Diff of the two buildlogs: -- --- b1/build.log 2020-07-10 01:44:46.383220067 +0000 +++ b2/build.log 2020-07-10 01:58:10.000121440 +0000 @@ -1,6 +1,9 @@ -I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 11 20:03:05 -12 2021 -I: pbuilder-time-stamp: 1628755385 +W: cgroups are not available on the host, not using them. +unshare: unshare failed: Cannot allocate memory +W: pbuilder: unshare CLONE_NEWNET not available +I: pbuilder: network access is available during build! +I: Current time: Fri Jul 10 15:44:50 +14 2020 +I: pbuilder-time-stamp: 1594345490 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +21,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Sep 4 01:22:38 2018 -12 +gpgv: Signature made Wed Sep 5 03:22:38 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,138 +31,171 @@ dpkg-source: info: unpacking garli_2.1-3.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/44624/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30017/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build2-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/30017/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30017/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 parallel=18' - 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]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.0.3(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 parallel=10' + 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='886187b003514e2ba2812192bafdf9b4' - 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='44624' - PS1='# ' - PS2='> ' + 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=30017 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.2UPB4U8Cl7/pbuilderrc_rBqZ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.2UPB4U8Cl7/b1 --logfile b1/build.log garli_2.1-3.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://85.184.249.68:3128' + 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.2UPB4U8Cl7/pbuilderrc_z2Zx --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.2UPB4U8Cl7/b2 --logfile b2/build.log garli_2.1-3.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://78.137.99.97:3128 I: uname -a - Linux profitbricks-build16-i386 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-9-686-pae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) i686 GNU/Linux I: ls -l /bin - total 5476 - -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown - -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp - -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash - -rwxr-xr-x 1 root root 120676 Feb 28 2019 date - -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd - -rwxr-xr-x 1 root root 100620 Feb 28 2019 df - -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir - -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 34532 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln - -rwxr-xr-x 1 root root 55400 Jul 26 2018 login - -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls - -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 42348 Jan 9 2019 more - -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount - -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm - -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 11 02:47 sh -> dash - -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty - -rwsr-xr-x 1 root root 71072 Jan 9 2019 su - -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync - -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar - -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch - -rwxr-xr-x 1 root root 34532 Feb 28 2019 true - -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount - -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/44624/tmp/hooks/D02_print_environment finished + total 5484 + -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown + -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp + -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash + -rwxr-xr-x 1 root root 120676 Mar 1 2019 date + -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd + -rwxr-xr-x 1 root root 100620 Mar 1 2019 df + -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir + -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 34532 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 30112 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln + -rwxr-xr-x 1 root root 55400 Jul 27 2018 login + -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls + -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 42348 Jan 10 2019 more + -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount + -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm + -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 10 15:47 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 9 22:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty + -rwsr-xr-x 1 root root 71072 Jan 10 2019 su + -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync + -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar + -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch + -rwxr-xr-x 1 root root 34532 Mar 1 2019 true + -rwxr-xr-x 1 root root 17768 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount + -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/30017/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -278,7 +314,7 @@ Get: 73 http://deb.debian.org/debian buster/main i386 openmpi-bin i386 3.1.3-11 [200 kB] Get: 74 http://deb.debian.org/debian buster/main i386 libopenmpi-dev i386 3.1.3-11 [963 kB] Get: 75 http://deb.debian.org/debian buster/main i386 ncl-tools i386 2.1.21+git20180827.c71b264-2 [206 kB] -Fetched 32.0 MB in 1s (25.5 MB/s) +Fetched 32.0 MB in 13s (2418 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) @@ -605,7 +641,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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 2.1-3 dpkg-buildpackage: info: source distribution unstable @@ -668,8 +704,8 @@ 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 @@ -748,7 +784,7 @@ config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build - make -j18 + make -j10 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' @@ -764,22 +800,12 @@ 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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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] outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 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 -ffile-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:337:20: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(modName, "model%d", modelNum); @@ -801,7 +827,6 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __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 -ffile-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 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] fscanf(inf, "%d %d", &num_taxa, &num_chars); @@ -874,6 +899,9 @@ 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] 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 -ffile-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 -ffile-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 -ffile-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 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] fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -909,6 +937,53 @@ 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] fread(dummy, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +garlimain.cpp: In function 'int SubGarliMain(int)': +garlimain.cpp:323:23: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] + else sprintf(temp, ".run%d", rank); + ^~~~~~~~ +garlimain.cpp:323:23: note: directive argument in the range [10, 2147483647] +In file included from /usr/include/stdio.h:873, + from /usr/include/c++/8/cstdio:42, + from /usr/include/c++/8/ext/string_conversions.h:43, + from /usr/include/c++/8/bits/basic_string.h:6400, + from /usr/include/c++/8/string:52, + from /usr/include/c++/8/bits/locale_classes.h:40, + from /usr/include/c++/8/bits/ios_base.h:41, + from /usr/include/c++/8/ios:42, + from /usr/include/c++/8/ostream:38, + from /usr/include/c++/8/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 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +garlimain.cpp:322:32: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] + if(rank < 10) sprintf(temp, ".run0%d", rank); + ^~~~~~~~~ +garlimain.cpp:322:32: note: directive argument in the range [-2147483648, 9] +In file included from /usr/include/stdio.h:873, + from /usr/include/c++/8/cstdio:42, + from /usr/include/c++/8/ext/string_conversions.h:43, + from /usr/include/c++/8/bits/basic_string.h:6400, + from /usr/include/c++/8/string:52, + from /usr/include/c++/8/bits/locale_classes.h:40, + from /usr/include/c++/8/bits/ios_base.h:41, + from /usr/include/c++/8/ios:42, + from /usr/include/c++/8/ostream:38, + from /usr/include/c++/8/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 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -940,6 +1015,25 @@ 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] 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 -ffile-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 -ffile-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 +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:19: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] + sprintf(oStr, "R(%d)", d + 1); + ^~~~~~~ +population.cpp:3066:19: note: directive argument in the range [1, 536870911] +In file included from /usr/include/stdio.h:873, + from /usr/include/c++/8/cstdio:42, + from /usr/include/c++/8/ext/string_conversions.h:43, + from /usr/include/c++/8/bits/basic_string.h:6400, + from /usr/include/c++/8/string:52, + from population.cpp:25: +/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __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 -ffile-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 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] fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1007,65 +1101,7 @@ 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] fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:19: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] - sprintf(oStr, "R(%d)", d + 1); - ^~~~~~~ -population.cpp:3066:19: note: directive argument in the range [1, 536870911] -In file included from /usr/include/stdio.h:873, - from /usr/include/c++/8/cstdio:42, - from /usr/include/c++/8/ext/string_conversions.h:43, - from /usr/include/c++/8/bits/basic_string.h:6400, - from /usr/include/c++/8/string:52, - from population.cpp:25: -/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:323:23: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] - else sprintf(temp, ".run%d", rank); - ^~~~~~~~ -garlimain.cpp:323:23: note: directive argument in the range [10, 2147483647] -In file included from /usr/include/stdio.h:873, - from /usr/include/c++/8/cstdio:42, - from /usr/include/c++/8/ext/string_conversions.h:43, - from /usr/include/c++/8/bits/basic_string.h:6400, - from /usr/include/c++/8/string:52, - from /usr/include/c++/8/bits/locale_classes.h:40, - from /usr/include/c++/8/bits/ios_base.h:41, - from /usr/include/c++/8/ios:42, - from /usr/include/c++/8/ostream:38, - from /usr/include/c++/8/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 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -garlimain.cpp:322:32: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] - if(rank < 10) sprintf(temp, ".run0%d", rank); - ^~~~~~~~~ -garlimain.cpp:322:32: note: directive argument in the range [-2147483648, 9] -In file included from /usr/include/stdio.h:873, - from /usr/include/c++/8/cstdio:42, - from /usr/include/c++/8/ext/string_conversions.h:43, - from /usr/include/c++/8/bits/basic_string.h:6400, - from /usr/include/c++/8/string:52, - from /usr/include/c++/8/bits/locale_classes.h:40, - from /usr/include/c++/8/bits/ios_base.h:41, - from /usr/include/c++/8/ios:42, - from /usr/include/c++/8/ostream:38, - from /usr/include/c++/8/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 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __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 -ffile-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 mpic++ -g -O2 -ffile-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 -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[4]: Leaving directory '/build/garli-2.1/src' Making all in tests @@ -1141,8 +1177,8 @@ 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 @@ -1219,7 +1255,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/garli-2.1' dh_auto_build - make -j18 + make -j10 make[1]: Entering directory '/build/garli-2.1' make all-recursive make[2]: Entering directory '/build/garli-2.1' @@ -1235,22 +1271,12 @@ 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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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] outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 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 -ffile-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:337:20: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(modName, "model%d", modelNum); @@ -1272,7 +1298,6 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __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 -ffile-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 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] fread((char *) this, 1, scalarSize, in); @@ -1334,6 +1359,20 @@ 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] 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 -ffile-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 +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::__cxx11::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] + 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] + fread(&ch, sizeof(char), 1, file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 