 pinv= 0.0070 eq freqs= 0.0001 rel rates= 0.0163 subset rates= 0.0000) -pass 14: -3350.4195 (branch= 0.0001 alpha= 0.0065 pinv= 0.0063 eq freqs= 0.0000 rel rates= 0.0143 subset rates= 0.0000) -pass 15: -3350.3951 (branch= 0.0000 alpha= 0.0061 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0126 subset rates= 0.0000) -pass 16: -3350.3736 (branch= 0.0000 alpha= 0.0056 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0108 subset rates= 0.0000) -pass 17: -3350.3549 (branch= 0.0000 alpha= 0.0050 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0093 subset rates= 0.0000) -pass 18: -3350.3386 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0079 subset rates= 0.0000) -pass 19: -3350.3244 (branch= 0.0000 alpha= 0.0039 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0068 subset rates= 0.0000) -pass 20: -3350.3120 (branch= 0.0000 alpha= 0.0034 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0059 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2509 (branch= 0.0000 alpha= 0.0174 pinv= 0.0157 eq freqs= 0.0001 rel rates= 0.0280 subset rates= 0.0000) - optimization up to ... -pass 40: -3350.2369 (branch= 0.0000 alpha= 0.0038 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0065 subset rates= 0.0000) +pass 1 : -3350.8331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0194 eq freqs= 0.0000 rel rates= 0.0259 subset rates= 0.0000) +pass 2 : -3350.7676 (branch= 0.0041 alpha= 0.0101 pinv= 0.0174 eq freqs= 0.0000 rel rates= 0.0338 subset rates= 0.0000) +pass 3 : -3350.7005 (branch= 0.0062 alpha= 0.0155 pinv= 0.0155 eq freqs= 0.0054 rel rates= 0.0220 subset rates= 0.0025) +pass 4 : -3350.6468 (branch= 0.0053 alpha= 0.0136 pinv= 0.0143 eq freqs= 0.0008 rel rates= 0.0197 subset rates= 0.0000) +pass 5 : -3350.5974 (branch= 0.0030 alpha= 0.0131 pinv= 0.0130 eq freqs= 0.0000 rel rates= 0.0181 subset rates= 0.0021) +pass 6 : -3350.5537 (branch= 0.0039 alpha= 0.0116 pinv= 0.0120 eq freqs= 0.0003 rel rates= 0.0146 subset rates= 0.0012) +pass 7 : -3350.5170 (branch= 0.0019 alpha= 0.0101 pinv= 0.0110 eq freqs= 0.0000 rel rates= 0.0136 subset rates= 0.0000) +pass 8 : -3350.4826 (branch= 0.0004 alpha= 0.0102 pinv= 0.0099 eq freqs= 0.0000 rel rates= 0.0128 subset rates= 0.0013) +pass 9 : -3350.4524 (branch= 0.0011 alpha= 0.0093 pinv= 0.0090 eq freqs= 0.0001 rel rates= 0.0107 subset rates= 0.0000) +pass 10: -3350.4262 (branch= 0.0002 alpha= 0.0084 pinv= 0.0080 eq freqs= 0.0000 rel rates= 0.0097 subset rates= 0.0000) +pass 11: -3350.4022 (branch= 0.0001 alpha= 0.0080 pinv= 0.0072 eq freqs= 0.0000 rel rates= 0.0087 subset rates= 0.0000) +pass 12: -3350.3809 (branch= 0.0000 alpha= 0.0073 pinv= 0.0064 eq freqs= 0.0000 rel rates= 0.0075 subset rates= 0.0000) +pass 13: -3350.3621 (branch= 0.0000 alpha= 0.0065 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0065 subset rates= 0.0000) +pass 14: -3350.3456 (branch= 0.0000 alpha= 0.0058 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0056 subset rates= 0.0000) +pass 15: -3350.3310 (branch= 0.0000 alpha= 0.0052 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0048 subset rates= 0.0000) +pass 16: -3350.3183 (branch= 0.0000 alpha= 0.0046 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 17: -3350.3070 (branch= 0.0000 alpha= 0.0040 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) +pass 18: -3350.2972 (branch= 0.0000 alpha= 0.0036 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) +pass 19: -3350.2886 (branch= 0.0000 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0026 subset rates= 0.0000) +pass 20: -3350.2811 (branch= 0.0000 alpha= 0.0027 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2439 (branch= 0.0000 alpha= 0.0137 pinv= 0.0124 eq freqs= 0.0000 rel rates= 0.0111 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2339 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0017 subset rates= 0.0000) +pass 40: -3350.2356 (branch= 0.0000 alpha= 0.0030 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0026 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2333 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 50: -3350.2339 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) optimization up to ... -pass 70: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 60: -3350.2336 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 73: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 67: -3350.2335 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2331 -Time used so far = 0 hours, 0 minutes and 13 seconds +Final score = -3350.2336 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.116, AG = 10.421, AT = 2.691, CG = 0.001, CT = 21.933, GT = 1.000 + AC = 3.119, AG = 10.423, AT = 2.692, CG = 0.001, CT = 21.907, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3329 0.2222 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5776 + 0.5780 with an invariant (invariable) site category, proportion estimated - 0.3657 + 0.3656 Substitution rate categories under this model: rate proportion - 0.0000 0.3657 - 0.0485 0.1586 - 0.2996 0.1586 - 0.8694 0.1586 - 2.7824 0.1586 + 0.0000 0.3656 + 0.0486 0.1586 + 0.2998 0.1586 + 0.8697 0.1586 + 2.7819 0.1586 Model 2 Number of states = 2 (binary data) @@ -12969,20 +13073,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2336 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.116 10.42 2.691 0.001 21.93 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.119 10.42 2.692 0.001 21.91 1 0.333 0.222 0.157 0.288 0.578 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.789 1.820 0.180 +rep 1: 0.788 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -13132,6 +13236,14 @@ 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 +500 -3323.6818 0.500 1 +600 -3323.3459 0.500 1 +Optimization precision reduced + Optimizing parameters... improved 1.812 lnL + Optimizing branchlengths... improved 0.023 lnL +700 -3321.3649 0.255 1 +800 -3321.0294 0.255 1 +900 -3321.0142 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13232,74 +13344,77 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 402, seed 1111909906, best lnL -3323.926 +Search rep 1 (of 2) generation 938, seed 2003812286, best lnL -3321.012 gen current_lnL precision last_tree_imp -402 -3323.9255 0.500 1 -500 -3323.6818 0.500 1 -600 -3323.3459 0.500 1 +938 -3321.0116 0.255 1 +1000 -3320.9667 0.255 1 +1100 -3320.8654 0.255 1 Optimization precision reduced - Optimizing parameters... improved 1.812 lnL - Optimizing branchlengths... improved 0.023 lnL -700 -3321.3650 0.255 1 -800 -3321.0294 0.255 1 + Optimizing parameters... improved 0.579 lnL + Optimizing branchlengths... improved 0.058 lnL +1200 -3320.1508 0.010 1 +1300 -3320.0931 0.010 1 +1400 -3320.0732 0.010 1 +1500 -3320.0216 0.010 1 +1600 -3320.0127 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3321.0275 +Current score = -3320.0113 Performing final optimizations... -pass 1 : -3320.3970 (branch= 0.0377 alpha= 0.0000 pinv= 0.0166 eq freqs= 0.0109 rel rates= 0.5404 ins/del rates= 0.0249) -pass 2 : -3319.9172 (branch= 0.0705 alpha= 0.0049 pinv= 0.0165 eq freqs= 0.0032 rel rates= 0.3665 ins/del rates= 0.0182) -pass 3 : -3319.5594 (branch= 0.0376 alpha= 0.0113 pinv= 0.0155 eq freqs= 0.0040 rel rates= 0.2782 ins/del rates= 0.0112) -pass 4 : -3319.2676 (branch= 0.0266 alpha= 0.0097 pinv= 0.0153 eq freqs= 0.0029 rel rates= 0.2265 ins/del rates= 0.0108) -pass 5 : -3319.0369 (branch= 0.0178 alpha= 0.0106 pinv= 0.0146 eq freqs= 0.0007 rel rates= 0.1801 ins/del rates= 0.0070) -pass 6 : -3318.8371 (branch= 0.0130 alpha= 0.0092 pinv= 0.0139 eq freqs= 0.0007 rel rates= 0.1575 ins/del rates= 0.0055) -pass 7 : -3318.6754 (branch= 0.0083 alpha= 0.0107 pinv= 0.0130 eq freqs= 0.0004 rel rates= 0.1259 ins/del rates= 0.0034) -pass 8 : -3318.5421 (branch= 0.0058 alpha= 0.0098 pinv= 0.0121 eq freqs= 0.0003 rel rates= 0.1028 ins/del rates= 0.0025) -pass 9 : -3318.4304 (branch= 0.0036 alpha= 0.0101 pinv= 0.0112 eq freqs= 0.0003 rel rates= 0.0849 ins/del rates= 0.0016) -pass 10: -3318.3353 (branch= 0.0025 alpha= 0.0093 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0710 ins/del rates= 0.0011) -pass 11: -3318.2569 (branch= 0.0017 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0576 ins/del rates= 0.0007) -pass 12: -3318.1911 (branch= 0.0011 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0472 ins/del rates= 0.0005) -pass 13: -3318.1351 (branch= 0.0007 alpha= 0.0077 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0393 ins/del rates= 0.0003) -pass 14: -3318.0873 (branch= 0.0005 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0327 ins/del rates= 0.0002) -pass 15: -3318.0469 (branch= 0.0003 alpha= 0.0067 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0268 ins/del rates= 0.0001) -pass 16: -3318.0122 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0225 ins/del rates= 0.0001) -pass 17: -3317.9822 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0192 ins/del rates= 0.0000) -pass 18: -3317.9562 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0164 ins/del rates= 0.0000) -pass 19: -3317.9336 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0139 ins/del rates= 0.0000) -pass 20: -3317.9141 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0119 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8169 (branch= 0.0001 alpha= 0.0212 pinv= 0.0196 eq freqs= 0.0001 rel rates= 0.0562 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7938 (branch= 0.0001 alpha= 0.0053 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0128 ins/del rates= 0.0000) +pass 1 : -3319.5718 (branch= 0.0142 alpha= 0.0000 pinv= 0.0150 eq freqs= 0.0000 rel rates= 0.3416 ins/del rates= 0.0687) +pass 2 : -3319.2722 (branch= 0.0272 alpha= 0.0160 pinv= 0.0159 eq freqs= 0.0095 rel rates= 0.2232 ins/del rates= 0.0076) +pass 3 : -3319.0397 (branch= 0.0288 alpha= 0.0144 pinv= 0.0153 eq freqs= 0.0000 rel rates= 0.1681 ins/del rates= 0.0059) +pass 4 : -3318.8568 (branch= 0.0156 alpha= 0.0106 pinv= 0.0148 eq freqs= 0.0022 rel rates= 0.1346 ins/del rates= 0.0050) +pass 5 : -3318.6965 (branch= 0.0117 alpha= 0.0117 pinv= 0.0140 eq freqs= 0.0011 rel rates= 0.1177 ins/del rates= 0.0041) +pass 6 : -3318.5684 (branch= 0.0073 alpha= 0.0113 pinv= 0.0131 eq freqs= 0.0005 rel rates= 0.0929 ins/del rates= 0.0030) +pass 7 : -3318.4601 (branch= 0.0046 alpha= 0.0108 pinv= 0.0122 eq freqs= 0.0006 rel rates= 0.0783 ins/del rates= 0.0019) +pass 8 : -3318.3679 (branch= 0.0031 alpha= 0.0102 pinv= 0.0113 eq freqs= 0.0001 rel rates= 0.0661 ins/del rates= 0.0013) +pass 9 : -3318.2875 (branch= 0.0024 alpha= 0.0093 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0571 ins/del rates= 0.0010) +pass 10: -3318.2187 (branch= 0.0016 alpha= 0.0089 pinv= 0.0095 eq freqs= 0.0001 rel rates= 0.0479 ins/del rates= 0.0007) +pass 11: -3318.1600 (branch= 0.0011 alpha= 0.0085 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0399 ins/del rates= 0.0005) +pass 12: -3318.1097 (branch= 0.0007 alpha= 0.0079 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0335 ins/del rates= 0.0003) +pass 13: -3318.0671 (branch= 0.0004 alpha= 0.0074 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0274 ins/del rates= 0.0002) +pass 14: -3318.0301 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0232 ins/del rates= 0.0001) +pass 15: -3317.9982 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0197 ins/del rates= 0.0001) +pass 16: -3317.9704 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0169 ins/del rates= 0.0000) +pass 17: -3317.9463 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0144 ins/del rates= 0.0000) +pass 18: -3317.9253 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0123 ins/del rates= 0.0000) +pass 19: -3317.9070 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0105 ins/del rates= 0.0000) +pass 20: -3317.8910 (branch= 0.0000 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0090 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8115 (branch= 0.0001 alpha= 0.0189 pinv= 0.0174 eq freqs= 0.0001 rel rates= 0.0431 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7926 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0099 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0031 ins/del rates= 0.0000) +pass 50: -3317.7882 (branch= 0.0000 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0024 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) +pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0005 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... -pass 74: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 73: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 14 seconds +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.064, AG = 10.254, AT = 2.652, CG = 0.001, CT = 21.517, GT = 1.000 + AC = 3.067, AG = 10.269, AT = 2.656, CG = 0.001, CT = 21.550, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3328 0.2223 0.1566 0.2882 + (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5751 + 0.5747 with an invariant (invariable) site category, proportion estimated - 0.3614 + 0.3612 Substitution rate categories under this model: rate proportion - 0.0000 0.3614 - 0.0480 0.1597 - 0.2981 0.1597 - 0.8681 0.1597 - 2.7858 0.1597 + 0.0000 0.3612 + 0.0479 0.1597 + 0.2979 0.1597 + 0.8678 0.1597 + 2.7863 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -13331,7 +13446,7 @@ Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.064 10.25 2.652 0.001 21.52 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.067 10.27 2.656 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -13460,13 +13575,44 @@ Optimization precision reduced Optimizing parameters... improved 1.264 lnL Optimizing branchlengths... improved 0.275 lnL -1200 -211.1653 0.010 1104 -1400 -211.1319 0.010 1104 +1200 -211.1652 0.010 1104 +1400 -211.1318 0.010 1104 1600 -211.0218 0.010 1104 1800 -210.9997 0.010 1104 -2000 -210.9460 0.010 1104 -2200 -210.8946 0.010 1104 -2400 -210.8864 0.010 1104 +2000 -210.9459 0.010 1104 +2200 -210.8945 0.010 1104 +2400 -210.8863 0.010 1104 +2600 -210.8436 0.010 1104 +2800 -210.8251 0.010 1104 +3000 -210.8190 0.010 1104 +3200 -210.7905 0.010 1104 +3400 -210.7553 0.010 1104 +3600 -210.7287 0.010 1104 +3800 -210.7084 0.010 1104 +4000 -210.6947 0.010 1104 +4200 -210.6742 0.010 1104 +4400 -210.6493 0.010 1104 +4600 -210.6258 0.010 1104 +4800 -210.5949 0.010 1104 +5000 -210.5740 0.010 1104 +5200 -210.5695 0.010 1104 +5400 -210.5461 0.010 1104 +5600 -210.5152 0.010 1104 +5800 -210.4823 0.010 1104 +6000 -210.4633 0.010 1104 +6200 -210.4596 0.010 1104 +6400 -210.4468 0.010 1104 +6600 -210.4215 0.010 1104 +6800 -210.3965 0.010 1104 +7000 -210.3384 0.010 1104 +7200 -210.3218 0.010 1104 +7400 -210.2807 0.010 1104 +7600 -210.2625 0.010 1104 +7800 -210.1873 0.010 1104 +8000 -210.1732 0.010 1104 +8200 -210.1282 0.010 1104 +8400 -210.1102 0.010 1104 +8600 -210.0896 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13546,41 +13692,44 @@ STARTING RUN Restarting from checkpoint... - generation 2560, seed 322414041, best lnL -210.849 + generation 8614, seed 166395651, best lnL -210.087 gen current_lnL precision last_tree_imp -2560 -210.8489 0.010 1104 -2600 -210.8436 0.010 1104 -2700 -210.8340 0.010 1104 -2800 -210.8250 0.010 1104 -2900 -210.8228 0.010 1104 -3000 -210.8189 0.010 1104 -3100 -210.8049 0.010 1104 -3200 -210.7905 0.010 1104 +8614 -210.0868 0.010 1104 +8700 -210.0566 0.010 1104 +8800 -210.0543 0.010 1104 +8900 -210.0535 0.010 1104 +9000 -210.0431 0.010 1104 +9100 -209.9813 0.010 1104 +9200 -209.9790 0.010 1104 +9300 -209.9616 0.010 1104 +9400 -209.9603 0.010 1104 +9500 -209.9581 0.010 1104 +9600 -209.9463 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.04347 +Improvement over last 500 gen = 0.03506 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.253, AG = 4.316, AT = 0.229, CG = 3.799, CT = 6.513, GT = 1.000 + AC = 5.196, AG = 8.877, AT = 0.234, CG = 9.299, CT = 14.385, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2299 0.3376 0.2132 0.2194 + (ACGT) 0.2351 0.3311 0.2101 0.2237 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.1008 + 1.9484 with an invariant (invariable) site category, proportion estimated - 0.1053 + 0.2068 Substitution rate categories under this model: rate proportion - 0.0000 0.1053 - 0.2110 0.2982 - 0.7362 0.2982 - 2.0528 0.2982 + 0.0000 0.2068 + 0.3480 0.2644 + 0.8452 0.2644 + 1.8067 0.2644 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... @@ -13588,15 +13737,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.7905 +Replicate 1 : -209.9463 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.253 4.316 0.2288 3.799 6.513 1 0.230 0.338 0.213 0.219 1.101 0.105 +rep 1: 5.196 8.877 0.234 9.299 14.38 1 0.235 0.331 0.210 0.224 1.948 0.207 Treelengths: TL -rep 1: 2.237 +rep 1: 2.329 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log @@ -13722,15 +13871,45 @@ 1200 -193.1176 0.500 694 Optimization precision reduced Optimizing parameters... improved 1.295 lnL - Optimizing branchlengths... improved 0.178 lnL -1400 -191.5424 0.010 1238 -1600 -191.4257 0.010 1238 -1800 -191.2922 0.010 1238 -2000 -191.1576 0.010 1979 -2200 -191.0934 0.010 1979 -2400 -190.9579 0.010 1979 -2600 -190.9301 0.010 1979 -2800 -190.8932 0.010 1979 + Optimizing branchlengths... improved 0.177 lnL +1400 -191.5427 0.010 1238 +1600 -191.4261 0.010 1238 +1800 -191.2927 0.010 1238 +2000 -191.1580 0.010 1979 +2200 -191.0939 0.010 1979 +2400 -190.9582 0.010 1979 +2600 -190.9310 0.010 1979 +2800 -190.8956 0.010 1979 +3000 -190.8859 0.010 1979 +3200 -190.8751 0.010 1979 +3400 -190.8601 0.010 1979 +3600 -190.8481 0.010 1979 +3800 -190.7803 0.010 1979 +4000 -190.7724 0.010 1979 +4200 -190.7222 0.010 1979 +4400 -190.7070 0.010 1979 +4600 -190.6711 0.010 1979 +4800 -190.6644 0.010 1979 +5000 -190.6534 0.010 1979 +5200 -190.6459 0.010 1979 +5400 -190.6442 0.010 1979 +5600 -190.6023 0.010 1979 +5800 -190.5545 0.010 1979 +6000 -190.5517 0.010 1979 +6200 -190.5474 0.010 1979 +6400 -190.5259 0.010 1979 +6600 -190.5060 0.010 1979 +6800 -190.5053 0.010 1979 +7000 -190.5032 0.010 1979 +7200 -190.4915 0.010 1979 +7400 -190.4895 0.010 1979 +7600 -190.4664 0.010 1979 +7800 -190.4626 0.010 1979 +8000 -190.4448 0.010 1979 +8200 -190.4365 0.010 1979 +8400 -190.4338 0.010 1979 +8600 -190.4323 0.010 1979 +8800 -190.3415 0.010 1979 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13811,51 +13990,35 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 2900, seed 621586136, best lnL -190.887 +Bootstrap rep 1 (of 1) generation 8989, seed 343313311, best lnL -190.315 gen current_lnL precision last_tree_imp -2900 -190.8874 0.010 1979 -3000 -190.8742 0.010 1979 -3100 -190.8656 0.010 1979 -3200 -190.8644 0.010 1979 -3300 -190.8608 0.010 1979 -3400 -190.8490 0.010 1979 -3500 -190.8375 0.010 1979 -3600 -190.8368 0.010 1979 -3700 -190.8127 0.010 1979 -3800 -190.7692 0.010 1979 -3900 -190.7626 0.010 1979 -4000 -190.7606 0.010 1979 -4100 -190.7295 0.010 1979 -4200 -190.7106 0.010 1979 -4300 -190.6995 0.010 1979 -4400 -190.6938 0.010 1979 -4500 -190.6695 0.010 1979 -4600 -190.6593 0.010 1979 -4700 -190.6591 0.010 1979 -4800 -190.6551 0.010 1979 +8989 -190.3147 0.010 1979 +9000 -190.3145 0.010 1979 +9100 -190.3117 0.010 1979 +9200 -190.3105 0.010 1979 Reached termination condition! last topological improvement at gen 1979 -Improvement over last 500 gen = 0.04439 +Improvement over last 500 gen = 0.04841 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.525, AG = 1.103, AT = 0.009, CG = 2.352, CT = 10.997, GT = 1.000 + AC = 0.911, AG = 1.790, AT = 0.009, CG = 4.211, CT = 21.627, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3118 0.3242 0.2589 0.1052 + (ACGT) 0.3161 0.3202 0.2599 0.1038 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 6.3206 + 6.6923 with an invariant (invariable) site category, proportion estimated - 0.1381 + 0.1453 Substitution rate