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 -ffile-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 -ffile-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 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] fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -1369,17 +1408,11 @@ 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] fread(dummy, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - fscanf(inf, "%d %d", &num_taxa, &num_chars); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::__cxx11::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] - 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] - fread(&ch, sizeof(char), 1, file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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, @@ -1411,6 +1444,9 @@ 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] 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 -ffile-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 -ffile-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 -ffile-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] fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1510,7 +1546,7 @@ # 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 -j18 check VERBOSE=1 + make -j10 check VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' @@ -4181,7 +4217,7 @@ 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 0 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4478,7 +4514,7 @@ 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 13 seconds +Time used = 0 hours, 0 minutes and 23 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4630,7 +4666,7 @@ 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 9 seconds +Time used = 0 hours, 0 minutes and 16 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4834,7 +4870,7 @@ pass 75: -3350.2333 (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 = -3350.2333 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5042,7 +5078,7 @@ pass 75: -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 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5359,7 +5395,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5525,7 +5561,7 @@ pass 14: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -5779,7 +5815,7 @@ pass 35: -13306.2062 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0005) Looking for minimum length branches... Final score = -13306.2062 -Time used = 0 hours, 0 minutes and 3 seconds +Time used = 0 hours, 0 minutes and 7 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6204,7 +6240,7 @@ pass 15: -467.6802 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6802 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6628,7 +6664,7 @@ pass 18: -477.6853 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6853 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7048,7 +7084,7 @@ pass 14: -464.5475 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5475 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7622,73 +7658,73 @@ Optimizing branchlengths... improved 0.015 lnL 1500 -210.8784 0.010 1215 2000 -210.6585 0.010 1215 -2500 -210.6112 0.010 1215 +2500 -210.6111 0.010 1215 3000 -210.5162 0.010 1215 Reached termination condition! last topological improvement at gen 1215 -Improvement over last 500 gen = 0.03349 +Improvement over last 500 gen = 0.03350 Current score = -210.5119 Performing final optimizations... -pass 1 : -210.1432 (branch= 0.0000 alpha= 0.0977 pinv= 0.2250 eq freqs= 0.0000 rel rates= 0.0461) -pass 2 : -209.5364 (branch= 0.0000 alpha= 0.3284 pinv= 0.2533 eq freqs= 0.0028 rel rates= 0.0223) -pass 3 : -209.3315 (branch= 0.0350 alpha= 0.1415 pinv= 0.0149 eq freqs= 0.0067 rel rates= 0.0067) -pass 4 : -209.2605 (branch= 0.0424 alpha= 0.0193 pinv= 0.0022 eq freqs= 0.0011 rel rates= 0.0061) -pass 5 : -209.2227 (branch= 0.0234 alpha= 0.0076 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0068) -pass 6 : -209.1994 (branch= 0.0110 alpha= 0.0027 pinv= 0.0010 eq freqs= 0.0002 rel rates= 0.0084) -pass 7 : -209.1780 (branch= 0.0082 alpha= 0.0019 pinv= 0.0003 eq freqs= 0.0004 rel rates= 0.0106) -pass 8 : -209.1599 (branch= 0.0046 alpha= 0.0010 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0118) -pass 9 : -209.1459 (branch= 0.0022 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0111) -pass 10: -209.1347 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) -pass 11: -209.1250 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0089) -pass 12: -209.1163 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) -pass 13: -209.1085 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) -pass 14: -209.1014 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) -pass 15: -209.0947 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) -pass 16: -209.0885 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) -pass 17: -209.0826 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) -pass 18: -209.0771 (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: -209.0670 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) - optimization up to ... -pass 30: -208.9996 (branch= 0.0075 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0584) - optimization up to ... -pass 40: -208.8389 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1219) - optimization up to ... -pass 50: -208.6970 (branch= 0.0133 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0058 rel rates= 0.1214) +pass 1 : -210.1438 (branch= 0.0000 alpha= 0.0976 pinv= 0.2246 eq freqs= 0.0000 rel rates= 0.0459) +pass 2 : -209.5246 (branch= 0.0000 alpha= 0.3298 pinv= 0.2626 eq freqs= 0.0030 rel rates= 0.0239) +pass 3 : -209.3277 (branch= 0.0368 alpha= 0.1313 pinv= 0.0151 eq freqs= 0.0070 rel rates= 0.0068) +pass 4 : -209.2566 (branch= 0.0487 alpha= 0.0134 pinv= 0.0018 eq freqs= 0.0011 rel rates= 0.0062) +pass 5 : -209.2196 (branch= 0.0233 alpha= 0.0065 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0069) +pass 6 : -209.1966 (branch= 0.0105 alpha= 0.0028 pinv= 0.0003 eq freqs= 0.0002 rel rates= 0.0091) +pass 7 : -209.1760 (branch= 0.0067 alpha= 0.0022 pinv= 0.0001 eq freqs= 0.0005 rel rates= 0.0111) +pass 8 : -209.1584 (branch= 0.0047 alpha= 0.0007 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0116) +pass 9 : -209.1452 (branch= 0.0019 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0108) +pass 10: -209.1342 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0098) +pass 11: -209.1248 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0088) +pass 12: -209.1161 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) +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: -209.0884 (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: -209.0717 (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= 0.0048) + optimization up to ... +pass 30: -208.9993 (branch= 0.0076 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0585) + optimization up to ... +pass 40: -208.8381 (branch= 0.0298 alpha= 0.0000 pinv= 0.0016 eq freqs= 0.0076 rel rates= 0.1223) + optimization up to ... +pass 50: -208.6967 (branch= 0.0132 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1210) optimization up to ... -pass 60: -208.6228 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0721) +pass 60: -208.6228 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0719) optimization up to ... -pass 70: -208.5736 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0486) +pass 70: -208.5735 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0487) optimization up to ... -pass 80: -208.5377 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0356) +pass 80: -208.5378 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0354) optimization up to ... -pass 90: -208.5106 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0268) +pass 90: -208.5105 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0270) optimization up to ... pass 100: -208.4894 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) optimization up to ... -pass 110: -208.4726 (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= 0.0000 rel rates= 0.0167) optimization up to ... -pass 120: -208.4587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) +pass 120: -208.4586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) optimization up to ... -pass 130: -208.4472 (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= 0.0113) optimization up to ... -pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) +pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) optimization up to ... -pass 150: -208.4292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) +pass 150: -208.4291 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... -pass 160: -208.4222 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) +pass 160: -208.4221 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) optimization up to ... -pass 170: -208.4160 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0062) +pass 170: -208.4160 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) optimization up to ... -pass 180: -208.4107 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) +pass 180: -208.4106 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) optimization up to ... -pass 190: -208.4059 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 190: -208.4060 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... -pass 200: -208.4017 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0042) +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: -208.3980 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) +pass 210: -208.3980 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0038) optimization up to ... -pass 220: -208.3946 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) +pass 220: -208.3946 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... @@ -7706,11 +7742,11 @@ optimization up to ... 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) +pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3708 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... @@ -7730,35 +7766,35 @@ optimization up to ... pass 420: -208.3630 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 440: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 450: -208.3609 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 450: -208.3608 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 490: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) +pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 498: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 494: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... -Final score = -208.3583 -Time used = 0 hours, 0 minutes and 4 seconds +Final score = -208.3586 +Time used = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.874, AG = 189.609, AT = 7.010, CG = 205.866, CT = 195.874, GT = 1.000 + AC = 121.819, AG = 187.983, AT = 6.950, CG = 204.100, CT = 194.203, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 999.9000 + 999.8998 with an invariant (invariable) site category, proportion estimated 0.2780 Substitution rate categories under this model: @@ -7777,11 +7813,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3583 +Replicate 1 : -208.3586 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: 122.9 189.6 7.01 205.9 195.9 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 121.8 188 6.95 204.1 194.2 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -7905,76 +7941,76 @@ Optimization precision reduced Optimizing parameters... improved 1.752 lnL Optimizing branchlengths... improved 0.106 lnL -1000 -212.3288 0.010 825 +1000 -212.3287 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 +3000 -211.6569 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 = 0.03822 -Current score = -211.2855 +Current score = -211.2854 Performing final optimizations... -pass 1 : -208.6656 (branch= 0.0000 alpha= 0.7666 pinv= 1.7492 eq freqs= 0.0076 rel rates= 0.0965) -pass 2 : -208.5490 (branch= 0.0744 alpha= 0.0044 pinv= 0.0000 eq freqs= 0.0121 rel rates= 0.0257) -pass 3 : -208.5063 (branch= 0.0127 alpha= 0.0052 pinv= 0.0020 eq freqs= 0.0000 rel rates= 0.0228) -pass 4 : -208.4811 (branch= 0.0036 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0208) -pass 5 : -208.4604 (branch= 0.0014 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0189) -pass 6 : -208.4415 (branch= 0.0007 alpha= 0.0006 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0176) -pass 7 : -208.4255 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0154) -pass 8 : -208.4107 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0144) -pass 9 : -208.3975 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0131) -pass 10: -208.3848 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0125) -pass 11: -208.3735 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0113) -pass 12: -208.3628 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0106) -pass 13: -208.3531 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) -pass 14: -208.3441 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) -pass 15: -208.3358 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) -pass 16: -208.3282 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) -pass 17: -208.3208 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) -pass 18: -208.3140 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0068) -pass 19: -208.3077 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0062) -pass 20: -208.3017 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0060) +pass 1 : -209.0424 (branch= 0.0000 alpha= 0.7553 pinv= 1.3974 eq freqs= 0.0059 rel rates= 0.0845) +pass 2 : -208.5683 (branch= 0.0369 alpha= 0.3859 pinv= 0.0105 eq freqs= 0.0116 rel rates= 0.0292) +pass 3 : -208.5075 (branch= 0.0315 alpha= 0.0023 pinv= 0.0000 eq freqs= 0.0018 rel rates= 0.0252) +pass 4 : -208.4824 (branch= 0.0032 alpha= 0.0000 pinv= 0.0017 eq freqs= 0.0000 rel rates= 0.0202) +pass 5 : -208.4603 (branch= 0.0027 alpha= 0.0011 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0179) +pass 6 : -208.4421 (branch= 0.0005 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0004 rel rates= 0.0172) +pass 7 : -208.4250 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0163) +pass 8 : -208.4104 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0143) +pass 9 : -208.3966 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0135) +pass 10: -208.3839 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0125) +pass 11: -208.3721 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0117) +pass 12: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0106) +pass 13: -208.3518 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) +pass 14: -208.3429 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0088) +pass 15: -208.3346 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) +pass 16: -208.3269 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) +pass 17: -208.3197 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0072) +pass 18: -208.3131 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 19: -208.3066 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) +pass 20: -208.3008 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... -pass 30: -208.2574 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0442) +pass 30: -208.2567 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0439) optimization up to ... -pass 40: -208.2297 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0276) +pass 40: -208.2292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0274) optimization up to ... -pass 50: -208.2108 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0188) +pass 50: -208.2104 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0188) optimization up to ... -pass 60: -208.1970 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) +pass 60: -208.1967 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... -pass 70: -208.1865 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 70: -208.1863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... -pass 80: -208.1783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) +pass 80: -208.1782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... -pass 90: -208.1717 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 90: -208.1715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) optimization up to ... -pass 100: -208.1662 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) +pass 100: -208.1661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... -pass 110: -208.1615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) +pass 110: -208.1614 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) optimization up to ... -pass 120: -208.1576 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) +pass 120: -208.1575 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... -pass 130: -208.1542 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 130: -208.1541 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... -pass 140: -208.1512 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) +pass 140: -208.1511 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 150: -208.1485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 160: -208.1462 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 160: -208.1461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... -pass 170: -208.1441 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) +pass 170: -208.1440 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 180: -208.1422 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 180: -208.1421 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 190: -208.1404 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 200: -208.1389 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 210: -208.1375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 210: -208.1374 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 220: -208.1361 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... @@ -7998,7 +8034,7 @@ 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 ... -pass 330: -208.1266 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 330: -208.1265 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 340: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... @@ -8011,13 +8047,13 @@ pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 22.235, AG = 32.309, AT = 0.001, CG = 36.395, CT = 80.289, GT = 1.000 + AC = 22.243, AG = 32.320, AT = 0.001, CG = 36.408, CT = 80.318, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: @@ -8045,7 +8081,7 @@ 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: 22.24 32.31 0.001 36.4 80.29 1 0.221 0.344 0.216 0.218 999.900 0.338 +rep 1: 22.24 32.32 0.001 36.41 80.32 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL @@ -8181,84 +8217,84 @@ 4500 -210.6277 0.010 2883 5000 -210.5647 0.010 2883 5500 -210.5012 0.010 2883 -6000 -210.3408 0.010 2883 +6000 -210.3409 0.010 2883 Reached termination condition! last topological improvement at gen 2883 -Improvement over last 500 gen = 0.04250 +Improvement over last 500 gen = 0.04252 Current score = -210.3311 Performing final optimizations... -pass 1 : -209.7266 (branch= 0.0039 alpha= 0.2014 pinv= 0.3304 eq freqs= 0.0000 rel rates= 0.0688) -pass 2 : -209.3745 (branch= 0.0154 alpha= 0.2666 pinv= 0.0439 eq freqs= 0.0000 rel rates= 0.0261) -pass 3 : -209.2639 (branch= 0.0491 alpha= 0.0389 pinv= 0.0119 eq freqs= 0.0057 rel rates= 0.0050) -pass 4 : -209.2206 (branch= 0.0230 alpha= 0.0131 pinv= 0.0000 eq freqs= 0.0018 rel rates= 0.0053) -pass 5 : -209.1742 (branch= 0.0276 alpha= 0.0091 pinv= 0.0012 eq freqs= 0.0023 rel rates= 0.0062) -pass 6 : -209.1460 (branch= 0.0112 alpha= 0.0055 pinv= 0.0003 eq freqs= 0.0006 rel rates= 0.0107) -pass 7 : -209.1250 (branch= 0.0068 alpha= 0.0031 pinv= 0.0000 eq freqs= 0.0010 rel rates= 0.0101) -pass 8 : -209.1117 (branch= 0.0035 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0090) -pass 9 : -209.1024 (branch= 0.0010 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0078) -pass 10: -209.0945 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0070) -pass 11: -209.0878 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0063) -pass 12: -209.0818 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) -pass 13: -209.0764 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) -pass 14: -209.0712 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) -pass 15: -209.0658 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) -pass 16: -209.0603 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0050) -pass 17: -209.0543 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) -pass 18: -209.0476 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) -pass 19: -209.0402 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) -pass 20: -209.0319 (branch= 0.0015 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) +pass 1 : -209.7266 (branch= 0.0039 alpha= 0.2015 pinv= 0.3303 eq freqs= 0.0000 rel rates= 0.0688) +pass 2 : -209.3675 (branch= 0.0154 alpha= 0.2696 pinv= 0.0479 eq freqs= 0.0000 rel rates= 0.0262) +pass 3 : -209.2588 (branch= 0.0550 alpha= 0.0315 pinv= 0.0111 eq freqs= 0.0060 rel rates= 0.0050) +pass 4 : -209.2138 (branch= 0.0247 alpha= 0.0127 pinv= 0.0000 eq freqs= 0.0018 rel rates= 0.0059) +pass 5 : -209.1729 (branch= 0.0242 alpha= 0.0072 pinv= 0.0011 eq freqs= 0.0025 rel rates= 0.0059) +pass 6 : -209.1450 (branch= 0.0112 alpha= 0.0049 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0112) +pass 7 : -209.1249 (branch= 0.0070 alpha= 0.0026 pinv= 0.0001 eq freqs= 0.0009 rel rates= 0.0095) +pass 8 : -209.1114 (branch= 0.0036 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0090) +pass 9 : -209.1022 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0077) +pass 10: -209.0944 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0070) +pass 11: -209.0876 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0063) +pass 12: -209.0816 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) +pass 13: -209.0762 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) +pass 14: -209.0710 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 15: -209.0658 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) +pass 16: -209.0602 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) +pass 17: -209.0541 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) +pass 18: -209.0475 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) +pass 19: -209.0400 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) +pass 20: -209.0318 (branch= 0.0015 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) optimization up to ... -pass 30: -208.8938 (branch= 0.0276 alpha= 0.0000 pinv= 0.0011 eq freqs= 0.0057 rel rates= 0.1039) +pass 30: -208.8943 (branch= 0.0275 alpha= 0.0000 pinv= 0.0011 eq freqs= 0.0057 rel rates= 0.1032) optimization up to ... -pass 40: -208.7302 (branch= 0.0198 alpha= 0.0000 pinv= 0.0018 eq freqs= 0.0074 rel rates= 0.1345) +pass 40: -208.7303 (branch= 0.0198 alpha= 0.0000 pinv= 0.0018 eq freqs= 0.0074 rel rates= 0.1351) optimization up to ... pass 50: -208.6429 (branch= 0.0022 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0013 rel rates= 0.0835) optimization up to ... pass 60: -208.5876 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0546) optimization up to ... -pass 70: -208.5481 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0392) +pass 70: -208.5480 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0391) optimization up to ... -pass 80: -208.5186 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0293) +pass 80: -208.5186 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0292) optimization up to ... pass 90: -208.4958 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0227) optimization up to ... pass 100: -208.4776 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0181) optimization up to ... -pass 110: -208.4629 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0146) +pass 110: -208.4628 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0146) optimization up to ... -pass 120: -208.4506 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0122) +pass 120: -208.4506 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0121) optimization up to ... pass 130: -208.4404 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0101) optimization up to ... pass 140: -208.4317 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0087) optimization up to ... -pass 150: -208.4243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) +pass 150: -208.4242 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) optimization up to ... -pass 160: -208.4179 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) +pass 160: -208.4179 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) optimization up to ... -pass 170: -208.4123 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) +pass 170: -208.4123 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) optimization up to ... -pass 180: -208.4074 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) +pass 180: -208.4074 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) optimization up to ... pass 190: -208.4031 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0043) optimization up to ... pass 200: -208.3992 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... -pass 210: -208.3957 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) +pass 210: -208.3958 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... -pass 220: -208.3925 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) +pass 220: -208.3926 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... -pass 230: -208.3897 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) +pass 230: -208.3898 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... -pass 240: -208.3871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) +pass 240: -208.3872 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 250: -208.3847 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 250: -208.3848 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... -pass 260: -208.3825 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) +pass 260: -208.3826 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... -pass 270: -208.3805 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) +pass 270: -208.3806 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 280: -208.3787 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3770 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... @@ -8272,7 +8308,7 @@ optimization up to ... pass 340: -208.3700 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 350: -208.3688 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 350: -208.3689 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 360: -208.3678 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... @@ -8298,24 +8334,22 @@ optimization up to ... 