categories under this model: rate proportion - 0.0000 0.1381 - 0.5491 0.2155 - 0.8300 0.2155 - 1.0805 0.2155 - 1.5403 0.2155 + 0.0000 0.1453 + 0.5601 0.2137 + 0.8358 0.2137 + 1.0797 0.2137 + 1.5244 0.2137 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. @@ -13865,15 +14028,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -190.6551 +Replicate 1 : -190.3105 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 0.5248 1.103 0.00911 2.352 11 1 0.312 0.324 0.259 0.105 6.321 0.138 +rep 1: 0.9112 1.79 0.008714 4.211 21.63 1 0.316 0.320 0.260 0.104 6.692 0.145 Treelengths: TL -rep 1: 2.271 +rep 1: 2.374 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -13996,15 +14159,82 @@ 3200 -213.1947 0.010 530 3400 -213.1684 0.010 530 3600 -213.1581 0.010 530 -NOTE: ****Specified time limit (5 seconds) reached... +3800 -213.0252 0.010 3769 +4000 -212.9705 0.010 3769 +4200 -212.9482 0.010 3769 +4400 -212.9233 0.010 3769 +4600 -212.8795 0.010 3769 +4800 -212.8767 0.010 3769 +5000 -212.8762 0.010 3769 +5200 -212.8557 0.010 3769 +5400 -212.8534 0.010 3769 +5600 -212.8187 0.010 3769 +5800 -212.7687 0.010 3769 +6000 -212.7263 0.010 3769 +6200 -212.7248 0.010 3769 +6400 -212.7244 0.010 3769 +6600 -212.7153 0.010 3769 +6800 -212.7057 0.010 3769 +7000 -212.7024 0.010 3769 +7200 -212.7018 0.010 3769 +7400 -212.6732 0.010 3769 +7600 -212.6697 0.010 3769 +7800 -212.6661 0.010 3769 +8000 -212.6648 0.010 3769 +8200 -212.6626 0.010 3769 +8400 -212.6613 0.010 3769 +8600 -212.6533 0.010 3769 +8800 -212.5987 0.010 3769 +9000 -212.5600 0.010 3769 +9200 -212.5460 0.010 3769 +9400 -212.5285 0.010 3769 +9600 -212.5057 0.010 3769 +9800 -212.4986 0.010 3769 +10000 -212.4929 0.010 3769 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +Model 1 + Number of states = 4 (nucleotide data) + Nucleotide Relative Rate Matrix: 6 rates + AC = 8.357, AG = 15.268, AT = 0.630, CG = 15.123, CT = 10.065, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2200 0.2879 0.1851 0.3070 + Rate Heterogeneity Model: + no rate heterogeneity + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 1 branches were collapsed. + +Saving site likelihoods to file ch.n.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + +####################################################### + +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -212.4929 + +Parameter estimates: + r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) +rep 1: 8.357 15.27 0.6302 15.12 10.06 1 0.220 0.288 0.185 0.307 + +Treelengths: + TL +rep 1: 1.726 + +Saving final tree from best search rep (#1) to ch.n.best.tre +Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log + +WARNING: Internal states inferred on tree from prematurely terminated search +####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -14075,46 +14305,17 @@ STARTING RUN Restarting from checkpoint... - generation 3740, seed 1276111451, best lnL -213.107 + generation 10001, seed 1459438551, best lnL -212.493 gen current_lnL precision last_tree_imp -3740 -213.1066 0.010 530 -3800 -213.0252 0.010 3769 -3900 -212.9946 0.010 3769 -4000 -212.9705 0.010 3769 -4100 -212.9705 0.010 3769 -4200 -212.9482 0.010 3769 -4300 -212.9260 0.010 3769 -4400 -212.9233 0.010 3769 -4500 -212.8900 0.010 3769 -4600 -212.8795 0.010 3769 -4700 -212.8767 0.010 3769 -4800 -212.8767 0.010 3769 -4900 -212.8762 0.010 3769 -5000 -212.8762 0.010 3769 -5100 -212.8650 0.010 3769 -5200 -212.8557 0.010 3769 -5300 -212.8535 0.010 3769 -5400 -212.8534 0.010 3769 -5500 -212.8217 0.010 3769 -5600 -212.8187 0.010 3769 -5700 -212.8107 0.010 3769 -5800 -212.7687 0.010 3769 -5900 -212.7273 0.010 3769 -6000 -212.7263 0.010 3769 -6100 -212.7249 0.010 3769 -6200 -212.7248 0.010 3769 -6300 -212.7245 0.010 3769 -Reached termination condition! -last topological improvement at gen 3769 -Improvement over last 500 gen = 0.04425 +10001 -212.4929 0.010 3769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 4.838, AG = 9.614, AT = 0.397, CG = 9.762, CT = 6.242, GT = 1.000 + AC = 8.357, AG = 15.268, AT = 0.630, CG = 15.123, CT = 10.065, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2212 0.2915 0.1818 0.3056 + (ACGT) 0.2200 0.2879 0.1851 0.3070 Rate Heterogeneity Model: no rate heterogeneity @@ -14127,15 +14328,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.7245 +Replicate 1 : -212.4929 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 4.838 9.614 0.397 9.762 6.242 1 0.221 0.291 0.182 0.306 +rep 1: 8.357 15.27 0.6302 15.12 10.06 1 0.220 0.288 0.185 0.307 Treelengths: TL -rep 1: 1.731 +rep 1: 1.726 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log @@ -14268,22 +14469,105 @@ 1600 -211.2007 0.010 1502 1800 -211.0869 0.010 1502 2000 -210.9688 0.010 1502 -2200 -210.8961 0.010 1502 +2200 -210.8960 0.010 1502 2400 -210.8906 0.010 1502 2600 -210.8173 0.010 1502 -2800 -210.7848 0.010 1502 -3000 -210.7511 0.010 2883 -3200 -210.7244 0.010 2883 +2800 -210.7847 0.010 1502 +3000 -210.7510 0.010 2883 +3200 -210.7243 0.010 2883 3400 -210.7006 0.010 2883 -NOTE: ****Specified time limit (5 seconds) reached... +3600 -210.6993 0.010 2883 +3800 -210.6779 0.010 2883 +4000 -210.6775 0.010 2883 +4200 -210.6762 0.010 2883 +4400 -210.6527 0.010 2883 +4600 -210.6397 0.010 2883 +4800 -210.5993 0.010 4692 +5000 -210.5909 0.010 4692 +5200 -210.5665 0.010 4692 +5400 -210.5211 0.010 4692 +5600 -210.5054 0.010 4692 +5800 -210.3943 0.010 4692 +6000 -210.3810 0.010 4692 +6200 -210.3787 0.010 4692 +6400 -210.3726 0.010 4692 +6600 -210.3694 0.010 4692 +6800 -210.3541 0.010 4692 +7000 -210.3464 0.010 4692 +7200 -210.3372 0.010 4692 +7400 -210.3335 0.010 4692 +7600 -210.3216 0.010 4692 +7800 -210.2529 0.010 4692 +8000 -210.2457 0.010 4692 +8200 -210.2413 0.010 4692 +8400 -210.2356 0.010 4692 +8600 -210.2042 0.010 4692 +8800 -210.1747 0.010 4692 +9000 -210.1244 0.010 4692 +9200 -210.1122 0.010 4692 +9400 -210.1016 0.010 4692 +9600 -210.0776 0.010 4692 +9800 -210.0722 0.010 4692 +10000 -210.0595 0.010 4692 + Optimizing parameters... improved 0.457 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +Model 1 + Number of states = 4 (nucleotide data) + Nucleotide Relative Rate Matrix: 6 rates + AC = 2.401, AG = 4.418, AT = 0.037, CG = 4.396, CT = 8.498, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2422 0.3365 0.2110 0.2103 + Rate Heterogeneity Model: + 4 discrete gamma distributed rate categories, alpha param estimated + 2.8812 + with an invariant (invariable) site category, proportion estimated + 0.2875 + Substitution rate categories under this model: + rate proportion + 0.0000 0.2875 + 0.3799 0.1781 + 0.7247 0.1781 + 1.0819 0.1781 + 1.8135 0.1781 + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 1 branches were collapsed. + + +NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with + a positive constraint, it is possible for a constrained branch itself to be collapsed. + If you care, be careful to check whether this has happened or turn off branch collapsing. + +Saving site likelihoods to file ch.n.const.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + +####################################################### + +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -209.6021 + +Parameter estimates: + r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv +rep 1: 2.401 4.418 0.03741 4.396 8.498 1 0.242 0.336 0.211 0.210 2.881 0.288 + +Treelengths: + TL +rep 1: 2.437 + +Saving final tree from best search rep (#1) to ch.n.const.best.tre +Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log + +WARNING: Internal states inferred on tree from prematurely terminated search +####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -14362,101 +14646,32 @@ STARTING RUN Restarting from checkpoint... - generation 3445, seed 1512055452, best lnL -210.701 + generation 10001, seed 1041095190, best lnL -209.602 gen current_lnL precision last_tree_imp -3445 -210.7006 0.010 2883 -3500 -210.7006 0.010 2883 -3600 -210.6993 0.010 2883 -3700 -210.6820 0.010 2883 -3800 -210.6779 0.010 2883 -3900 -210.6776 0.010 2883 -4000 -210.6776 0.010 2883 -4100 -210.6766 0.010 2883 -4200 -210.6762 0.010 2883 -4300 -210.6651 0.010 2883 -4400 -210.6527 0.010 2883 -4500 -210.6527 0.010 2883 -4600 -210.6397 0.010 2883 -4700 -210.6055 0.010 4692 -4800 -210.5993 0.010 4692 -4900 -210.5915 0.010 4692 -5000 -210.5909 0.010 4692 -5100 -210.5860 0.010 4692 -5200 -210.5665 0.010 4692 -5300 -210.5269 0.010 4692 -5400 -210.5211 0.010 4692 -5500 -210.5077 0.010 4692 -5600 -210.5055 0.010 4692 -5700 -210.4303 0.010 4692 -5800 -210.3722 0.010 5799 -5900 -210.3503 0.010 5804 -6000 -210.3155 0.010 5804 -6100 -210.3123 0.010 5804 -6200 -210.3116 0.010 5804 -6300 -210.3110 0.010 5804 -6400 -210.2916 0.010 5804 -6500 -210.2907 0.010 5804 -6600 -210.2893 0.010 5804 -6700 -210.2758 0.010 5804 -6800 -210.2693 0.010 5804 -6900 -210.2692 0.010 5804 -7000 -210.2665 0.010 5804 -7100 -210.2645 0.010 5804 -7200 -210.2556 0.010 5804 -7300 -210.2320 0.010 5804 -7400 -210.2316 0.010 5804 -7500 -210.2316 0.010 5804 -7600 -210.2218 0.010 5804 -7700 -210.1853 0.010 5804 -7800 -210.1524 0.010 7792 -7900 -210.1490 0.010 7792 -8000 -210.1487 0.010 7792 -8100 -210.1386 0.010 7792 -8200 -210.1320 0.010 7792 -8300 -210.1172 0.010 7792 -8400 -210.0705 0.010 8327 -8500 -210.0550 0.010 8414 -8600 -210.0541 0.010 8414 -8700 -210.0396 0.010 8414 -8800 -210.0387 0.010 8414 -8900 -210.0300 0.010 8414 -9000 -210.0297 0.010 8414 -9100 -210.0296 0.010 8414 -9200 -210.0210 0.010 8414 -9300 -210.0178 0.010 8414 -9400 -210.0175 0.010 8414 -9500 -210.0085 0.010 8414 -9600 -210.0085 0.010 8414 -9700 -210.0081 0.010 8414 -9800 -209.9733 0.010 8414 -9900 -209.9711 0.010 8414 -10000 -209.9708 0.010 8414 - Optimizing parameters... improved 0.535 lnL - Optimizing branchlengths... improved 0.003 lnL -NOTE: ****Specified generation limit (10000) reached... +10001 -209.6021 0.010 4692 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.482, AG = 4.593, AT = 0.040, CG = 4.596, CT = 8.835, GT = 1.000 + AC = 2.401, AG = 4.418, AT = 0.037, CG = 4.396, CT = 8.498, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2393 0.3376 0.2118 0.2112 + (ACGT) 0.2422 0.3365 0.2110 0.2103 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.2038 + 2.8812 with an invariant (invariable) site category, proportion estimated - 0.3019 + 0.2875 Substitution rate categories under this model: rate proportion - 0.0000 0.3019 - 0.4652 0.1745 - 0.7820 0.1745 - 1.0843 0.1745 - 1.6685 0.1745 + 0.0000 0.2875 + 0.3799 0.1781 + 0.7247 0.1781 + 1.0819 0.1781 + 1.8135 0.1781 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with @@ -14464,31 +14679,24 @@ If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.4331 +Replicate 1 : -209.6021 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.482 4.593 0.03999 4.596 8.835 1 0.239 0.338 0.212 0.211 4.204 0.302 +rep 1: 2.401 4.418 0.03741 4.396 8.498 1 0.242 0.336 0.211 0.210 2.881 0.288 Treelengths: TL -rep 1: 2.422 +rep 1: 2.437 Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/p.3diff.conf @@ -14689,6 +14897,25 @@ Optimization precision reduced Optimizing parameters... improved 0.055 lnL Optimizing branchlengths... improved 0.000 lnL +700 -13181.7193 0.402 1 +800 -13181.6899 0.402 1 +900 -13181.6040 0.402 1 +1000 -13181.4969 0.402 1 +1100 -13181.4426 0.402 1 +Optimization precision reduced + Optimizing parameters... improved 0.019 lnL + Optimizing branchlengths... improved 0.000 lnL +1200 -13181.4112 0.304 1 +1300 -13181.3755 0.304 1 +1400 -13181.3694 0.304 1 +1500 -13181.3534 0.304 1 +1600 -13181.3306 0.304 1 +Optimization precision reduced + Optimizing parameters... improved 0.011 lnL + Optimizing branchlengths... improved 0.000 lnL +1700 -13181.3200 0.206 1 +1800 -13181.3027 0.206 1 +1900 -13181.2988 0.206 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14811,75 +15038,72 @@ Subset 3: Random seed for bootstrap reweighting: 1903425807 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 699, seed 1219341124, best lnL -13181.719 +Bootstrap rep 1 (of 1) generation 1929, seed 1480359060, best lnL -13181.299 gen current_lnL precision last_tree_imp -699 -13181.7193 0.402 1 -700 -13181.7193 0.402 1 -800 -13181.6899 0.402 1 -900 -13181.6040 0.402 1 -NOTE: ****Specified time limit (1 seconds) reached... +1929 -13181.2988 0.206 1 +2000 -13181.2934 0.206 1 +NOTE: ****Specified generation limit (2000) reached... -MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.971, AG = 3.147, AT = 1.158, CG = 1.158, CT = 2.621, GT = 1.000 + AC = 2.076, AG = 3.225, AT = 1.199, CG = 1.199, CT = 2.700, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3056 0.1863 0.2743 0.2338 + (ACGT) 0.3051 0.1870 0.2737 0.2342 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3873 + 0.3878 Substitution rate categories under this model: rate proportion - 0.0149 0.2500 - 0.1722 0.2500 - 0.7171 0.2500 - 3.0958 0.2500 + 0.0150 0.2500 + 0.1726 0.2500 + 0.7177 0.2500 + 3.0948 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 3.865, AG = 4.815, AT = 0.741, CG = 4.815, CT = 3.865, GT = 1.000 + AC = 3.839, AG = 4.683, AT = 0.735, CG = 4.683, CT = 3.839, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2518 0.1565 0.1900 0.4017 + (ACGT) 0.2505 0.1555 0.1902 0.4037 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.4402 + 0.4489 Substitution rate categories under this model: rate proportion - 0.0229 0.2500 - 0.2111 0.2500 - 0.7714 0.2500 - 2.9946 0.2500 + 0.0243 0.2500 + 0.2172 0.2500 + 0.7792 0.2500 + 2.9793 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 7.154, AT = 5.573, CG = 1.042, CT = 7.154, GT = 1.000 + AC = 1.000, AG = 7.121, AT = 5.573, CG = 1.050, CT = 7.121, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1615 0.3400 0.2956 0.2029 + (ACGT) 0.1612 0.3394 0.2965 0.2029 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.5455 + 4.8773 with an invariant (invariable) site category, proportion estimated - 0.0109 + 0.0123 Substitution rate categories under this model: rate proportion - 0.0000 0.0109 - 0.4820 0.2473 - 0.7922 0.2473 - 1.0840 0.2473 - 1.6418 0.2473 + 0.0000 0.0123 + 0.4969 0.2469 + 0.8010 0.2469 + 1.0835 0.2469 + 1.6186 0.2469 Subset rate multipliers: 0.53 0.28 2.20 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. ->>>Terminated Bootstrap rep 1 (of 1) <<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -14889,25 +15113,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13181.5027 (TERMINATED PREMATURELY) +Replicate 1 : -13181.2934 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 1.971 3.147 1.158 1.158 2.621 1 0.306 0.186 0.274 0.234 0.387 +rep 1: 2.076 3.225 1.199 1.199 2.7 1 0.305 0.187 0.274 0.234 0.388 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 3.865 4.815 0.7412 4.815 3.865 1 0.252 0.157 0.190 0.402 0.440 +rep 1: 3.839 4.683 0.7351 4.683 3.839 1 0.251 0.156 0.190 0.404 0.449 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 7.154 5.573 1.042 7.154 1 0.161 0.340 0.296 0.203 4.546 0.011 +rep 1: 1 7.121 5.573 1.05 7.121 1 0.161 0.339 0.296 0.203 4.877 0.012 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.677 0.526 0.278 2.196 +rep 1: 1.667 0.526 0.278 2.196 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -15097,6 +15321,133 @@ 2200 -467.7210 0.010 76 2300 -467.7209 0.010 76 2400 -467.7201 0.010 76 +2500 -467.7198 0.010 76 +2600 -467.7198 0.010 76 +2700 -467.7190 0.010 76 +2800 -467.7182 0.010 76 +2900 -467.7178 0.010 76 +3000 -467.7177 0.010 76 +3100 -467.7174 0.010 76 +3200 -467.7172 0.010 76 +3300 -467.7171 0.010 76 +3400 -467.7171 0.010 76 +Reached termination condition! +last topological improvement at gen 76 +Improvement over last 500 gen = 0.00073 +Current score = -467.7171 +Performing final optimizations... +pass 1 : -467.7125 (branch= 0.0000 subset rates= 0.0046) +pass 2 : -467.6943 (branch= 0.0182 subset rates= 0.0000) +pass 3 : -467.6943 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -467.6901 (branch= 0.0042 subset rates= 0.0000) +pass 5 : -467.6873 (branch= 0.0017 subset rates= 0.0010) +pass 6 : -467.6844 (branch= 0.0019 subset rates= 0.0010) +pass 7 : -467.6817 (branch= 0.0009 subset rates= 0.0018) +pass 8 : -467.6811 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -467.6808 (branch= 0.0003 subset rates= 0.0000) +pass 10: -467.6807 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6806 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6805 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6805 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6805 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -467.6805 +Time used so far = 0 hours, 0 minutes and 3 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.79 1.48 2.14 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=864977241 + +Initial ln Likelihood: -614.0831 +optimizing: starting branch lengths, subset rates... +pass 1:+ 127.392 (branch= 121.24 scale= 1.98 subset rates= 4.16) +pass 2:+ 15.988 (branch= 15.02 scale= 0.02 subset rates= 0.96) +pass 3:+ 2.694 (branch= 2.46 scale= 0.04 subset rates= 0.20) +pass 4:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.039 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -467.8364 +gen current_lnL precision last_tree_imp +0 -467.8364 0.010 0 +100 -467.8012 0.010 0 +200 -467.7834 0.010 0 +300 -467.7718 0.010 0 +400 -467.7465 0.010 0 +500 -467.7421 0.010 0 +600 -467.7393 0.010 0 +700 -467.7358 0.010 0 +800 -467.7328 0.010 0 +900 -467.7314 0.010 0 +1000 -467.7285 0.010 0 +1100 -467.7271 0.010 0 +1200 -467.7201 0.010 0 +1300 -467.7189 0.010 0 +1400 -467.7172 0.010 0 +1500 -467.7147 0.010 0 +1600 -467.7146 0.010 0 +1700 -467.7131 0.010 0 +1800 -467.7122 0.010 0 +1900 -467.7122 0.010 0 +2000 -467.7119 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15222,40 +15573,54 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 2430, seed 1526162433, best lnL -467.720 +Search rep 2 (of 5) generation 2030, seed 1985580474, best lnL -467.712 gen current_lnL precision last_tree_imp -2430 -467.7201 0.010 76 -2500 -467.7198 0.010 76 -2600 -467.7198 0.010 76 -2700 -467.7190 0.010 76 -2800 -467.7182 0.010 76 -2900 -467.7178 0.010 76 -3000 -467.7177 0.010 76 -3100 -467.7174 0.010 76 -3200 -467.7172 0.010 76 -3300 -467.7171 0.010 76 -3400 -467.7171 0.010 76 +2030 -467.7119 0.010 0 +2100 -467.7104 0.010 0 +2200 -467.7087 0.010 0 +2300 -467.7087 0.010 0 +2400 -467.7083 0.010 0 +2500 -467.7076 0.010 0 +2600 -467.7072 0.010 0 +2700 -467.7072 0.010 0 +2800 -467.7066 0.010 0 +2900 -467.7065 0.010 0 +3000 -467.7064 0.010 0 +3100 -467.7058 0.010 0 +3200 -467.7050 0.010 0 +3300 -467.7035 0.010 0 +3400 -467.7028 0.010 0 +3500 -467.7023 0.010 0 +3600 -467.7019 0.010 0 +3700 -467.7017 0.010 0 +3800 -467.7017 0.010 0 +3900 -467.7013 0.010 0 +4000 -467.7004 0.010 0 +4100 -467.7001 0.010 0 +4200 -467.7001 0.010 0 +4300 -467.6998 0.010 0 +4400 -467.6997 0.010 0 +4500 -467.6997 0.010 0 Reached termination condition! -last topological improvement at gen 76 +last topological improvement at gen 0 Improvement over last 500 gen = 0.00073 -Current score = -467.7171 +Current score = -467.6997 Performing final optimizations... -pass 1 : -467.7101 (branch= 0.0000 subset rates= 0.0070) -pass 2 : -467.6919 (branch= 0.0182 subset rates= 0.0000) -pass 3 : -467.6883 (branch= 0.0036 subset rates= 0.0000) -pass 4 : -467.6845 (branch= 0.0037 subset rates= 0.0000) -pass 5 : -467.6832 (branch= 0.0013 subset rates= 0.0000) -pass 6 : -467.6814 (branch= 0.0019 subset rates= 0.0000) -pass 7 : -467.6806 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -467.6802 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -467.6800 (branch= 0.0002 subset rates= 0.0000) -pass 10: -467.6799 (branch= 0.0001 subset rates= 0.0000) -pass 11: -467.6798 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6797 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6797 