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 480: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... -pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 490: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 500: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) - optimization up to ... -pass 503: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) +pass 499: -208.3582 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... -Final score = -208.3583 -Time used = 0 hours, 0 minutes and 4 seconds +Final score = -208.3582 +Time used = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.984, AG = 190.260, AT = 7.020, CG = 206.234, CT = 196.107, GT = 1.000 + AC = 123.189, AG = 190.592, AT = 7.041, CG = 206.593, CT = 196.456, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2034 0.2835 + (ACGT) 0.2225 0.2906 0.2034 0.2834 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 @@ -8342,11 +8376,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3583 +Replicate 1 : -208.3582 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: 123 190.3 7.02 206.2 196.1 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 123.2 190.6 7.041 206.6 196.5 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -8473,144 +8507,144 @@ Optimization precision reduced Optimizing parameters... improved 1.494 lnL Optimizing branchlengths... improved 0.350 lnL -1500 -210.9424 0.010 1230 +1500 -210.9425 0.010 1230 2000 -210.7769 0.010 1230 2500 -210.6534 0.010 1230 -3000 -210.6026 0.010 1230 +3000 -210.6127 0.010 1230 Reached termination condition! last topological improvement at gen 1230 -Improvement over last 500 gen = 0.04159 -Current score = -210.5932 +Improvement over last 500 gen = 0.03867 +Current score = -210.5967 Performing final optimizations... -pass 1 : -210.1854 (branch= 0.0000 alpha= 0.1339 pinv= 0.2107 eq freqs= 0.0000 rel rates= 0.0632) -pass 2 : -209.5577 (branch= 0.0093 alpha= 0.3569 pinv= 0.2378 eq freqs= 0.0050 rel rates= 0.0188) -pass 3 : -209.3366 (branch= 0.0381 alpha= 0.1426 pinv= 0.0183 eq freqs= 0.0077 rel rates= 0.0145) -pass 4 : -209.2576 (branch= 0.0465 alpha= 0.0211 pinv= 0.0031 eq freqs= 0.0034 rel rates= 0.0047) -pass 5 : -209.2070 (branch= 0.0350 alpha= 0.0093 pinv= 0.0011 eq freqs= 0.0003 rel rates= 0.0049) -pass 6 : -209.1762 (branch= 0.0179 alpha= 0.0051 pinv= 0.0002 eq freqs= 0.0004 rel rates= 0.0071) -pass 7 : -209.1503 (branch= 0.0101 alpha= 0.0035 pinv= 0.0003 eq freqs= 0.0009 rel rates= 0.0111) -pass 8 : -209.1295 (branch= 0.0070 alpha= 0.0016 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0113) -pass 9 : -209.1160 (branch= 0.0029 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0099) -pass 10: -209.1058 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0086) -pass 11: -209.0974 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0076) -pass 12: -209.0901 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0068) -pass 13: -209.0837 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) -pass 14: -209.0778 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) -pass 15: -209.0724 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) -pass 16: -209.0673 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) -pass 17: -209.0625 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 18: -209.0578 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) -pass 19: -209.0528 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 20: -209.0474 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 1 : -210.1951 (branch= 0.0000 alpha= 0.1301 pinv= 0.2107 eq freqs= 0.0000 rel rates= 0.0609) +pass 2 : -209.5752 (branch= 0.0039 alpha= 0.3416 pinv= 0.2383 eq freqs= 0.0033 rel rates= 0.0327) +pass 3 : -209.3376 (branch= 0.0533 alpha= 0.1438 pinv= 0.0210 eq freqs= 0.0088 rel rates= 0.0106) +pass 4 : -209.2576 (branch= 0.0496 alpha= 0.0230 pinv= 0.0015 eq freqs= 0.0022 rel rates= 0.0038) +pass 5 : -209.2075 (branch= 0.0344 alpha= 0.0093 pinv= 0.0012 eq freqs= 0.0004 rel rates= 0.0049) +pass 6 : -209.1727 (branch= 0.0201 alpha= 0.0062 pinv= 0.0003 eq freqs= 0.0011 rel rates= 0.0070) +pass 7 : -209.1462 (branch= 0.0108 alpha= 0.0041 pinv= 0.0002 eq freqs= 0.0006 rel rates= 0.0108) +pass 8 : -209.1248 (branch= 0.0075 alpha= 0.0017 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0112) +pass 9 : -209.1113 (branch= 0.0031 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0096) +pass 10: -209.1012 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0084) +pass 11: -209.0929 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0074) +pass 12: -209.0858 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) +pass 13: -209.0796 (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: -209.0638 (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: -209.0541 (branch= 0.0001 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: -209.0432 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) optimization up to ... -pass 30: -208.9473 (branch= 0.0174 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0033 rel rates= 0.0788) +pass 30: -208.9355 (branch= 0.0194 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0038 rel rates= 0.0838) optimization up to ... -pass 40: -208.7707 (branch= 0.0281 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0088 rel rates= 0.1377) +pass 40: -208.7593 (branch= 0.0269 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1386) optimization up to ... -pass 50: -208.6638 (branch= 0.0053 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0028 rel rates= 0.0981) +pass 50: -208.6580 (branch= 0.0043 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0024 rel rates= 0.0941) optimization up to ... -pass 60: -208.6017 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0611) +pass 60: -208.5979 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0592) optimization up to ... -pass 70: -208.5584 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0429) +pass 70: -208.5556 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0418) optimization up to ... -pass 80: -208.5264 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0317) +pass 80: -208.5243 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0311) optimization up to ... -pass 90: -208.5018 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0244) +pass 90: -208.5002 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0239) optimization up to ... -pass 100: -208.4825 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0192) +pass 100: -208.4811 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0189) optimization up to ... -pass 110: -208.4669 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0155) +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: -208.4540 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0128) +pass 120: -208.4531 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0126) optimization up to ... -pass 130: -208.4432 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) +pass 130: -208.4426 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... -pass 140: -208.4341 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) +pass 140: -208.4334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) optimization up to ... -pass 150: -208.4263 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) +pass 150: -208.4257 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) optimization up to ... -pass 160: -208.4196 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) +pass 160: -208.4191 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) optimization up to ... -pass 170: -208.4138 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) +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: -208.4088 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 180: -208.4083 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... -pass 190: -208.4043 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) +pass 190: -208.4039 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... -pass 200: -208.4003 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) +pass 200: -208.3999 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... -pass 210: -208.3967 (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: -208.3935 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) +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: -208.3906 (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: -208.3879 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) +pass 240: -208.3876 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 250: -208.3855 (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: -208.3833 (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: -208.3812 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) +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: -208.3793 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +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: -208.3775 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +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: -208.3759 (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: -208.3744 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) +pass 310: -208.3742 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... -pass 320: -208.3729 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3728 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) +pass 330: -208.3715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 340: -208.3704 (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: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 350: -208.3691 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 360: -208.3680 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 370: -208.3670 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 380: -208.3660 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +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: -208.3642 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 410: -208.3635 (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: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +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 440: -208.3613 (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 450: -208.3606 (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 460: -208.3600 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +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 470: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 480: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) +pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +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 500: -208.3583 (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 502: -208.3583 (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 = -208.3583 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.954, AG = 190.236, AT = 7.029, CG = 206.205, CT = 196.088, GT = 1.000 + AC = 122.709, AG = 189.839, AT = 7.004, CG = 205.775, CT = 195.674, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2034 0.2834 + (ACGT) 0.2225 0.2906 0.2034 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 @@ -8641,7 +8675,7 @@ 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: 123 190.2 7.029 206.2 196.1 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.7 189.8 7.004 205.8 195.7 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -11313,15 +11347,6 @@ 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 -1500 -98.6821 0.500 1029 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11418,11 +11443,16 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1520, seed 924178076, best lnL -98.664 +Bootstrap rep 1 (of 1) generation 640, seed 2080244240, best lnL -99.264 gen current_lnL precision last_tree_imp -1520 -98.6643 0.500 1029 +640 -99.2638 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... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -11434,37 +11464,41 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.8297 + 0.6652 with an invariant (invariable) site category, proportion estimated - 0.0493 + 0.0626 Substitution rate categories under this model: rate proportion - 0.0000 0.0493 - 0.1485 0.3169 - 0.6610 0.3169 - 2.1906 0.3169 + 0.0000 0.0626 + 0.1054 0.3125 + 0.5916 0.3125 + 2.3030 0.3125 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 : -98.6643 +Replicate 1 : -98.8740 Parameter estimates: alpha pinv -rep 1: 0.830 0.049 +rep 1: 0.665 0.063 Treelengths: TL -rep 1: 1.733 +rep 1: 1.521 Saving best tree to bootstrap file ch.a.G3.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf @@ -11586,14 +11620,6 @@ 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 -900 -110.5555 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11680,9 +11706,17 @@ STARTING RUN Restarting from checkpoint... - generation 944, seed 580258994, best lnL -110.538 + generation 463, seed 787518119, best lnL -111.904 gen current_lnL precision last_tree_imp -944 -110.5385 0.010 707 +463 -111.9042 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 +900 -110.5555 0.010 707 1000 -110.5065 0.010 707 NOTE: ****Specified generation limit (1000) reached... @@ -11864,23 +11898,6 @@ 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 -3000 -111.6815 0.010 563 -3100 -111.6815 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11966,9 +11983,9 @@ STARTING RUN Restarting from checkpoint... - generation 3105, seed 1703492673, best lnL -111.682 + generation 1477, seed 138374867, best lnL -111.682 gen current_lnL precision last_tree_imp -3105 -111.6815 0.010 563 +1477 -111.6819 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -11984,7 +12001,7 @@ no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... @@ -11992,14 +12009,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6815 +Replicate 1 : -111.6819 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.607 +rep 1: 2.608 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 @@ -12129,15 +12146,6 @@ 10 -207.1401 0.500 10 20 -205.6892 0.500 18 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 @@ -12224,11 +12232,19 @@ STARTING RUN Restarting from checkpoint... - generation 126, seed 66613685, best lnL -205.250 + generation 30, seed 48961654, best lnL -205.650 gen current_lnL precision last_tree_imp -126 -205.2505 0.500 121 +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 +NOTE: ****Specified generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates @@ -12253,31 +12269,38 @@ 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion - 0.0473 0.5211 + 0.0490 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 : -205.2505 +Replicate 1 : -205.3829 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.047 0.521 0.499 0.479 1.586 3.999 0.04 2.453 3.968 1 +rep 1: 0.049 0.521 0.499 0.479 1.586 3.999 0.04 2.453 3.968 1 Treelengths: TL -rep 1: 7.702 +rep 1: 7.371 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 @@ -12407,15 +12430,6 @@ 20 -199.5203 0.500 13 30 -199.4495 0.500 13 40 -197.8338 0.500 31 -50 -197.8131 0.500 31 -60 -197.7840 0.500 31 -70 -197.6626 0.500 61 -80 -197.6022 0.500 61 -90 -197.5770 0.500 61 -100 -197.5676 0.500 61 -110 -197.4217 0.500 101 -120 -197.4217 0.500 101 -130 -197.4217 0.500 101 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12503,16 +12517,23 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 134, seed 699723792, best lnL -197.422 +Bootstrap rep 1 (of 1) generation 46, seed 2067029090, best lnL -197.813 gen current_lnL precision last_tree_imp -134 -197.4217 0.500 101 +46 -197.8131 0.500 31 +50 -197.8131 0.500 31 +60 -197.7840 0.500 31 +70 -197.6626 0.500 61 +80 -197.6022 0.500 61 +90 -197.5770 0.500 61 +100 -197.5676 0.500 61 +NOTE: ****Specified generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.154177 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 2.497, AG = 4.055, AT = 0.007, CG = 2.637, CT = 2.184, GT = 1.000 + AC = 2.497, AG = 4.006, AT = 0.007, CG = 2.637, CT = 2.184, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -12536,23 +12557,27 @@ 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 : -197.4217 +Replicate 1 : -197.5676 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.154 1.000 2.497 4.055 0.00742 2.637 2.184 1 +rep 1: 0.154 1.000 2.497 4.006 0.00742 2.637 2.184 1 Treelengths: TL -rep 1: 7.461 +rep 1: 7.474 Saving best tree to bootstrap file ch.c.