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6797 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.6997 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.6876 (branch= 0.0121 subset rates= 0.0000) +pass 3 : -467.6830 (branch= 0.0046 subset rates= 0.0000) +pass 4 : -467.6821 (branch= 0.0009 subset rates= 0.0000) +pass 5 : -467.6811 (branch= 0.0010 subset rates= 0.0000) +pass 6 : -467.6804 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -467.6793 (branch= 0.0012 subset rates= 0.0000) +pass 8 : -467.6789 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -467.6786 (branch= 0.0002 subset rates= 0.0000) +pass 10: -467.6785 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6784 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6784 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6797 +Final score = -467.6784 Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL @@ -15284,13 +15649,13 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.15 + 0.79 1.48 2.17 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 1 (of 5)<<< +>>>Completed Search rep 2 (of 5)<<< ->>>Search rep 2 (of 5)<<< +>>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -15319,51 +15684,72 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=864977241 +Starting with seed=1668858692 -Initial ln Likelihood: -614.0831 +Initial ln Likelihood: -630.9240 optimizing: starting branch lengths, subset rates... -pass 1:+ 127.392 (branch= 121.24 scale= 1.98 subset rates= 4.16) -pass 2:+ 15.988 (branch= 15.02 scale= 0.02 subset rates= 0.96) -pass 3:+ 2.694 (branch= 2.46 scale= 0.04 subset rates= 0.20) -pass 4:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.039 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 1:+ 146.355 (branch= 140.50 scale= 1.37 subset rates= 4.49) +pass 2:+ 13.169 (branch= 11.99 scale= 0.01 subset rates= 1.16) +pass 3:+ 3.305 (branch= 3.17 scale= 0.00 subset rates= 0.14) +pass 4:+ 0.249 (branch= 0.25 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.025 (branch= 0.03 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8364 +lnL after optimization: -467.8215 gen current_lnL precision last_tree_imp -0 -467.8364 0.010 0 -100 -467.8012 0.010 0 -200 -467.7834 0.010 0 -300 -467.7718 0.010 0 -400 -467.7465 0.010 0 -500 -467.7421 0.010 0 -600 -467.7393 0.010 0 -700 -467.7358 0.010 0 -800 -467.7328 0.010 0 -900 -467.7314 0.010 0 -1000 -467.7285 0.010 0 -1100 -467.7271 0.010 0 -1200 -467.7201 0.010 0 -1300 -467.7189 0.010 0 +0 -467.8215 0.010 0 +100 -467.7946 0.010 0 +200 -467.7839 0.010 0 +300 -467.7684 0.010 0 +400 -467.7555 0.010 0 +500 -467.7486 0.010 0 +600 -467.7440 0.010 0 +700 -467.7414 0.010 0 +800 -467.7400 0.010 0 +900 -467.7390 0.010 0 +1000 -467.7341 0.010 0 +1100 -467.7306 0.010 0 +1200 -467.7273 0.010 0 +1300 -467.7266 0.010 0 +1400 -467.7226 0.010 0 +1500 -467.7189 0.010 0 +1600 -467.7178 0.010 0 +1700 -467.7172 0.010 0 +1800 -467.7161 0.010 0 +1900 -467.7149 0.010 0 +2000 -467.7133 0.010 0 +2100 -467.7125 0.010 0 +2200 -467.7116 0.010 0 +2300 -467.7116 0.010 0 +2400 -467.7114 0.010 0 +2500 -467.7111 0.010 0 +2600 -467.7100 0.010 0 +2700 -467.7097 0.010 0 +2800 -467.7096 0.010 0 +2900 -467.7093 0.010 0 +3000 -467.7084 0.010 0 +3100 -467.7084 0.010 0 +3200 -467.7073 0.010 0 +3300 -467.7073 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7175 +Current score = -467.7069 Performing final optimizations... -pass 1 : -467.7175 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.7016 (branch= 0.0159 subset rates= 0.0000) -pass 3 : -467.6927 (branch= 0.0088 subset rates= 0.0000) -pass 4 : -467.6844 (branch= 0.0084 subset rates= 0.0000) -pass 5 : -467.6821 (branch= 0.0023 subset rates= 0.0000) -pass 6 : -467.6801 (branch= 0.0020 subset rates= 0.0000) -pass 7 : -467.6796 (branch= 0.0005 subset rates= 0.0000) -pass 8 : -467.6793 (branch= 0.0003 subset rates= 0.0000) +pass 1 : -467.7069 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.6925 (branch= 0.0144 subset rates= 0.0000) +pass 3 : -467.6885 (branch= 0.0039 subset rates= 0.0000) +pass 4 : -467.6861 (branch= 0.0024 subset rates= 0.0000) +pass 5 : -467.6843 (branch= 0.0014 subset rates= 0.0004) +pass 6 : -467.6817 (branch= 0.0025 subset rates= 0.0001) +pass 7 : -467.6804 (branch= 0.0014 subset rates= 0.0000) +pass 8 : -467.6793 (branch= 0.0010 subset rates= 0.0000) pass 9 : -467.6790 (branch= 0.0003 subset rates= 0.0000) -pass 10: -467.6789 (branch= 0.0001 subset rates= 0.0000) -pass 11: -467.6788 (branch= 0.0000 subset rates= 0.0000) -pass 12: -467.6788 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6788 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6788 (branch= 0.0000 subset rates= 0.0000) +pass 10: -467.6789 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6788 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6786 (branch= 0.0000 subset rates= 0.0001) +pass 13: -467.6786 (branch= 0.0001 subset rates= 0.0000) +pass 14: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6785 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6788 +Final score = -467.6785 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15392,11 +15778,11 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.16 + 0.78 1.48 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 2 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -15404,13 +15790,14 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -467.6797 -Replicate 2 : -467.6788 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -467.6805 +Replicate 2 : -467.6784 (best) (same topology as 1) +Replicate 3 : -467.6785 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -15425,8 +15812,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.839 0.789 1.480 2.149 -rep 2: 3.840 0.788 1.479 2.162 +rep 1: 3.839 0.788 1.483 2.140 +rep 2: 3.841 0.787 1.480 2.172 +rep 3: 3.845 0.785 1.484 2.181 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -15613,6 +16001,140 @@ 2000 -477.4746 0.010 373 2100 -477.4736 0.010 373 2200 -477.4729 0.010 373 +2300 -477.4726 0.010 373 +2400 -477.4723 0.010 373 +2500 -477.4720 0.010 373 +2600 -477.4708 0.010 373 +2700 -477.4705 0.010 373 +2800 -477.4703 0.010 373 +2900 -477.4703 0.010 373 +3000 -477.4700 0.010 373 +3100 -477.4699 0.010 373 +Reached termination condition! +last topological improvement at gen 373 +Improvement over last 500 gen = 0.00098 +Current score = -477.4699 +Performing final optimizations... +pass 1 : -477.4696 (branch= 0.0000 subset rates= 0.0002) +pass 2 : -477.4427 (branch= 0.0269 subset rates= 0.0000) +pass 3 : -477.4390 (branch= 0.0038 subset rates= 0.0000) +pass 4 : -477.4361 (branch= 0.0028 subset rates= 0.0000) +pass 5 : -477.4350 (branch= 0.0011 subset rates= 0.0000) +pass 6 : -477.4343 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -477.4332 (branch= 0.0011 subset rates= 0.0000) +pass 8 : -477.4324 (branch= 0.0008 subset rates= 0.0000) +pass 9 : -477.4321 (branch= 0.0004 subset rates= 0.0000) +pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4317 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.4317 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4317 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4317 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -477.4317 +Time used so far = 0 hours, 0 minutes and 3 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.63 1.92 2.74 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 7 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=200420059 + +Initial ln Likelihood: -656.4902 +optimizing: starting branch lengths, subset rates... +pass 1:+ 148.906 (branch= 137.62 scale= 1.92 subset rates= 9.37) +pass 2:+ 19.722 (branch= 15.83 scale= 0.00 subset rates= 3.89) +pass 3:+ 3.558 (branch= 2.11 scale= 0.00 subset rates= 1.45) +pass 4:+ 2.462 (branch= 2.03 scale= 0.00 subset rates= 0.44) +pass 5:+ 3.227 (branch= 3.23 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.746 (branch= 0.71 scale= 0.01 subset rates= 0.02) +pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -477.8529 +gen current_lnL precision last_tree_imp +0 -477.8529 0.010 0 +100 -477.7882 0.010 74 +200 -477.7667 0.010 74 +300 -477.7488 0.010 74 +400 -477.7425 0.010 74 +500 -477.7296 0.010 74 +600 -477.7269 0.010 74 +700 -477.7207 0.010 74 +800 -477.7196 0.010 74 +900 -477.7188 0.010 74 +1000 -477.7137 0.010 74 +1100 -477.7096 0.010 74 +1200 -477.7092 0.010 74 +1300 -477.7061 0.010 74 +1400 -477.7037 0.010 74 +1500 -477.7021 0.010 74 +1600 -477.7005 0.010 74 +1700 -477.6995 0.010 74 +1800 -477.6986 0.010 74 +1900 -477.6979 0.010 74 +2000 -477.6963 0.010 74 +2100 -477.3761 0.010 2081 +2200 -477.3593 0.010 2170 +2300 -477.3535 0.010 2170 +2400 -477.3473 0.010 2170 +2500 -477.3427 0.010 2170 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15738,41 +16260,72 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 2212, seed 51095155, best lnL -477.473 +Search rep 2 (of 5) generation 2552, seed 1822272353, best lnL -477.334 gen current_lnL precision last_tree_imp -2212 -477.4729 0.010 373 -2300 -477.4726 0.010 373 -2400 -477.4723 0.010 373 -2500 -477.4720 0.010 373 -2600 -477.4708 0.010 373 -2700 -477.4705 0.010 373 -2800 -477.4703 0.010 373 -2900 -477.4703 0.010 373 -3000 -477.4700 0.010 373 -3100 -477.4699 0.010 373 +2552 -477.3342 0.010 2170 +2600 -477.3277 0.010 2170 +2700 -477.3252 0.010 2170 +2800 -477.3168 0.010 2170 +2900 -477.3153 0.010 2170 +3000 -477.3138 0.010 2170 +3100 -477.3121 0.010 2170 +3200 -477.3114 0.010 2170 +3300 -477.3111 0.010 2170 +3400 -477.3104 0.010 2170 +3500 -477.3097 0.010 2170 +3600 -477.3097 0.010 2170 +3700 -477.3095 0.010 2170 +3800 -477.3086 0.010 2170 +3900 -477.3085 0.010 2170 +4000 -477.3085 0.010 2170 +4100 -477.3065 0.010 2170 +4200 -477.3065 0.010 2170 +4300 -477.3063 0.010 2170 +4400 -477.3057 0.010 2170 +4500 -477.3053 0.010 2170 +4600 -477.3047 0.010 2170 +4700 -477.3046 0.010 2170 +4800 -477.3043 0.010 2170 +4900 -477.3039 0.010 2170 +5000 -477.3038 0.010 2170 + Optimizing parameters... improved 0.072 lnL + Optimizing branchlengths... improved 0.000 lnL +5100 -477.2302 0.010 2170 +5200 -477.2293 0.010 2170 +5300 -477.2275 0.010 2170 +5400 -477.2272 0.010 2170 +5500 -477.2270 0.010 2170 +5600 -477.2270 0.010 2170 +5700 -477.2267 0.010 2170 +5800 -477.2258 0.010 2170 +5900 -477.2253 0.010 2170 +6000 -477.2253 0.010 2170 +6100 -477.2250 0.010 2170 +6200 -477.2250 0.010 2170 +6300 -477.2245 0.010 2170 +6400 -477.2244 0.010 2170 Reached termination condition! -last topological improvement at gen 373 -Improvement over last 500 gen = 0.00098 -Current score = -477.4699 +last topological improvement at gen 2170 +Improvement over last 500 gen = 0.00096 +Current score = -477.2244 Performing final optimizations... -pass 1 : -477.4699 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -477.4430 (branch= 0.0269 subset rates= 0.0000) -pass 3 : -477.4391 (branch= 0.0038 subset rates= 0.0000) -pass 4 : -477.4363 (branch= 0.0028 subset rates= 0.0000) -pass 5 : -477.4352 (branch= 0.0011 subset rates= 0.0000) -pass 6 : -477.4345 (branch= 0.0006 subset rates= 0.0000) -pass 7 : -477.4333 (branch= 0.0012 subset rates= 0.0000) -pass 8 : -477.4325 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -477.4322 (branch= 0.0003 subset rates= 0.0000) -pass 10: -477.4318 (branch= 0.0002 subset rates= 0.0001) -pass 11: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2244 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.2186 (branch= 0.0058 subset rates= 0.0000) +pass 3 : -477.2083 (branch= 0.0102 subset rates= 0.0000) +pass 4 : -477.2083 (branch= 0.0000 subset rates= 0.0000) +pass 5 : -477.2071 (branch= 0.0012 subset rates= 0.0000) +pass 6 : -477.2056 (branch= 0.0015 subset rates= 0.0000) +pass 7 : -477.2051 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -477.2048 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -477.2046 (branch= 0.0002 subset rates= 0.0000) +pass 10: -477.2045 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.2044 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4316 -Time used so far = 0 hours, 0 minutes and 8 seconds +Final score = -477.2044 +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -15800,13 +16353,13 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.74 + 0.63 1.94 2.62 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Completed Search rep 1 (of 5)<<< +>>>Completed Search rep 2 (of 5)<<< ->>>Search rep 2 (of 5)<<< +>>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -15835,58 +16388,51 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=200420059 +Starting with seed=956850881 -Initial ln Likelihood: -656.4902 +Initial ln Likelihood: -633.0120 optimizing: starting branch lengths, subset rates... -pass 1:+ 148.906 (branch= 137.62 scale= 1.92 subset rates= 9.37) -pass 2:+ 19.722 (branch= 15.83 scale= 0.00 subset rates= 3.89) -pass 3:+ 3.558 (branch= 2.11 scale= 0.00 subset rates= 1.45) -pass 4:+ 2.462 (branch= 2.03 scale= 0.00 subset rates= 0.44) -pass 5:+ 3.227 (branch= 3.23 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.746 (branch= 0.71 scale= 0.01 subset rates= 0.02) -pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8529 +pass 1:+ 138.344 (branch= 127.75 scale= 0.81 subset rates= 9.78) +pass 2:+ 11.907 (branch= 7.96 scale= 0.00 subset rates= 3.94) +pass 3:+ 3.578 (branch= 2.45 scale= 0.00 subset rates= 1.13) +pass 4:+ 1.011 (branch= 0.71 scale= 0.02 subset rates= 0.28) +pass 5:+ 0.286 (branch= 0.27 scale= 0.00 subset rates= 0.01) +pass 6:+ 0.028 (branch= 0.03 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -477.8578 gen current_lnL precision last_tree_imp -0 -477.8529 0.010 0 -100 -477.7882 0.010 74 -200 -477.7667 0.010 74 -300 -477.7488 0.010 74 -400 -477.7425 0.010 74 -500 -477.7296 0.010 74 -600 -477.7269 0.010 74 -700 -477.7207 0.010 74 -800 -477.7196 0.010 74 -900 -477.7188 0.010 74 -1000 -477.7137 0.010 74 -1100 -477.7096 0.010 74 -1200 -477.7092 0.010 74 -1300 -477.7061 0.010 74 -1400 -477.7037 0.010 74 -1500 -477.7021 0.010 74 -1600 -477.7005 0.010 74 +0 -477.8578 0.010 0 +100 -477.8234 0.010 13 +200 -477.6998 0.010 195 +300 -477.4389 0.010 251 +400 -477.4187 0.010 251 +500 -477.4041 0.010 251 +600 -477.3408 0.010 509 +700 -477.3216 0.010 509 +800 -477.3135 0.010 509 +900 -477.3070 0.010 509 +1000 -477.3044 0.010 509 +1100 -477.2932 0.010 509 +1200 -477.2889 0.010 509 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.7005 +Current score = -477.2857 Performing final optimizations... -pass 1 : -477.6829 (branch= 0.0117 subset rates= 0.0060) -pass 2 : -477.6506 (branch= 0.0234 subset rates= 0.0089) -pass 3 : -477.6390 (branch= 0.0114 subset rates= 0.0002) -pass 4 : -477.6288 (branch= 0.0102 subset rates= 0.0000) -pass 5 : -477.6246 (branch= 0.0042 subset rates= 0.0000) -pass 6 : -477.6206 (branch= 0.0036 subset rates= 0.0004) -pass 7 : -477.6189 (branch= 0.0018 subset rates= 0.0000) -pass 8 : -477.6179 (branch= 0.0010 subset rates= 0.0000) -pass 9 : -477.6174 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.6171 (branch= 0.0003 subset rates= 0.0000) -pass 11: -477.6170 (branch= 0.0002 subset rates= 0.0000) -pass 12: -477.6169 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.6168 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.6168 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.6168 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.6168 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2695 (branch= 0.0101 subset rates= 0.0061) +pass 2 : -477.2456 (branch= 0.0223 subset rates= 0.0016) +pass 3 : -477.2199 (branch= 0.0258 subset rates= 0.0000) +pass 4 : -477.2174 (branch= 0.0018 subset rates= 0.0006) +pass 5 : -477.2151 (branch= 0.0024 subset rates= 0.0000) +pass 6 : -477.2135 (branch= 0.0015 subset rates= 0.0000) +pass 7 : -477.2130 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -477.2126 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -477.2122 (branch= 0.0004 subset rates= 0.0000) +pass 10: -477.2120 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.2120 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2119 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2119 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.2119 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.6168 +Final score = -477.2119 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15915,11 +16461,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.75 + 0.64 1.91 2.62 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 2 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -15927,13 +16473,14 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -477.4316 (best) -Replicate 2 : -477.6168 (TERMINATED PREMATURELY) +Replicate 1 : -477.4317 +Replicate 2 : -477.2044 (best) +Replicate 3 : -477.2119 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -15948,10 +16495,11 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.929 0.632 1.915 2.738 -rep 2: 4.894 0.633 1.907 2.748 +rep 1: 4.931 0.631 1.918 2.738 +rep 2: 4.698 0.634 1.941 2.622 +rep 3: 4.670 0.643 1.908 2.617 -Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre +Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf @@ -16142,6 +16690,101 @@ 2200 -484.5816 0.010 661 2300 -484.5814 0.010 661 2400 -484.5805 0.010 661 +2500 -484.5795 0.010 661 +2600 -484.5795 0.010 661 +2700 -484.5788 0.010 661 +2800 -484.5788 0.010 661 +2900 -484.5786 0.010 661 +3000 -484.5785 0.010 661 +Reached termination condition! +last topological improvement at gen 661 +Improvement over last 500 gen = 0.00096 +Current score = -484.5785 +Performing final optimizations... +pass 1 : -484.5735 (branch= 0.0050 subset rates= 0.0000) +pass 2 : -484.5566 (branch= 0.0169 subset rates= 0.0000) +pass 3 : -484.5504 (branch= 0.0062 subset rates= 0.0000) +pass 4 : -484.5486 (branch= 0.0017 subset rates= 0.0000) +pass 5 : -484.5454 (branch= 0.0032 subset rates= 0.0000) +pass 6 : -484.5447 (branch= 0.0006 subset rates= 0.0001) +pass 7 : -484.5438 (branch= 0.0008 subset rates= 0.0001) +pass 8 : -484.5435 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -484.5434 (branch= 0.0001 subset rates= 0.0000) +pass 10: -484.5434 (branch= 0.0000 subset rates= 0.0000) +pass 11: -484.5433 (branch= 0.0001 subset rates= 0.0000) +pass 12: -484.5433 (branch= 0.0000 subset rates= 0.0000) +pass 13: -484.5433 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -484.5433 +Time used so far = 0 hours, 0 minutes and 3 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.66 2.00 2.95 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 7 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=1313877241 + +Initial ln Likelihood: -686.5027 +optimizing: starting branch lengths, subset rates... +pass 1:+ 166.870 (branch= 157.13 scale= 0.42 subset rates= 9.32) +pass 2:+ 14.235 (branch= 9.89 scale= 0.00 subset rates= 4.35) +pass 3:+ 8.232 (branch= 7.09 scale= 0.00 subset rates= 1.14) +pass 4:+ 0.513 (branch= 0.40 scale= 0.00 subset rates= 0.12) +pass 5:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -496.6412 +gen current_lnL precision last_tree_imp +0 -496.6412 0.010 0 +100 -495.7046 0.010 100 +200 -492.2695 0.010 104 +300 -491.3099 0.010 275 +400 -491.3011 0.010 275 +500 -488.1091 0.010 468 +600 -486.3446 0.010 593 +700 -485.6174 0.010 682 +800 -484.6671 0.010 730 +900 -484.6498 0.010 730 +1000 -484.6388 0.010 730 +1100 -484.6348 0.010 730 +1200 -484.6180 0.010 730 +1300 -484.6124 0.010 730 +1400 -484.6006 0.010 730 +1500 -484.5961 0.010 730 +1600 -484.5957 0.010 730 +1700 -484.5889 0.010 730 +1800 -484.5871 0.010 730 +1900 -484.5831 0.010 730 +2000 -484.5826 0.010 730 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16270,37 +16913,55 @@ Subset 3: Random seed for bootstrap reweighting: 585640194 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 2433, seed 593977190, best lnL -484.580 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 2048, seed 1981579071, best lnL -484.583 gen current_lnL precision last_tree_imp -2433 -484.5803 0.010 661 -2500 -484.5795 0.010 661 -2600 -484.5795 0.010 661 -2700 -484.5788 0.010 661 -2800 -484.5788 0.010 661 -2900 -484.5786 0.010 661 -3000 -484.5785 0.010 661 +2048 -484.5826 0.010 730 +2100 -484.5811 0.010 730 +2200 -484.5802 0.010 730 +2300 -484.5798 0.010 730 +2400 -484.5794 0.010 730 +2500 -484.5789 0.010 730 +2600 -484.5779 0.010 730 +2700 -484.5772 0.010 730 +2800 -484.5759 0.010 730 +2900 -484.5752 0.010 730 +3000 -484.5749 0.010 730 +3100 -484.5737 0.010 730 +3200 -484.5736 0.010 730 +3300 -484.5727 0.010 730 +3400 -484.5726 0.010 730 +3500 -484.5723 0.010 730 +3600 -484.5719 0.010 730 +3700 -484.5714 0.010 730 +3800 -484.5713 0.010 730 +3900 -484.5701 0.010 730 +4000 -484.5698 0.010 730 +4100 -484.5698 0.010 730 +4200 -484.5696 0.010 730 +4300 -484.5695 0.010 730 +4400 -484.5695 0.010 730 Reached termination condition! -last topological improvement at gen 661 -Improvement over last 500 gen = 0.00096 -Current score = -484.5785 +last topological improvement at gen 730 +Improvement over last 500 gen = 0.00058 +Current score = -484.5695 Performing final optimizations... -pass 1 : -484.5735 (branch= 0.0050 subset rates= 0.0000) -pass 2 : -484.5566 (branch= 0.0169 subset rates= 0.0000) -pass 3 : -484.5504 (branch= 0.0062 subset rates= 0.0000) -pass 4 : -484.5486 (branch= 0.0017 subset rates= 0.0000) -pass 5 : -484.5454 (branch= 0.0032 subset rates= 0.0000) -pass 6 : -484.5448 (branch= 0.0006 subset rates= 0.0000) -pass 7 : -484.5441 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -484.5438 (branch= 0.0003 subset rates= 0.0001) -pass 9 : -484.5435 (branch= 0.0002 subset rates= 0.0000) -pass 10: -484.5434 (branch= 0.0001 subset rates= 0.0000) -pass 11: -484.5434 (branch= 0.0001 subset rates= 0.0000) -pass 12: -484.5434 (branch= 0.0000 subset rates= 0.0000) -pass 13: -484.5434 (branch= 0.0000 subset rates= 0.0000) -pass 14: -484.5434 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -484.5645 (branch= 0.0051 subset rates= 0.0000) +pass 2 : -484.5518 (branch= 0.0127 subset rates= 0.0000) +pass 3 : -484.5463 (branch= 0.0052 subset rates= 0.0003) +pass 4 : -484.5447 (branch= 0.0015 subset rates= 0.0000) +pass 5 : -484.5447 (branch= 0.0000 subset rates= 0.0000) +pass 6 : -484.5439 (branch= 0.0008 subset rates= 0.0000) +pass 7 : -484.5437 (branch= 0.0003 subset rates= 0.0000) +pass 8 : -484.5433 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -484.5431 (branch= 0.0001 subset rates= 0.0000) +pass 10: -484.5430 (branch= 0.0002 subset rates= 0.0000) +pass 11: -484.5429 (branch= 0.0000 subset rates= 0.0000) +pass 12: -484.5429 (branch= 0.0000 subset rates= 0.0000) +pass 13: -484.5429 (branch= 0.0000 subset rates= 0.0000) +pass 14: -484.5429 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -484.5434 -Time used so far = 0 hours, 0 minutes and 7 seconds +Final score = -484.5429 +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16328,64 +16989,85 @@ no rate heterogeneity Subset rate multipliers: - 0.66 2.00 2.94 + 0.66 2.00 2.96 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< ->>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus -Starting with seed=1313877241 +Starting with seed=913733743 -Initial ln Likelihood: -686.5027 +Initial ln Likelihood: -630.3171 optimizing: starting branch lengths, subset rates... -pass 1:+ 166.870 (branch= 157.13 scale= 0.42 subset rates= 9.32) -pass 2:+ 14.235 (branch= 9.89 scale= 0.00 subset rates= 4.35) -pass 3:+ 8.232 (branch= 7.09 scale= 0.00 subset rates= 1.14) -pass 4:+ 0.513 (branch= 0.40 scale= 0.00 subset rates= 0.12) -pass 5:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -496.6412 +pass 1:+ 121.154 (branch= 111.55 scale= 0.31 subset rates= 9.29) +pass 2:+ 10.711 (branch= 7.08 scale= 0.07 subset rates= 3.55) +pass 3:+ 1.556 (branch= 0.57 scale= 0.00 subset rates= 0.98) +pass 4:+ 0.226 (branch= 0.11 scale= 0.00 subset rates= 0.11) +pass 5:+ 0.080 (branch= 0.06 scale= 0.02 subset rates= 0.00) +pass 6:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -496.5791 gen current_lnL precision last_tree_imp -0 -496.6412 0.010 0 -100 -495.7046 0.010 100 -200 -492.2695 0.010 104 -300 -491.3099 0.010 275 -400 -491.3011 0.010 275 -500 -488.1091 0.010 468 -600 -486.3446 0.010 593 -700 -485.6174 0.010 682 -800 -484.6671 0.010 730 -900 -484.6498 0.010 730 -1000 -484.6388 0.010 730 -1100 -484.6348 0.010 730 -1200 -484.6180 0.010 730 -1300 -484.6124 0.010 730 -1400 -484.6006 0.010 730 -1500 -484.5961 0.010 730 -1600 -484.5957 0.010 730 -1700 -484.5889 0.010 730 -1800 -484.5871 0.010 730 -1900 -484.5831 0.010 730 -2000 -484.5826 0.010 730 +0 -496.5791 0.010 0 +100 -494.6348 0.010 85 +200 -492.4115 0.010 162 +300 -488.9487 0.010 268 +400 -487.9189 0.010 383 +500 -487.4739 0.010 454 +600 -487.4323 0.010 588 +700 -486.5291 0.010 691 +800 -485.7575 0.010 706 +900 -485.6990 0.010 890 +1000 -485.6947 0.010 890 +1100 -485.6879 0.010 890 +1200 -485.6824 0.010 890 +1300 -485.6810 0.010 890 +1400 -485.6803 0.010 890 +1500 -485.6775 0.010 890 +1600 -485.6763 0.010 890 +1700 -485.6752 0.010 890 +1800 -485.6731 0.010 890 +1900 -485.6725 0.010 890 +2000 -485.6721 0.010 890 +2100 -485.6717 0.010 890 +2200 -485.6713 0.010 890 +2300 -485.6701 0.010 890 +2400 -485.6696 0.010 890 +2500 -485.6692 0.010 890 +2600 -485.6686 0.010 890 +2700 -485.6683 0.010 890 +2800 -485.6670 0.010 890 +2900 -485.6666 0.010 890 +3000 -485.6660 0.010 890 +3100 -485.6660 0.010 890 +3200 -485.6652 0.010 890 +3300 -485.6648 0.010 890 +3400 -485.6648 0.010 890 +3500 -485.6647 0.010 890 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -484.5820 +Current score = -485.6647 Performing final optimizations... -pass 1 : -484.5745 (branch= 0.0075 subset rates= 0.0000) -pass 2 : -484.5615 (branch= 0.0129 subset rates= 0.0001) -pass 3 : -484.5525 (branch= 0.0089 subset rates= 0.0000) -pass 4 : -484.5489 (branch= 0.0036 subset rates= 0.0000) -pass 5 : -484.5470 (branch= 0.0019 subset rates= 0.0000) -pass 6 : -484.5453 (branch= 0.0016 subset rates= 0.0001) -pass 7 : -484.5439 (branch= 0.0014 subset rates= 0.0000) -pass 8 : -484.5437 (branch= 0.0002 subset rates= 0.0000) -pass 9 : -484.5434 (branch= 0.0002 subset rates= 0.0000) -pass 10: -484.5434 (branch= 0.0000 subset rates= 0.0000) -pass 11: -484.5434 (branch= 0.0000 subset rates= 0.0000) -pass 12: -484.5434 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -485.6570 (branch= 0.0058 subset rates= 0.0018) +pass 2 : -485.6394 (branch= 0.0144 subset rates= 0.0032) +pass 3 : -485.6317 (branch= 0.0077 subset rates= 0.0000) +pass 4 : -485.6298 (branch= 0.0019 subset rates= 0.0000) +pass 5 : -485.6288 (branch= 0.0010 subset rates= 0.0000) +pass 6 : -485.6261 (branch= 0.0028 subset rates= 0.0000) +pass 7 : -485.6253 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -485.6241 (branch= 0.0012 subset rates= 0.0000) +pass 9 : -485.6236 (branch= 0.0005 subset rates= 0.0000) +pass 10: -485.6218 (branch= 0.0002 subset rates= 0.0015) +pass 11: -485.6216 (branch= 0.0003 subset rates= 0.0000) +pass 12: -485.6211 (branch= 0.0001 subset rates= 0.0003) +pass 13: -485.6210 (branch= 0.0001 subset rates= 0.0000) +pass 14: -485.6210 (branch= 0.0000 subset rates= 0.0000) +pass 15: -485.6209 (branch= 0.0001 subset rates= 0.0000) +pass 16: -485.6208 (branch= 0.0000 subset rates= 0.0000) +pass 17: -485.6208 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -484.5434 +Final score = -485.6208 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16414,11 +17096,11 @@ no rate heterogeneity Subset rate multipliers: - 0.66 1.99 2.95 + 0.63 2.07 3.16 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -16426,13 +17108,14 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -484.5434 (best) -Replicate 2 : -484.5434 (TERMINATED PREMATURELY) +Replicate 1 : -484.5433 +Replicate 2 : -484.5429 (best) +Replicate 3 : -485.6208 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16447,10 +17130,11 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.520 0.660 2.003 2.943 -rep 2: 3.517 0.663 1.989 2.951 +rep 1: 3.519 0.661 1.999 2.948 +rep 2: 3.520 0.660 2.001 2.958 +rep 3: 3.753 0.633 2.070 3.156 -Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#2) to bootstrap file ch.p.mkv.ssr.boot.tre ####################################################### TREEFILES PASS @@ -16612,29 +17296,154 @@ pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8625 +lnL after optimization: -474.8624 gen current_lnL precision last_tree_imp -0 -474.8625 0.010 0 +0 -474.8624 0.010 0 100 -474.7511 0.010 68 200 -474.7182 0.010 68 300 -474.6978 0.010 68 400 -474.6394 0.010 329 500 -474.1558 0.010 455 -600 -474.1354 0.010 560 -700 -474.0346 0.010 653 -800 -474.0227 0.010 653 -900 -474.0142 0.010 653 -1000 -474.0141 0.010 653 -1100 -474.0133 0.010 653 -1200 -474.0074 0.010 653 -1300 -474.0012 0.010 653 -1400 -473.9963 0.010 653 -1500 -473.9956 0.010 653 -1600 -473.9943 0.010 653 -1700 -473.9892 0.010 653 -1800 -473.9875 0.010 653 -1900 -473.9864 0.010 653 +600 -474.1352 0.010 560 +700 -474.0440 0.010 653 +800 -474.0207 0.010 653 +900 -474.0163 0.010 653 +1000 -474.0114 0.010 653 +1100 -474.0075 0.010 653 +1200 -474.0047 0.010 653 +1300 -474.0024 0.010 653 +1400 -473.9997 0.010 653 +1500 -473.9958 0.010 653 +1600 -473.9927 0.010 653 +1700 -473.9906 0.010 653 +1800 -473.9878 0.010 653 +1900 -473.9868 0.010 653 2000 -473.9850 0.010 653 +2100 -473.9839 0.010 653 +2200 -473.9829 0.010 653 +2300 -473.9815 0.010 653 +2400 -473.9808 0.010 653 +2500 -473.9808 0.010 653 +2600 -473.9795 0.010 653 +2700 -473.9785 0.010 653 +2800 -473.9777 0.010 653 +2900 -473.9774 0.010 653 +3000 -473.9767 0.010 653 +3100 -473.9766 0.010 653 +3200 -473.9765 0.010 653 +3300 -473.9764 0.010 653 +3400 -473.9763 0.010 653 +3500 -473.9761 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00053 +Current score = -473.9761 +Performing final optimizations... +pass 1 : -473.9741 (branch= 0.0001 subset rates= 0.0020) +pass 2 : -473.9555 (branch= 0.0185 subset rates= 0.0000) +pass 3 : -473.9555 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9555 (branch= 0.0000 subset rates= 0.0000) +pass 5 : -473.9537 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -473.9523 (branch= 0.0004 subset rates= 0.0009) +pass 7 : -473.9516 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -473.9511 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -473.9509 (branch= 0.0003 subset rates= 0.0000) +pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9507 +Time used so far = 0 hours, 0 minutes and 4 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.59 2.07 2.80 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=966839612 + +Initial ln Likelihood: -700.9766 +optimizing: starting branch lengths, subset rates... +pass 1:+ 200.092 (branch= 188.08 scale= 2.23 subset rates= 9.79) +pass 2:+ 16.922 (branch= 12.34 scale= 0.03 subset rates= 4.55) +pass 3:+ 7.545 (branch= 5.75 scale= 0.00 subset rates= 1.79) +pass 4:+ 1.489 (branch= 0.84 scale= 0.00 subset rates= 0.65) +pass 5:+ 0.091 (branch= 0.04 scale= 0.01 subset rates= 0.04) +pass 6:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8235 +gen current_lnL precision last_tree_imp +0 -474.8235 0.010 0 +100 -474.7995 0.010 0 +200 -474.7019 0.010 199 +300 -474.6990 0.010 199 +400 -474.6893 0.010 199 +500 -474.5617 0.010 476 +600 -474.5541 0.010 476 +700 -474.5467 0.010 476 +800 -474.5377 0.010 476 +900 -474.5302 0.010 476 +1000 -474.5273 0.010 476 +1100 -474.5253 0.010 476 +1200 -474.5238 0.010 476 +1300 -474.5142 0.010 476 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16760,147 +17569,83 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 2006, seed 789984249, best lnL -473.985 +Search rep 2 (of 5) generation 1380, seed 274794359, best lnL -474.514 gen current_lnL precision last_tree_imp -2006 -473.9850 0.010 653 -2100 -473.9828 0.010 653 -2200 -473.9822 0.010 653 -2300 -473.9814 0.010 653 -2400 -473.9805 0.010 653 -2500 -473.9799 0.010 653 -2600 -473.9793 0.010 653 -2700 -473.9788 0.010 653 -2800 -473.9777 0.010 653 -2900 -473.9774 0.010 653 -3000 -473.9773 0.010 653 -3100 -473.9769 0.010 653 -3200 -473.9766 0.010 653 -3300 -473.9764 0.010 653 -3400 -473.9760 0.010 653 -3500 -473.9759 0.010 653 -3600 -473.9759 0.010 653 -3700 -473.9757 0.010 653 -Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00096 -Current score = -473.9757 -Performing final optimizations... -pass 1 : -473.9746 (branch= 0.0001 subset rates= 0.0010) -pass 2 : -473.9563 (branch= 0.0183 subset rates= 0.0000) -pass 3 : -473.9563 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9554 (branch= 0.0009 subset rates= 0.0000) -pass 5 : -473.9550 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -473.9534 (branch= 0.0007 subset rates= 0.0009) -pass 7 : -473.9529 (branch= 0.0005 subset rates= 0.0000) -pass 8 : -473.9526 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -473.9522 (branch= 0.0004 subset rates= 0.0000) -pass 10: -473.9511 (branch= 0.0001 subset rates= 0.0010) -pass 11: -473.9511 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9510 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9510 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9509 (branch= 0.0000 subset rates= 0.0001) -Looking for minimum length branches... -Final score = -473.9509 -Time used so far = 0 hours, 0 minutes and 10 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.59 2.07 2.79 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=74284197 - -Initial ln Likelihood: -646.1143 -optimizing: starting branch lengths, subset rates... -pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) -pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) -pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) -pass 4:+ 2.491 (branch= 1.89 scale= 0.00 subset rates= 0.61) -pass 5:+ 0.683 (branch= 0.62 scale= 0.02 subset rates= 0.05) -pass 6:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8187 -gen current_lnL precision last_tree_imp -0 -474.8187 0.010 0 -100 -474.7244 0.010 55 -200 -474.7117 0.010 55 -300 -474.6999 0.010 55 -400 -474.5534 0.010 345 +1380 -474.5136 0.010 476 +1400 -474.5122 0.010 476 +1500 -474.5086 0.010 476 +1600 -474.5067 0.010 476 +1700 -474.5062 0.010 476 +1800 -474.5050 0.010 476 +1900 -474.5037 0.010 476 +2000 -474.5011 0.010 476 +2100 -474.5010 0.010 476 +2200 -474.4999 0.010 476 +2300 -474.4990 0.010 476 +2400 -474.4948 0.010 476 +2500 -474.4942 0.010 476 +2600 -474.4908 0.010 476 +2700 -474.4901 0.010 476 +2800 -474.4892 0.010 476 +2900 -474.4882 0.010 476 +3000 -474.4860 0.010 476 +3100 -474.4848 0.010 476 +3200 -474.4848 0.010 476 +3300 -474.4827 0.010 476 +3400 -474.4817 0.010 476 +3500 -474.4803 0.010 476 +3600 -474.4801 0.010 476 +3700 -474.4800 0.010 476 +3800 -474.4794 0.010 476 +3900 -474.4785 0.010 476 +4000 -474.4783 0.010 476 +4100 -474.4783 0.010 476 +4200 -474.4768 0.010 476 +4300 -474.4760 0.010 476 +4400 -474.4748 0.010 476 +4500 -474.4731 0.010 476 +4600 -474.4723 0.010 476 +4700 -474.4705 0.010 476 +4800 -474.4700 0.010 476 +4900 -474.4683 0.010 476 +5000 -474.4682 0.010 476 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +5100 -474.4680 0.010 476 +5200 -474.4680 0.010 476 +5300 -474.4676 0.010 476 +5400 -474.4666 0.010 476 +5500 -474.4662 0.010 476 +5600 -474.4650 0.010 476 +5700 -474.4646 0.010 476 +5800 -474.4640 0.010 476 +5900 -474.4640 0.010 476 +6000 -474.4638 0.010 476 +6100 -474.4629 0.010 476 +6200 -474.4628 0.010 476 +6300 -474.4616 0.010 476 +6400 -474.4616 0.010 476 +6500 -474.4611 0.010 476 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.2047 +Current score = -474.4609 Performing final optimizations... -pass 1 : -474.1519 (branch= 0.0483 subset rates= 0.0044) -pass 2 : -474.0731 (branch= 0.0740 subset rates= 0.0048) -pass 3 : -474.0509 (branch= 0.0221 subset rates= 0.0000) -pass 4 : -474.0457 (branch= 0.0053 subset rates= 0.0000) -pass 5 : -474.0392 (branch= 0.0064 subset rates= 0.0000) -pass 6 : -474.0372 (branch= 0.0020 subset rates= 0.0000) -pass 7 : -474.0362 (branch= 0.0010 subset rates= 0.0000) -pass 8 : -474.0356 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -474.0353 (branch= 0.0003 subset rates= 0.0000) -pass 10: -474.0353 (branch= 0.0001 subset rates= 0.0000) -pass 11: -474.0343 (branch= 0.0000 subset rates= 0.0010) -pass 12: -474.0342 (branch= 0.0000 subset rates= 0.0000) -pass 13: -474.0342 (branch= 0.0000 subset rates= 0.0000) -pass 14: -474.0342 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4551 (branch= 0.0058 subset rates= 0.0000) +pass 2 : -474.4458 (branch= 0.0094 subset rates= 0.0000) +pass 3 : -474.4375 (branch= 0.0083 subset rates= 0.0000) +pass 4 : -474.4350 (branch= 0.0025 subset rates= 0.0000) +pass 5 : -474.4332 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -474.4323 (branch= 0.0009 subset rates= 0.0000) +pass 7 : -474.4309 (branch= 0.0014 subset rates= 0.0000) +pass 8 : -474.4299 (branch= 0.0010 subset rates= 0.0000) +pass 9 : -474.4295 (branch= 0.0004 subset rates= 0.0000) +pass 10: -474.4294 (branch= 0.0001 subset rates= 0.0000) +pass 11: -474.4293 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4292 (branch= 0.0000 subset rates= 0.0000) +pass 13: -474.4292 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4292 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4292 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -474.0342 +Final score = -474.4292 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16929,9 +17674,9 @@ no rate heterogeneity Subset rate multipliers: - 0.60 2.04 2.79 + 0.59 2.03 2.89 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. >>>Terminated Search rep 2 (of 5)<<< @@ -16946,8 +17691,8 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -473.9509 (best) -Replicate 2 : -474.0342 (TERMINATED PREMATURELY) +Replicate 1 : -473.9507 (best) +Replicate 2 : -474.4292 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16962,8 +17707,8 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.349 0.588 2.070 2.791 -rep 2: 4.338 0.596 2.037 2.790 +rep 1: 4.350 0.588 2.066 2.804 +rep 2: 4.595 0.590 2.034 2.888 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -16981,13 +17726,13 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j10 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j18 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/garli-2.1' Making install in src make[2]: Entering directory '/build/garli-2.1/src' make[3]: Entering directory '/build/garli-2.1/src' make[3]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/garli-2.1/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/garli-2.1/debian/tmp/usr/bin' /usr/bin/install -c Garli '/build/garli-2.1/debian/tmp/usr/bin' make install-exec-hook make[4]: Entering directory '/build/garli-2.1/src' @@ -17030,23 +17775,25 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-4_i386.deb'. -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-4_all.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-4_i386.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-4_i386.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-4_i386.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-4_i386.deb'. +dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-4_i386.deb'. +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../garli_2.1-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/59425/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/59425/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/17799 and its subdirectories -I: Current time: Sat Jun 12 15:36:57 -12 2021 -I: pbuilder-time-stamp: 1623555417 +I: removing directory /srv/workspace/pbuilder/59425 and its subdirectories +I: Current time: Sun Jul 17 00:04:49 +14 2022 +I: pbuilder-time-stamp: 1657965889