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -12711,24 +12736,10 @@ 900 -3353.8938 0.255 0 1000 -3353.6942 0.255 0 Optimization precision reduced - Optimizing parameters... improved 0.830 lnL + Optimizing parameters... improved 0.829 lnL Optimizing branchlengths... improved 0.084 lnL -1100 -3352.7252 0.010 0 -1200 -3352.6788 0.010 0 -1300 -3352.5571 0.010 0 -1400 -3352.3179 0.010 0 -1500 -3352.2784 0.010 0 -1600 -3352.1763 0.010 0 -1700 -3352.1640 0.010 0 -1800 -3352.0839 0.010 0 -1900 -3351.7359 0.010 0 -2000 -3351.6703 0.010 0 -2100 -3351.4847 0.010 0 -2200 -3351.3012 0.010 0 -2300 -3351.2536 0.010 0 -2400 -3351.2181 0.010 0 -2500 -3351.1260 0.010 0 -2600 -3351.0633 0.010 0 +1100 -3352.7266 0.010 0 +1200 -3352.6808 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12832,88 +12843,74 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 2677, seed 1130685511, best lnL -3351.063 +Search rep 1 (of 2) generation 1239, seed 2081090418, best lnL -3352.559 gen current_lnL precision last_tree_imp -2677 -3351.0633 0.010 0 -2700 -3351.0630 0.010 0 -2800 -3351.0576 0.010 0 -2900 -3351.0142 0.010 0 -3000 -3351.0142 0.010 0 -3100 -3351.0015 0.010 0 -3200 -3350.9822 0.010 0 -3300 -3350.9797 0.010 0 -3400 -3350.9764 0.010 0 -3500 -3350.9762 0.010 0 -3600 -3350.9756 0.010 0 -3700 -3350.9427 0.010 0 -3800 -3350.9285 0.010 0 -3900 -3350.8684 0.010 0 -4000 -3350.8684 0.010 0 -4100 -3350.8587 0.010 0 -4200 -3350.8532 0.010 0 -4300 -3350.8530 0.010 0 -4400 -3350.8489 0.010 0 -4500 -3350.8489 0.010 0 -4600 -3350.8176 0.010 0 -4700 -3350.8156 0.010 0 -4800 -3350.8156 0.010 0 -4900 -3350.8156 0.010 0 +1239 -3352.5589 0.010 0 +1300 -3352.5589 0.010 0 +1400 -3352.3202 0.010 0 +1500 -3352.2806 0.010 0 +1600 -3352.1793 0.010 0 +1700 -3352.1671 0.010 0 +1800 -3352.0841 0.010 0 +1900 -3351.7374 0.010 0 +2000 -3351.6717 0.010 0 +2100 -3351.4901 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.8156 +Current score = -3351.4298 Performing final optimizations... -pass 1 : -3350.7663 (branch= 0.0000 alpha= 0.0000 pinv= 0.0239 eq freqs= 0.0001 rel rates= 0.0252 subset rates= 0.0000) -pass 2 : -3350.7090 (branch= 0.0028 alpha= 0.0101 pinv= 0.0167 eq freqs= 0.0000 rel rates= 0.0263 subset rates= 0.0014) -pass 3 : -3350.6541 (branch= 0.0073 alpha= 0.0164 pinv= 0.0147 eq freqs= 0.0000 rel rates= 0.0166 subset rates= 0.0000) -pass 4 : -3350.6005 (branch= 0.0056 alpha= 0.0139 pinv= 0.0138 eq freqs= 0.0016 rel rates= 0.0155 subset rates= 0.0032) -pass 5 : -3350.5574 (branch= 0.0049 alpha= 0.0120 pinv= 0.0127 eq freqs= 0.0000 rel rates= 0.0123 subset rates= 0.0012) -pass 6 : -3350.5202 (branch= 0.0032 alpha= 0.0111 pinv= 0.0116 eq freqs= 0.0000 rel rates= 0.0113 subset rates= 0.0000) -pass 7 : -3350.4854 (branch= 0.0010 alpha= 0.0107 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0108 subset rates= 0.0017) -pass 8 : -3350.4557 (branch= 0.0018 alpha= 0.0096 pinv= 0.0095 eq freqs= 0.0000 rel rates= 0.0088 subset rates= 0.0000) -pass 9 : -3350.4286 (branch= 0.0002 alpha= 0.0088 pinv= 0.0085 eq freqs= 0.0000 rel rates= 0.0087 subset rates= 0.0010) -pass 10: -3350.4047 (branch= 0.0010 alpha= 0.0081 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0071 subset rates= 0.0000) -pass 11: -3350.3839 (branch= 0.0001 alpha= 0.0071 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0066 subset rates= 0.0000) -pass 12: -3350.3650 (branch= 0.0000 alpha= 0.0068 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0059 subset rates= 0.0000) -pass 13: -3350.3482 (branch= 0.0000 alpha= 0.0061 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0051 subset rates= 0.0000) -pass 14: -3350.3334 (branch= 0.0000 alpha= 0.0055 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0045 subset rates= 0.0000) -pass 15: -3350.3203 (branch= 0.0000 alpha= 0.0049 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0039 subset rates= 0.0000) -pass 16: -3350.3088 (branch= 0.0000 alpha= 0.0043 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0033 subset rates= 0.0000) -pass 17: -3350.2987 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0029 subset rates= 0.0000) -pass 18: -3350.2899 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0025 subset rates= 0.0000) -pass 19: -3350.2821 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0022 subset rates= 0.0000) -pass 20: -3350.2754 (branch= 0.0000 alpha= 0.0026 pinv= 0.0023 eq freqs= 0.0000 rel rates= 0.0018 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2422 (branch= 0.0000 alpha= 0.0127 pinv= 0.0115 eq freqs= 0.0000 rel rates= 0.0089 subset rates= 0.0000) +pass 1 : -3351.2917 (branch= 0.0075 alpha= 0.0000 pinv= 0.0109 eq freqs= 0.0163 rel rates= 0.0931 subset rates= 0.0103) +pass 2 : -3351.1452 (branch= 0.0140 alpha= 0.0090 pinv= 0.0198 eq freqs= 0.0000 rel rates= 0.1011 subset rates= 0.0026) +pass 3 : -3351.0227 (branch= 0.0141 alpha= 0.0173 pinv= 0.0177 eq freqs= 0.0023 rel rates= 0.0691 subset rates= 0.0021) +pass 4 : -3350.9234 (branch= 0.0058 alpha= 0.0142 pinv= 0.0162 eq freqs= 0.0000 rel rates= 0.0620 subset rates= 0.0011) +pass 5 : -3350.8332 (branch= 0.0071 alpha= 0.0149 pinv= 0.0149 eq freqs= 0.0013 rel rates= 0.0510 subset rates= 0.0010) +pass 6 : -3350.7583 (branch= 0.0040 alpha= 0.0134 pinv= 0.0139 eq freqs= 0.0002 rel rates= 0.0435 subset rates= 0.0000) +pass 7 : -3350.6919 (branch= 0.0007 alpha= 0.0128 pinv= 0.0126 eq freqs= 0.0002 rel rates= 0.0385 subset rates= 0.0015) +pass 8 : -3350.6339 (branch= 0.0024 alpha= 0.0117 pinv= 0.0116 eq freqs= 0.0003 rel rates= 0.0320 subset rates= 0.0000) +pass 9 : -3350.5827 (branch= 0.0006 alpha= 0.0110 pinv= 0.0105 eq freqs= 0.0000 rel rates= 0.0281 subset rates= 0.0010) +pass 10: -3350.5381 (branch= 0.0011 alpha= 0.0099 pinv= 0.0103 eq freqs= 0.0001 rel rates= 0.0231 subset rates= 0.0000) +pass 11: -3350.4990 (branch= 0.0002 alpha= 0.0091 pinv= 0.0092 eq freqs= 0.0000 rel rates= 0.0206 subset rates= 0.0000) +pass 12: -3350.4648 (branch= 0.0001 alpha= 0.0085 pinv= 0.0078 eq freqs= 0.0000 rel rates= 0.0178 subset rates= 0.0000) +pass 13: -3350.4348 (branch= 0.0000 alpha= 0.0078 pinv= 0.0070 eq freqs= 0.0000 rel rates= 0.0152 subset rates= 0.0000) +pass 14: -3350.4085 (branch= 0.0000 alpha= 0.0070 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0129 subset rates= 0.0000) +pass 15: -3350.3856 (branch= 0.0000 alpha= 0.0063 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0110 subset rates= 0.0000) +pass 16: -3350.3656 (branch= 0.0000 alpha= 0.0056 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0094 subset rates= 0.0000) +pass 17: -3350.3481 (branch= 0.0000 alpha= 0.0050 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0080 subset rates= 0.0000) +pass 18: -3350.3328 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0069 subset rates= 0.0000) +pass 19: -3350.3195 (branch= 0.0000 alpha= 0.0039 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0059 subset rates= 0.0000) +pass 20: -3350.3079 (branch= 0.0000 alpha= 0.0034 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0051 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2503 (branch= 0.0000 alpha= 0.0174 pinv= 0.0157 eq freqs= 0.0001 rel rates= 0.0244 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2349 (branch= 0.0000 alpha= 0.0027 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0021 subset rates= 0.0000) +pass 40: -3350.2371 (branch= 0.0000 alpha= 0.0039 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2334 (branch= 0.0000 alpha= 0.0005 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) +pass 50: -3350.2342 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0014 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 60: -3350.2337 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) optimization up to ... -pass 62: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 69: -3350.2335 (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 so far = 0 hours, 0 minutes and 12 seconds +Final score = -3350.2335 +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.114, AG = 10.418, AT = 2.692, CG = 0.001, CT = 21.923, GT = 1.000 + AC = 3.112, AG = 10.403, AT = 2.686, CG = 0.001, CT = 21.870, 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 - 0.5768 + 0.5786 with an invariant (invariable) site category, proportion estimated - 0.3654 + 0.3659 Substitution rate categories under this model: rate proportion - 0.0000 0.3654 - 0.0484 0.1587 - 0.2991 0.1587 - 0.8690 0.1587 - 2.7835 0.1587 + 0.0000 0.3659 + 0.0487 0.1585 + 0.3002 0.1585 + 0.8700 0.1585 + 2.7811 0.1585 Model 2 Number of states = 2 (binary data) @@ -12938,20 +12935,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2332 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2335 (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: 3.114 10.42 2.692 0.001 21.92 1 0.333 0.222 0.157 0.288 0.577 0.365 +rep 1: 3.112 10.4 2.686 0.001 21.87 1 0.333 0.222 0.157 0.288 0.579 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 ####################################################### @@ -13101,14 +13098,6 @@ 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 -3321.3650 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 @@ -13209,77 +13198,74 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 981, seed 1374777045, best lnL -3320.968 +Search rep 1 (of 2) generation 412, seed 413260545, best lnL -3323.925 gen current_lnL precision last_tree_imp -981 -3320.9684 0.255 1 -1000 -3320.9667 0.255 1 -1100 -3320.8654 0.255 1 +412 -3323.9255 0.500 1 +500 -3323.6818 0.500 1 +600 -3323.3459 0.500 1 Optimization precision reduced - Optimizing parameters... improved 0.578 lnL - Optimizing branchlengths... improved 0.059 lnL -1200 -3320.1480 0.010 1 -1300 -3320.0909 0.010 1 -1400 -3320.0771 0.010 1 -1500 -3320.0233 0.010 1 -1600 -3320.0144 0.010 1 + Optimizing parameters... improved 1.812 lnL + Optimizing branchlengths... improved 0.023 lnL +700 -3321.3650 0.255 1 +800 -3321.0294 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.0128 +Current score = -3321.0142 Performing final optimizations... -pass 1 : -3319.5647 (branch= 0.0143 alpha= 0.0000 pinv= 0.0157 eq freqs= 0.0000 rel rates= 0.3488 ins/del rates= 0.0692) -pass 2 : -3319.2664 (branch= 0.0265 alpha= 0.0171 pinv= 0.0157 eq freqs= 0.0088 rel rates= 0.2228 ins/del rates= 0.0074) -pass 3 : -3319.0356 (branch= 0.0288 alpha= 0.0141 pinv= 0.0152 eq freqs= 0.0000 rel rates= 0.1667 ins/del rates= 0.0059) -pass 4 : -3318.8546 (branch= 0.0153 alpha= 0.0108 pinv= 0.0148 eq freqs= 0.0020 rel rates= 0.1331 ins/del rates= 0.0049) -pass 5 : -3318.6962 (branch= 0.0114 alpha= 0.0118 pinv= 0.0140 eq freqs= 0.0012 rel rates= 0.1161 ins/del rates= 0.0040) -pass 6 : -3318.5682 (branch= 0.0072 alpha= 0.0112 pinv= 0.0131 eq freqs= 0.0005 rel rates= 0.0929 ins/del rates= 0.0030) -pass 7 : -3318.4590 (branch= 0.0049 alpha= 0.0104 pinv= 0.0122 eq freqs= 0.0005 rel rates= 0.0792 ins/del rates= 0.0020) -pass 8 : -3318.3654 (branch= 0.0032 alpha= 0.0103 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0673 ins/del rates= 0.0014) -pass 9 : -3318.2854 (branch= 0.0025 alpha= 0.0093 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0567 ins/del rates= 0.0010) -pass 10: -3318.2169 (branch= 0.0016 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0001 rel rates= 0.0476 ins/del rates= 0.0007) -pass 11: -3318.1584 (branch= 0.0011 alpha= 0.0085 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0397 ins/del rates= 0.0005) -pass 12: -3318.1082 (branch= 0.0007 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0334 ins/del rates= 0.0003) -pass 13: -3318.0657 (branch= 0.0004 alpha= 0.0073 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0273 ins/del rates= 0.0002) -pass 14: -3318.0291 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0230 ins/del rates= 0.0001) -pass 15: -3317.9973 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0197 ins/del rates= 0.0001) -pass 16: -3317.9696 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0168 ins/del rates= 0.0000) -pass 17: -3317.9455 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0143 ins/del rates= 0.0000) -pass 18: -3317.9246 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0122 ins/del rates= 0.0000) -pass 19: -3317.9064 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0105 ins/del rates= 0.0000) -pass 20: -3317.8906 (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: -3317.8114 (branch= 0.0001 alpha= 0.0189 pinv= 0.0173 eq freqs= 0.0001 rel rates= 0.0428 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7925 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0099 ins/del rates= 0.0000) +pass 1 : -3320.3923 (branch= 0.0389 alpha= 0.0000 pinv= 0.0127 eq freqs= 0.0124 rel rates= 0.5409 ins/del rates= 0.0170) +pass 2 : -3319.9264 (branch= 0.0583 alpha= 0.0041 pinv= 0.0163 eq freqs= 0.0044 rel rates= 0.3662 ins/del rates= 0.0167) +pass 3 : -3319.5589 (branch= 0.0456 alpha= 0.0095 pinv= 0.0157 eq freqs= 0.0066 rel rates= 0.2751 ins/del rates= 0.0150) +pass 4 : -3319.2697 (branch= 0.0314 alpha= 0.0109 pinv= 0.0152 eq freqs= 0.0018 rel rates= 0.2186 ins/del rates= 0.0113) +pass 5 : -3319.0371 (branch= 0.0189 alpha= 0.0099 pinv= 0.0147 eq freqs= 0.0009 rel rates= 0.1806 ins/del rates= 0.0076) +pass 6 : -3318.8424 (branch= 0.0144 alpha= 0.0095 pinv= 0.0139 eq freqs= 0.0007 rel rates= 0.1504 ins/del rates= 0.0058) +pass 7 : -3318.6778 (branch= 0.0092 alpha= 0.0101 pinv= 0.0130 eq freqs= 0.0005 rel rates= 0.1279 ins/del rates= 0.0039) +pass 8 : -3318.5441 (branch= 0.0060 alpha= 0.0100 pinv= 0.0122 eq freqs= 0.0003 rel rates= 0.1027 ins/del rates= 0.0026) +pass 9 : -3318.4304 (branch= 0.0040 alpha= 0.0099 pinv= 0.0113 eq freqs= 0.0003 rel rates= 0.0865 ins/del rates= 0.0017) +pass 10: -3318.3354 (branch= 0.0026 alpha= 0.0096 pinv= 0.0111 eq freqs= 0.0003 rel rates= 0.0703 ins/del rates= 0.0011) +pass 11: -3318.2572 (branch= 0.0017 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0571 ins/del rates= 0.0007) +pass 12: -3318.1916 (branch= 0.0011 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0468 ins/del rates= 0.0005) +pass 13: -3318.1357 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0390 ins/del rates= 0.0003) +pass 14: -3318.0880 (branch= 0.0005 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0325 ins/del rates= 0.0002) +pass 15: -3318.0476 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0266 ins/del rates= 0.0001) +pass 16: -3318.0130 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0224 ins/del rates= 0.0001) +pass 17: -3317.9830 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0190 ins/del rates= 0.0000) +pass 18: -3317.9569 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0162 ins/del rates= 0.0000) +pass 19: -3317.9343 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0138 ins/del rates= 0.0000) +pass 20: -3317.9146 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0118 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8171 (branch= 0.0001 alpha= 0.0216 pinv= 0.0199 eq freqs= 0.0001 rel rates= 0.0559 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7939 (branch= 0.0001 alpha= 0.0054 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0128 ins/del rates= 0.0000) optimization up to ... -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) +pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0012 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0031 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0006 ins/del rates= 0.0000) +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) optimization up to ... -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) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 72: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 74: -3317.7870 (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 = -3317.7870 -Time used so far = 0 hours, 0 minutes and 12 seconds +Time used so far = 0 hours, 0 minutes and 14 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.068, AG = 10.276, AT = 2.660, CG = 0.001, CT = 21.563, GT = 1.000 + AC = 3.067, AG = 10.266, AT = 2.657, CG = 0.001, CT = 21.547, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5745 + 0.5750 with an invariant (invariable) site category, proportion estimated - 0.3611 + 0.3613 Substitution rate categories under this model: rate proportion - 0.0000 0.3611 - 0.0479 0.1597 - 0.2978 0.1597 - 0.8677 0.1597 - 2.7866 0.1597 + 0.0000 0.3613 + 0.0480 0.1597 + 0.2981 0.1597 + 0.8680 0.1597 + 2.7858 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -13311,7 +13297,7 @@ 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: 3.068 10.28 2.66 0.001 21.56 1 0.333 0.222 0.157 0.288 0.574 0.361 +rep 1: 3.067 10.27 2.657 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -13444,39 +13430,7 @@ 1400 -211.1319 0.010 1104 1600 -211.0218 0.010 1104 1800 -210.9997 0.010 1104 -2000 -210.9459 0.010 1104 -2200 -210.8945 0.010 1104 -2400 -210.8864 0.010 1104 -2600 -210.8436 0.010 1104 -2800 -210.8251 0.010 1104 -3000 -210.8189 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 -210.6741 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 -210.5694 0.010 1104 -5400 -210.5461 0.010 1104 -5600 -210.5134 0.010 1104 -5800 -210.4817 0.010 1104 -6000 -210.4626 0.010 1104 -6200 -210.4591 0.010 1104 -6400 -210.4379 0.010 1104 -6600 -210.4142 0.010 1104 -6800 -210.3877 0.010 1104 -7000 -210.3299 0.010 1104 -7200 -210.2824 0.010 1104 -7400 -210.2491 0.010 1104 -7600 -210.2189 0.010 1104 -7800 -210.1676 0.010 1104 -8000 -210.1659 0.010 1104 -8200 -210.1029 0.010 1104 -8400 -210.0891 0.010 1104 +2000 -210.9460 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13556,76 +13510,66 @@ STARTING RUN Restarting from checkpoint... - generation 8540, seed 50858180, best lnL -210.086 + generation 2007, seed 1122703520, best lnL -210.946 gen current_lnL precision last_tree_imp -8540 -210.0863 0.010 1104 -8600 -210.0634 0.010 1104 -8700 -210.0289 0.010 1104 -8800 -210.0035 0.010 8716 -8900 -210.0028 0.010 8716 -9000 -209.9601 0.010 8716 -9100 -209.9394 0.010 8716 -9200 -209.9371 0.010 8716 -9300 -209.9252 0.010 8716 -9400 -209.9226 0.010 8716 -9500 -209.9207 0.010 8716 -9600 -209.9191 0.010 8716 -9700 -209.9036 0.010 8716 -9800 -209.8885 0.010 8716 -9900 -209.8795 0.010 8716 -10000 -209.8438 0.010 8716 - Optimizing parameters... improved 0.517 lnL - Optimizing branchlengths... improved 0.016 lnL -NOTE: ****Specified generation limit (10000) reached... +2007 -210.9460 0.010 1104 +2100 -210.9365 0.010 1104 +2200 -210.8946 0.010 1104 +2300 -210.8921 0.010 1104 +2400 -210.8864 0.010 1104 +2500 -210.8674 0.010 1104 +2600 -210.8436 0.010 1104 +2700 -210.8339 0.010 1104 +2800 -210.8250 0.010 1104 +2900 -210.8228 0.010 1104 +3000 -210.8188 0.010 1104 +3100 -210.8049 0.010 1104 +3200 -210.7905 0.010 1104 +Reached termination condition! +last topological improvement at gen 1104 +Improvement over last 500 gen = 0.04346 -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 = 5.724, AG = 9.822, AT = 0.264, CG = 10.186, CT = 15.645, GT = 1.000 + AC = 2.253, AG = 4.316, AT = 0.229, CG = 3.799, CT = 6.513, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2335 0.3288 0.2090 0.2286 + (ACGT) 0.2299 0.3376 0.2132 0.2194 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 4.4410 + 1.1008 with an invariant (invariable) site category, proportion estimated - 0.2922 + 0.1054 Substitution rate categories under this model: rate proportion - 0.0000 0.2922 - 0.5325 0.2359 - 0.9305 0.2359 - 1.5369 0.2359 + 0.0000 0.1054 + 0.2110 0.2982 + 0.7362 0.2982 + 2.0528 0.2982 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.n.G3.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 : -209.3108 +Replicate 1 : -210.7905 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: 5.724 9.822 0.2637 10.19 15.65 1 0.233 0.329 0.209 0.229 4.441 0.292 +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 Treelengths: TL -rep 1: 2.261 +rep 1: 2.237 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 -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G4.conf @@ -13748,41 +13692,13 @@ Optimization precision reduced Optimizing parameters... improved 1.296 lnL Optimizing branchlengths... improved 0.178 lnL -1400 -191.5418 0.010 1238 -1600 -191.4251 0.010 1238 -1800 -191.2916 0.010 1238 -2000 -191.1570 0.010 1979 -2200 -191.0929 0.010 1979 -2400 -190.9574 0.010 1979 -2600 -190.9303 0.010 1979 -2800 -190.8949 0.010 1979 -3000 -190.8851 0.010 1979 -3200 -190.8743 0.010 1979 -3400 -190.8594 0.010 1979 -3600 -190.8474 0.010 1979 -3800 -190.7797 0.010 1979 -4000 -190.7718 0.010 1979 -4200 -190.7235 0.010 1979 -4400 -190.7059 0.010 1979 -4600 -190.6719 0.010 1979 -4800 -190.6648 0.010 1979 -5000 -190.6613 0.010 1979 -5200 -190.6537 0.010 1979 -5400 -190.6508 0.010 1979 -5600 -190.6086 0.010 1979 -5800 -190.5583 0.010 1979 -6000 -190.5560 0.010 1979 -6200 -190.5543 0.010 1979 -6400 -190.5350 0.010 1979 -6600 -190.5160 0.010 1979 -6800 -190.5151 0.010 1979 -7000 -190.5131 0.010 1979 -7200 -190.5038 0.010 1979 -7400 -190.5007 0.010 1979 -7600 -190.4772 0.010 1979 -7800 -190.4734 0.010 1979 -8000 -190.4606 0.010 1979 -8200 -190.4509 0.010 1979 +1400 -191.5419 0.010 1238 +1600 -191.4252 0.010 1238 +1800 -191.2917 0.010 1238 +2000 -191.1572 0.010 1979 +2200 -191.0930 0.010 1979 +2400 -190.9575 0.010 1979 +2600 -190.9304 0.010 1979 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13863,55 +13779,78 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 8312, seed 882771591, best lnL -190.447 +Bootstrap rep 1 (of 1) generation 2698, seed 839693891, best lnL -190.907 gen current_lnL precision last_tree_imp -8312 -190.4466 0.010 1979 -8400 -190.4424 0.010 1979 -Reached termination condition! -last topological improvement at gen 1979 -Improvement over last 500 gen = 0.02962 +2698 -190.9069 0.010 1979 +2700 -190.9069 0.010 1979 +2800 -190.8950 0.010 1979 +2900 -190.8884 0.010 1979 +3000 -190.8852 0.010 1979 +3100 -190.8748 0.010 1979 +3200 -190.8744 0.010 1979 +3300 -190.8717 0.010 1979 +3400 -190.8595 0.010 1979 +3500 -190.8477 0.010 1979 +3600 -190.8475 0.010 1979 +3700 -190.8232 0.010 1979 +3800 -190.7798 0.010 1979 +3900 -190.7726 0.010 1979 +4000 -190.7719 0.010 1979 +4100 -190.7375 0.010 1979 +4200 -190.7218 0.010 1979 +4300 -190.7125 0.010 1979 +4400 -190.7065 0.010 1979 +4500 -190.6832 0.010 1979 +4600 -190.6707 0.010 1979 +4700 -190.6700 0.010 1979 +NOTE: ****Specified time limit (5 seconds) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.692, AG = 1.400, AT = 0.008, CG = 3.105, CT = 16.808, GT = 1.000 + AC = 0.515, AG = 1.091, AT = 0.009, CG = 2.298, CT = 10.746, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3162 0.3207 0.2602 0.1030 + (ACGT) 0.3123 0.3239 0.2587 0.1051 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 7.1508 + 6.3337 with an invariant (invariable) site category, proportion estimated - 0.1426 + 0.1316 Substitution rate categories under this model: rate proportion - 0.0000 0.1426 - 0.5726 0.2144 - 0.8422 0.2144 - 1.0786 0.2144 - 1.5066 0.2144 + 0.0000 0.1316 + 0.5495 0.2171 + 0.8302 0.2171 + 1.0805 0.2171 + 1.5397 0.2171 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were 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!*** + ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -190.4424 +Replicate 1 : -190.6700 (TERMINATED PREMATURELY) 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: 0.6925 1.4 0.008411 3.105 16.81 1 0.316 0.321 0.260 0.103 7.151 0.143 +rep 1: 0.5153 1.091 0.008553 2.298 10.75 1 0.312 0.324 0.259 0.105 6.334 0.132 Treelengths: TL -rep 1: 2.393 +rep 1: 2.268 Saving best tree to bootstrap file ch.n.G4.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf @@ -14027,85 +13966,15 @@ 2600 -213.2282 0.010 530 2800 -213.2194 0.010 530 3000 -213.2001 0.010 530 -3200 -213.1945 0.010 530 -3400 -213.1681 0.010 530 -3600 -213.1581 0.010 530 -3800 -213.0251 0.010 3769 -4000 -212.9704 0.010 3769 -4200 -212.9482 0.010 3769 -4400 -212.9233 0.010 3769 -4600 -212.8793 0.010 3769 -4800 -212.8765 0.010 3769 -5000 -212.8760 0.010 3769 -5200 -212.8556 0.010 3769 -5400 -212.8533 0.010 3769 -5600 -212.8185 0.010 3769 -5800 -212.7686 0.010 3769 -6000 -212.7263 0.010 3769 -6200 -212.7248 0.010 3769 -6400 -212.7244 0.010 3769 -6600 -212.7154 0.010 3769 -6800 -212.7057 0.010 3769 -7000 -212.7025 0.010 3769 -7200 -212.7020 0.010 3769 -7400 -212.6750 0.010 3769 -7600 -212.6701 0.010 3769 -7800 -212.6661 0.010 3769 -8000 -212.6646 0.010 3769 -8200 -212.6594 0.010 3769 -8400 -212.6591 0.010 3769 -8600 -212.6389 0.010 3769 -8800 -212.5865 0.010 3769 -9000 -212.5495 0.010 3769 -9200 -212.5340 0.010 3769 -9400 -212.5173 0.010 3769 -9600 -212.4987 0.010 3769 -9800 -212.4933 0.010 3769 -10000 -212.4847 0.010 3769 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 8.255, AG = 15.546, AT = 0.648, CG = 15.523, CT = 10.081, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2186 0.2862 0.1832 0.3120 - Rate Heterogeneity Model: - no rate heterogeneity - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be 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 : -212.4847 - -Parameter estimates: - r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 8.255 15.55 0.6481 15.52 10.08 1 0.219 0.286 0.183 0.312 - -Treelengths: - TL -rep 1: 1.718 - -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 +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +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. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -14176,17 +14045,22 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 1459438551, best lnL -212.485 + generation 3060, seed 17452919, best lnL -213.200 gen current_lnL precision last_tree_imp -10001 -212.4847 0.010 3769 +3060 -213.1996 0.010 530 +3100 -213.1996 0.010 530 +3200 -213.1945 0.010 530 +Reached termination condition! +last topological improvement at gen 530 +Improvement over last 500 gen = 0.03032 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 8.255, AG = 15.546, AT = 0.648, CG = 15.523, CT = 10.081, GT = 1.000 + AC = 2.795, AG = 5.882, AT = 0.224, CG = 5.585, CT = 3.606, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2186 0.2862 0.1832 0.3120 + (ACGT) 0.2245 0.2962 0.1812 0.2981 Rate Heterogeneity Model: no rate heterogeneity @@ -14199,15 +14073,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.4847 +Replicate 1 : -213.1945 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 8.255 15.55 0.6481 15.52 10.08 1 0.219 0.286 0.183 0.312 +rep 1: 2.795 5.882 0.2243 5.585 3.606 1 0.224 0.296 0.181 0.298 Treelengths: TL -rep 1: 1.718 +rep 1: 1.732 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 @@ -14337,108 +14211,23 @@ Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL -1600 -211.2007 0.010 1502 -1800 -211.0869 0.010 1502 +1600 -211.2008 0.010 1502 +1800 -211.0870 0.010 1502 2000 -210.9689 0.010 1502 2200 -210.8961 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 -3400 -210.7006 0.010 2883 -3600 -210.6994 0.010 2883 -3800 -210.6779 0.010 2883 -4000 -210.6776 0.010 2883 -4200 -210.6505 0.010 2883 -4400 -210.6307 0.010 2883 -4600 -210.6209 0.010 2883 -4800 -210.5769 0.010 2883 -5000 -210.5647 0.010 2883 -5200 -210.5368 0.010 2883 -5400 -210.5093 0.010 2883 -5600 -210.4832 0.010 2883 -5800 -210.3736 0.010 2883 -6000 -210.3408 0.010 2883 -6200 -210.3320 0.010 2883 -6400 -210.3259 0.010 2883 -6600 -210.2891 0.010 2883 -6800 -210.2616 0.010 2883 -7000 -210.2579 0.010 2883 -7200 -210.2571 0.010 2883 -7400 -210.2287 0.010 2883 -7600 -210.2174 0.010 2883 -7800 -210.1381 0.010 7783 -8000 -210.1299 0.010 7783 -8200 -210.1281 0.010 7783 -8400 -210.1159 0.010 7783 -8600 -210.0639 0.010 7783 -8800 -209.9971 0.010 7783 -9000 -209.9555 0.010 7783 -9200 -209.9334 0.010 7783 -9400 -209.9323 0.010 7783 -9600 -209.9203 0.010 7783 -9800 -209.8722 0.010 7783 -10000 -209.8518 0.010 9910 - Optimizing parameters... improved 0.457 lnL - Optimizing branchlengths... improved 0.003 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 2.499, AG = 4.559, AT = 0.044, CG = 4.642, CT = 9.030, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2432 0.3351 0.2122 0.2095 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 4.9167 - with an invariant (invariable) site category, proportion estimated - 0.3056 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3056 - 0.4986 0.1736 - 0.8019 0.1736 - 1.0834 0.1736 - 1.6160 0.1736 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be 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 : -209.3920 - -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: 2.499 4.559 0.04385 4.642 9.03 1 0.243 0.335 0.212 0.210 4.917 0.306 - -Treelengths: - TL -rep 1: 2.434 - -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 +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +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. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -14517,29 +14306,65 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 99464361, best lnL -209.392 + generation 3000, seed 1252193405, best lnL -210.751 gen current_lnL precision last_tree_imp -10001 -209.3920 0.010 9910 +3000 -210.7511 0.010 2883 +3100 -210.7475 0.010 2883 +3200 -210.7244 0.010 2883 +3300 -210.7026 0.010 2883 +3400 -210.7007 0.010 2883 +3500 -210.7006 0.010 2883 +3600 -210.6994 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 -210.6582 0.010 2883 +4200 -210.6506 0.010 2883 +4300 -210.6473 0.010 2883 +4400 -210.6307 0.010 2883 +4500 -210.6277 0.010 2883 +4600 -210.6209 0.010 2883 +4700 -210.5908 0.010 2883 +4800 -210.5769 0.010 2883 +4900 -210.5673 0.010 2883 +5000 -210.5647 0.010 2883 +5100 -210.5566 0.010 2883 +5200 -210.5368 0.010 2883 +5300 -210.5127 0.010 2883 +5400 -210.5093 0.010 2883 +5500 -210.5012 0.010 2883 +5600 -210.4832 0.010 2883 +5700 -210.4041 0.010 2883 +5800 -210.3736 0.010 2883 +5900 -210.3639 0.010 2883 +6000 -210.3409 0.010 2883 +6100 -210.3321 0.010 2883 +6200 -210.3320 0.010 2883 +6300 -210.3311 0.010 2883 +Reached termination condition! +last topological improvement at gen 2883 +Improvement over last 500 gen = 0.04252 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.499, AG = 4.559, AT = 0.044, CG = 4.642, CT = 9.030, GT = 1.000 + AC = 2.168, AG = 4.001, AT = 0.207, CG = 3.857, CT = 7.378, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2432 0.3351 0.2122 0.2095 + (ACGT) 0.2427 0.3358 0.2126 0.2089 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.9167 + 1.4302 with an invariant (invariable) site category, proportion estimated - 0.3056 + 0.1984 Substitution rate categories under this model: rate proportion - 0.0000 0.3056 - 0.4986 0.1736 - 0.8019 0.1736 - 1.0834 0.1736 - 1.6160 0.1736 + 0.0000 0.1984 + 0.2143 0.2004 + 0.5765 0.2004 + 1.0460 0.2004 + 2.1631 0.2004 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -14555,15 +14380,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.3920 +Replicate 1 : -210.3311 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: 2.499 4.559 0.04385 4.642 9.03 1 0.243 0.335 0.212 0.210 4.917 0.306 +rep 1: 2.168 4.001 0.2071 3.857 7.378 1 0.243 0.336 0.213 0.209 1.430 0.198 Treelengths: TL -rep 1: 2.434 +rep 1: 2.397 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 @@ -14769,24 +14594,6 @@ 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 -13181.4425 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 @@ -14909,72 +14716,74 @@ Subset 3: Random seed for bootstrap reweighting: 1903425807 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1921, seed 873215730, best lnL -13181.299 +Bootstrap rep 1 (of 1) generation 741, seed 1045877365, best lnL -13181.696 gen current_lnL precision last_tree_imp -1921 -13181.2988 0.206 1 -2000 -13181.2934 0.206 1 -NOTE: ****Specified generation limit (2000) reached... +741 -13181.6962 0.402 1 +800 -13181.6899 0.402 1 +900 -13181.6040 0.402 1 +NOTE: ****Specified time limit (1 seconds) reached... -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 2.076, AG = 3.225, AT = 1.199, CG = 1.199, CT = 2.700, GT = 1.000 + AC = 1.971, AG = 3.147, AT = 1.158, CG = 1.158, CT = 2.621, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3051 0.1870 0.2737 0.2342 + (ACGT) 0.3064 0.1908 0.2684 0.2344 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3878 + 0.3873 Substitution rate categories under this model: rate proportion - 0.0150 0.2500 - 0.1726 0.2500 - 0.7177 0.2500 - 3.0948 0.2500 + 0.0149 0.2500 + 0.1722 0.2500 + 0.7171 0.2500 + 3.0958 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 = 3.839, AG = 4.683, AT = 0.735, CG = 4.683, CT = 3.839, GT = 1.000 + AC = 3.865, AG = 4.717, AT = 0.741, CG = 4.717, CT = 3.865, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2505 0.1555 0.1902 0.4037 + (ACGT) 0.2518 0.1565 0.1900 0.4017 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.4489 + 0.4311 Substitution rate categories under this model: rate proportion - 0.0243 0.2500 - 0.2172 0.2500 - 0.7792 0.2500 - 2.9793 0.2500 + 0.0215 0.2500 + 0.2046 0.2500 + 0.7629 0.2500 + 3.0110 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 = 7.121, AT = 5.573, CG = 1.050, CT = 7.121, GT = 1.000 + AC = 1.000, AG = 7.154, AT = 5.573, CG = 1.042, CT = 7.154, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1612 0.3394 0.2965 0.2029 + (ACGT) 0.1615 0.3400 0.2956 0.2029 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.8773 + 4.5456 with an invariant (invariable) site category, proportion estimated - 0.0123 + 0.0109 Substitution rate categories under this model: rate proportion - 0.0000 0.0123 - 0.4969 0.2469 - 0.8010 0.2469 - 1.0835 0.2469 - 1.6186 0.2469 + 0.0000 0.0109 + 0.4820 0.2473 + 0.7922 0.2473 + 1.0840 0.2473 + 1.6418 0.2473 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!*** @@ -14984,25 +14793,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13181.2934 +Replicate 1 : -13181.5540 (TERMINATED PREMATURELY) 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: 2.076 3.225 1.199 1.199 2.7 1 0.305 0.187 0.274 0.234 0.388 +rep 1: 1.971 3.147 1.158 1.158 2.621 1 0.306 0.191 0.268 0.234 0.387 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: 3.839 4.683 0.7351 4.683 3.839 1 0.251 0.156 0.190 0.404 0.449 +rep 1: 3.865 4.717 0.7412 4.717 3.865 1 0.252 0.157 0.190 0.402 0.431 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 7.121 5.573 1.05 7.121 1 0.161 0.339 0.296 0.203 4.877 0.012 +rep 1: 1 7.154 5.573 1.042 7.154 1 0.161 0.340 0.296 0.203 4.546 0.011 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.667 0.526 0.278 2.196 +rep 1: 1.677 0.526 0.278 2.196 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -15193,131 +15002,6 @@ 2300 -467.7241 0.010 76 2400 -467.7235 0.010 76 2500 -467.7229 0.010 76 -2600 -467.7226 0.010 76 -2700 -467.7217 0.010 76 -2800 -467.7209 0.010 76 -2900 -467.7205 0.010 76 -3000 -467.7204 0.010 76 -3100 -467.7198 0.010 76 -3200 -467.7198 0.010 76 -3300 -467.7197 0.010 76 -3400 -467.7196 0.010 76 -Reached termination condition! -last topological improvement at gen 76 -Improvement over last 500 gen = 0.00092 -Current score = -467.7196 -Performing final optimizations... -pass 1 : -467.7172 (branch= 0.0000 subset rates= 0.0024) -pass 2 : -467.6984 (branch= 0.0188 subset rates= 0.0000) -pass 3 : -467.6918 (branch= 0.0019 subset rates= 0.0047) -pass 4 : -467.6875 (branch= 0.0043 subset rates= 0.0000) -pass 5 : -467.6832 (branch= 0.0025 subset rates= 0.0018) -pass 6 : -467.6823 (branch= 0.0009 subset rates= 0.0000) -pass 7 : -467.6816 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -467.6807 (branch= 0.0009 subset rates= 0.0000) -pass 9 : -467.6804 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6802 (branch= 0.0001 subset rates= 0.0000) -pass 11: -467.6802 (branch= 0.0000 subset rates= 0.0000) -pass 12: -467.6802 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6801 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6801 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -467.6801 -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=1713359200 - -Initial ln Likelihood: -593.3879 -optimizing: starting branch lengths, subset rates... -pass 1:+ 107.964 (branch= 101.79 scale= 1.42 subset rates= 4.75) -pass 2:+ 11.667 (branch= 10.49 scale= 0.04 subset rates= 1.14) -pass 3:+ 5.232 (branch= 5.12 scale= 0.00 subset rates= 0.11) -pass 4:+ 0.672 (branch= 0.66 scale= 0.01 subset rates= 0.00) -pass 5:+ 0.009 (branch= 0.01 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8440 -gen current_lnL precision last_tree_imp -0 -467.8440 0.010 0 -100 -467.8193 0.010 0 -200 -467.8062 0.010 0 -300 -467.7944 0.010 0 -400 -467.7821 0.010 0 -500 -467.7782 0.010 0 -600 -467.7738 0.010 0 -700 -467.7593 0.010 0 -800 -467.7569 0.010 0 -900 -467.7530 0.010 0 -1000 -467.7455 0.010 0 -1100 -467.7432 0.010 0 -1200 -467.7409 0.010 0 -1300 -467.7394 0.010 0 -1400 -467.7383 0.010 0 -1500 -467.7372 0.010 0 -1600 -467.7367 0.010 0 -1700 -467.7352 0.010 0 -1800 -467.7350 0.010 0 -1900 -467.7346 0.010 0 -2000 -467.7345 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15443,43 +15127,40 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 2066, seed 1580754273, best lnL -467.733 +Search rep 1 (of 5) generation 2556, seed 1277470040, best lnL -467.723 gen current_lnL precision last_tree_imp -2066 -467.7328 0.010 0 -2100 -467.7327 0.010 0 -2200 -467.7310 0.010 0 -2300 -467.7308 0.010 0 -2400 -467.7301 0.010 0 -2500 -467.7296 0.010 0 -2600 -467.7295 0.010 0 -2700 -467.7292 0.010 0 -2800 -467.7288 0.010 0 -2900 -467.7286 0.010 0 -3000 -467.7286 0.010 0 +2556 -467.7226 0.010 76 +2600 -467.7226 0.010 76 +2700 -467.7217 0.010 76 +2800 -467.7209 0.010 76 +2900 -467.7205 0.010 76 +3000 -467.7204 0.010 76 +3100 -467.7198 0.010 76 +3200 -467.7198 0.010 76 +3300 -467.7197 0.010 76 +3400 -467.7196 0.010 76 Reached termination condition! -last topological improvement at gen 0 -Improvement over last 500 gen = 0.00098 -Current score = -467.7286 +last topological improvement at gen 76 +Improvement over last 500 gen = 0.00092 +Current score = -467.7196 Performing final optimizations... -pass 1 : -467.7286 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.7106 (branch= 0.0163 subset rates= 0.0017) -pass 3 : -467.6992 (branch= 0.0114 subset rates= 0.0000) -pass 4 : -467.6927 (branch= 0.0065 subset rates= 0.0000) -pass 5 : -467.6890 (branch= 0.0037 subset rates= 0.0000) -pass 6 : -467.6851 (branch= 0.0039 subset rates= 0.0000) -pass 7 : -467.6835 (branch= 0.0016 subset rates= 0.0000) -pass 8 : -467.6822 (branch= 0.0013 subset rates= 0.0000) -pass 9 : -467.6811 (branch= 0.0006 subset rates= 0.0006) -pass 10: -467.6807 (branch= 0.0004 subset rates= 0.0000) -pass 11: -467.6793 (branch= 0.0003 subset rates= 0.0011) -pass 12: -467.6789 (branch= 0.0004 subset rates= 0.0000) -pass 13: -467.6788 (branch= 0.0001 subset rates= 0.0000) -pass 14: -467.6788 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6788 (branch= 0.0000 subset rates= 0.0000) -pass 16: -467.6788 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7137 (branch= 0.0000 subset rates= 0.0059) +pass 2 : -467.6933 (branch= 0.0188 subset rates= 0.0016) +pass 3 : -467.6894 (branch= 0.0040 subset rates= 0.0000) +pass 4 : -467.6860 (branch= 0.0034 subset rates= 0.0000) +pass 5 : -467.6842 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -467.6835 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -467.6825 (branch= 0.0010 subset rates= 0.0000) +pass 8 : -467.6822 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -467.6817 (branch= 0.0004 subset rates= 0.0000) +pass 10: -467.6816 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6815 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6815 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6814 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6792 (branch= 0.0000 subset rates= 0.0023) Looking for minimum length branches... -Final score = -467.6788 -Time used so far = 0 hours, 0 minutes and 7 seconds +Final score = -467.6786 +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -15511,145 +15192,9 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed 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 - 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=975681204 - -Initial ln Likelihood: -590.4310 -optimizing: starting branch lengths, subset rates... -pass 1:+ 111.273 (branch= 106.41 scale= 0.38 subset rates= 4.49) -pass 2:+ 8.172 (branch= 7.22 scale= 0.00 subset rates= 0.95) -pass 3:+ 2.417 (branch= 2.22 scale= 0.00 subset rates= 0.20) -pass 4:+ 0.650 (branch= 0.62 scale= 0.01 subset rates= 0.01) -pass 5:+ 0.055 (branch= 0.06 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8634 -gen current_lnL precision last_tree_imp -0 -467.8634 0.010 0 -100 -467.8021 0.010 75 -200 -467.7941 0.010 75 -300 -467.7861 0.010 75 -400 -467.7719 0.010 75 -500 -467.7604 0.010 75 -600 -467.7549 0.010 75 -700 -467.7496 0.010 75 -800 -467.7453 0.010 75 -900 -467.7390 0.010 75 -1000 -467.7316 0.010 75 -1100 -467.7258 0.010 75 -1200 -467.7230 0.010 75 -1300 -467.7214 0.010 75 -1400 -467.7209 0.010 75 -1500 -467.7188 0.010 75 -1600 -467.7182 0.010 75 -1700 -467.7170 0.010 75 -1800 -467.7145 0.010 75 -1900 -467.7131 0.010 75 -2000 -467.7124 0.010 75 -2100 -467.7113 0.010 75 -2200 -467.7100 0.010 75 -2300 -467.7090 0.010 75 -2400 -467.7076 0.010 75 -2500 -467.7075 0.010 75 -2600 -467.7061 0.010 75 -2700 -467.7051 0.010 75 -2800 -467.7047 0.010 75 -2900 -467.7046 0.010 75 -3000 -467.7035 0.010 75 -3100 -467.7032 0.010 75 -3200 -467.7031 0.010 75 -3300 -467.7029 0.010 75 -3400 -467.7021 0.010 75 -3500 -467.7019 0.010 75 -3600 -467.7017 0.010 75 -3700 -467.7015 0.010 75 -3800 -467.7014 0.010 75 -3900 -467.7012 0.010 75 -Reached termination condition! -last topological improvement at gen 75 -Improvement over last 500 gen = 0.00086 -Current score = -467.7012 -Performing final optimizations... -pass 1 : -467.7012 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.6886 (branch= 0.0121 subset rates= 0.0005) -pass 3 : -467.6838 (branch= 0.0032 subset rates= 0.0015) -pass 4 : -467.6807 (branch= 0.0030 subset rates= 0.0001) -pass 5 : -467.6802 (branch= 0.0003 subset rates= 0.0001) -pass 6 : -467.6799 (branch= 0.0003 subset rates= 0.0000) -pass 7 : -467.6794 (branch= 0.0005 subset rates= 0.0000) -pass 8 : -467.6786 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -467.6784 (branch= 0.0001 subset rates= 0.0000) -pass 10: -467.6783 (branch= 0.0001 subset rates= 0.0000) -pass 11: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 11 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 2.19 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 3 (of 5)<<< +>>>Completed Search rep 1 (of 5)<<< ->>>Search rep 4 (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 @@ -15678,40 +15223,57 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=1874639928 +Starting with seed=1713359200 -Initial ln Likelihood: -652.9712 +Initial ln Likelihood: -593.3879 optimizing: starting branch lengths, subset rates... -pass 1:+ 171.187 (branch= 165.01 scale= 1.78 subset rates= 4.40) -pass 2:+ 10.107 (branch= 9.13 scale= 0.07 subset rates= 0.90) -pass 3:+ 3.154 (branch= 2.92 scale= 0.04 subset rates= 0.19) -pass 4:+ 0.668 (branch= 0.67 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8557 +pass 1:+ 107.964 (branch= 101.79 scale= 1.42 subset rates= 4.75) +pass 2:+ 11.667 (branch= 10.49 scale= 0.04 subset rates= 1.14) +pass 3:+ 5.232 (branch= 5.12 scale= 0.00 subset rates= 0.11) +pass 4:+ 0.672 (branch= 0.66 scale= 0.01 subset rates= 0.00) +pass 5:+ 0.009 (branch= 0.01 scale= 0.00 subset rates= 0.00) +lnL after optimization: -467.8440 gen current_lnL precision last_tree_imp -0 -467.8557 0.010 0 -100 -467.8288 0.010 0 -200 -467.8053 0.010 168 -300 -467.7929 0.010 168 +0 -467.8440 0.010 0 +100 -467.8193 0.010 0 +200 -467.8062 0.010 0 +300 -467.7944 0.010 0 +400 -467.7821 0.010 0 +500 -467.7782 0.010 0 +600 -467.7738 0.010 0 +700 -467.7593 0.010 0 +800 -467.7569 0.010 0 +900 -467.7530 0.010 0 +1000 -467.7455 0.010 0 +1100 -467.7432 0.010 0 +1200 -467.7409 0.010 0 +1300 -467.7394 0.010 0 +1400 -467.7383 0.010 0 +1500 -467.7372 0.010 0 +1600 -467.7367 0.010 0 +1700 -467.7352 0.010 0 +1800 -467.7350 0.010 0 +1900 -467.7346 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7807 +Current score = -467.7345 Performing final optimizations... -pass 1 : -467.7738 (branch= 0.0069 subset rates= 0.0000) -pass 2 : -467.7215 (branch= 0.0508 subset rates= 0.0016) -pass 3 : -467.7039 (branch= 0.0175 subset rates= 0.0000) -pass 4 : -467.6873 (branch= 0.0166 subset rates= 0.0000) -pass 5 : -467.6830 (branch= 0.0043 subset rates= 0.0000) -pass 6 : -467.6808 (branch= 0.0022 subset rates= 0.0000) -pass 7 : -467.6797 (branch= 0.0011 subset rates= 0.0000) -pass 8 : -467.6793 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -467.6791 (branch= 0.0002 subset rates= 0.0000) -pass 10: -467.6790 (branch= 0.0001 subset rates= 0.0000) -pass 11: -467.6790 (branch= 0.0001 subset rates= 0.0000) +pass 1 : -467.7317 (branch= 0.0000 subset rates= 0.0028) +pass 2 : -467.7118 (branch= 0.0199 subset rates= 0.0000) +pass 3 : -467.7017 (branch= 0.0101 subset rates= 0.0000) +pass 4 : -467.6903 (branch= 0.0113 subset rates= 0.0000) +pass 5 : -467.6870 (branch= 0.0033 subset rates= 0.0000) +pass 6 : -467.6838 (branch= 0.0032 subset rates= 0.0000) +pass 7 : -467.6812 (branch= 0.0020 subset rates= 0.0006) +pass 8 : -467.6799 (branch= 0.0013 subset rates= 0.0000) +pass 9 : -467.6792 (branch= 0.0007 subset rates= 0.0000) +pass 10: -467.6791 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6789 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6789 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6789 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6788 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6788 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6789 +Final score = -467.6788 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15740,11 +15302,11 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.49 2.17 + 0.78 1.49 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 4 (of 5)<<< +>>>Terminated Search rep 2 (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!*** @@ -15752,15 +15314,13 @@ ####################################################### -Completed 4 replicate search(es) (of 5). +Completed 2 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 : -467.6801 -Replicate 2 : -467.6788 (same topology as 1) -Replicate 3 : -467.6782 (best) (same topology as 1) -Replicate 4 : -467.6789 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -467.6786 (best) +Replicate 2 : -467.6788 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -15775,12 +15335,10 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.840 0.788 1.485 2.144 -rep 2: 3.840 0.788 1.476 2.166 -rep 3: 3.842 0.787 1.475 2.187 -rep 4: 3.842 0.786 1.485 2.165 +rep 1: 3.839 0.788 1.476 2.174 +rep 2: 3.846 0.784 1.487 2.184 -Saving final tree from best search rep (#3) to ch.p.mk.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf @@ -15964,134 +15522,6 @@ 1900 -477.2551 0.010 555 2000 -477.2538 0.010 555 2100 -477.2531 0.010 555 -2200 -477.2523 0.010 555 -2300 -477.2517 0.010 555 -2400 -477.2508 0.010 555 -2500 -477.2503 0.010 555 -2600 -477.2501 0.010 555 -2700 -477.2499 0.010 555 -2800 -477.2497 0.010 555 -2900 -477.2496 0.010 555 -3000 -477.2495 0.010 555 -Reached termination condition! -last topological improvement at gen 555 -Improvement over last 500 gen = 0.00075 -Current score = -477.2495 -Performing final optimizations... -pass 1 : -477.2439 (branch= 0.0000 subset rates= 0.0056) -pass 2 : -477.2217 (branch= 0.0222 subset rates= 0.0000) -pass 3 : -477.2193 (branch= 0.0024 subset rates= 0.0000) -pass 4 : -477.2171 (branch= 0.0022 subset rates= 0.0000) -pass 5 : -477.2163 (branch= 0.0008 subset rates= 0.0000) -pass 6 : -477.2149 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -477.2143 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -477.2140 (branch= 0.0002 subset rates= 0.0000) -pass 9 : -477.2139 (branch= 0.0001 subset rates= 0.0000) -pass 10: -477.2138 (branch= 0.0000 subset rates= 0.0000) -pass 11: -477.2138 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2138 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2138 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.2137 -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: - 0.64 1.90 2.66 -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 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=1868627139 - -Initial ln Likelihood: -672.1746 -optimizing: starting branch lengths, subset rates... -pass 1:+ 166.816 (branch= 153.64 scale= 2.81 subset rates= 10.36) -pass 2:+ 20.204 (branch= 16.12 scale= 0.00 subset rates= 4.08) -pass 3:+ 5.370 (branch= 4.00 scale= 0.00 subset rates= 1.37) -pass 4:+ 1.615 (branch= 1.32 scale= 0.00 subset rates= 0.29) -pass 5:+ 0.256 (branch= 0.24 scale= 0.00 subset rates= 0.02) -pass 6:+ 0.059 (branch= 0.04 scale= 0.01 subset rates= 0.00) -pass 7:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8421 -gen current_lnL precision last_tree_imp -0 -477.8421 0.010 0 -100 -477.8029 0.010 0 -200 -477.5627 0.010 179 -300 -477.5493 0.010 179 -400 -477.5271 0.010 179 -500 -477.5135 0.010 179 -600 -477.5063 0.010 179 -700 -477.4980 0.010 179 -800 -477.4957 0.010 179 -900 -477.4945 0.010 179 -1000 -477.4934 0.010 179 -1100 -477.4898 0.010 179 -1200 -477.4865 0.010 179 -1300 -477.4826 0.010 179 -1400 -477.4823 0.010 179 -1500 -477.4812 0.010 179 -1600 -477.4806 0.010 179 -1700 -477.4796 0.010 179 -1800 -477.4785 0.010 179 -1900 -477.4781 0.010 179 -2000 -477.4779 0.010 179 -2100 -477.4767 0.010 179 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16217,53 +15647,38 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 2155, seed 945481183, best lnL -477.477 +Search rep 1 (of 5) generation 2135, seed 209444461, best lnL -477.252 gen current_lnL precision last_tree_imp -2155 -477.4767 0.010 179 -2200 -477.4767 0.010 179 -2300 -477.4763 0.010 179 -2400 -477.4755 0.010 179 -2500 -477.4750 0.010 179 -2600 -477.4744 0.010 179 -2700 -477.4742 0.010 179 -2800 -477.4733 0.010 179 -2900 -477.4729 0.010 179 -3000 -477.4728 0.010 179 -3100 -477.4726 0.010 179 -3200 -477.4720 0.010 179 -3300 -477.4710 0.010 179 -3400 -477.4709 0.010 179 -3500 -477.4705 0.010 179 -3600 -477.4700 0.010 179 -3700 -477.4695 0.010 179 -3800 -477.4692 0.010 179 -3900 -477.4692 0.010 179 -4000 -477.4692 0.010 179 -4100 -477.4691 0.010 179 +2135 -477.2523 0.010 555 +2200 -477.2523 0.010 555 +2300 -477.2517 0.010 555 +2400 -477.2508 0.010 555 +2500 -477.2503 0.010 555 +2600 -477.2501 0.010 555 +2700 -477.2499 0.010 555 +2800 -477.2497 0.010 555 +2900 -477.2496 0.010 555 +3000 -477.2495 0.010 555 Reached termination condition! -last topological improvement at gen 179 -Improvement over last 500 gen = 0.00091 -Current score = -477.4691 +last topological improvement at gen 555 +Improvement over last 500 gen = 0.00075 +Current score = -477.2495 Performing final optimizations... -pass 1 : -477.4621 (branch= 0.0069 subset rates= 0.0000) -pass 2 : -477.4564 (branch= 0.0054 subset rates= 0.0004) -pass 3 : -477.4419 (branch= 0.0145 subset rates= 0.0000) -pass 4 : -477.4379 (branch= 0.0040 subset rates= 0.0000) -pass 5 : -477.4355 (branch= 0.0024 subset rates= 0.0000) -pass 6 : -477.4346 (branch= 0.0009 subset rates= 0.0000) -pass 7 : -477.4335 (branch= 0.0011 subset rates= 0.0000) -pass 8 : -477.4333 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -477.4331 (branch= 0.0001 subset rates= 0.0000) -pass 10: -477.4330 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.4329 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4323 (branch= 0.0000 subset rates= 0.0005) -pass 13: -477.4321 (branch= 0.0002 subset rates= 0.0000) -pass 14: -477.4320 (branch= 0.0001 subset rates= 0.0000) -pass 15: -477.4319 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4319 (branch= 0.0000 subset rates= 0.0000) -pass 17: -477.4319 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2439 (branch= 0.0000 subset rates= 0.0056) +pass 2 : -477.2217 (branch= 0.0222 subset rates= 0.0000) +pass 3 : -477.2193 (branch= 0.0024 subset rates= 0.0000) +pass 4 : -477.2171 (branch= 0.0022 subset rates= 0.0000) +pass 5 : -477.2163 (branch= 0.0008 subset rates= 0.0000) +pass 6 : -477.2149 (branch= 0.0014 subset rates= 0.0000) +pass 7 : -477.2143 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -477.2140 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -477.2139 (branch= 0.0001 subset rates= 0.0000) +pass 10: -477.2138 (branch= 0.0000 subset rates= 0.0000) +pass 11: -477.2138 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2138 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2138 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4319 +Final score = -477.2137 Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL @@ -16292,143 +15707,13 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.92 2.72 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. - ->>>Completed 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 - 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=1218838684 - -Initial ln Likelihood: -680.2864 -optimizing: starting branch lengths, subset rates... -pass 1:+ 180.486 (branch= 168.28 scale= 2.46 subset rates= 9.75) -pass 2:+ 16.075 (branch= 12.31 scale= 0.00 subset rates= 3.76) -pass 3:+ 3.306 (branch= 2.03 scale= 0.00 subset rates= 1.28) -pass 4:+ 1.417 (branch= 1.16 scale= 0.00 subset rates= 0.25) -pass 5:+ 0.900 (branch= 0.86 scale= 0.02 subset rates= 0.03) -pass 6:+ 0.203 (branch= 0.20 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.043 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8562 -gen current_lnL precision last_tree_imp -0 -477.8562 0.010 0 -100 -477.4130 0.010 64 -200 -477.3245 0.010 114 -300 -477.3153 0.010 114 -400 -477.3002 0.010 114 -500 -477.2952 0.010 114 -600 -477.2896 0.010 114 -700 -477.2767 0.010 114 -800 -477.2754 0.010 114 -900 -477.2729 0.010 114 -1000 -477.2722 0.010 114 -1100 -477.2694 0.010 114 -1200 -477.2674 0.010 114 -1300 -477.2662 0.010 114 -1400 -477.2651 0.010 114 -1500 -477.2636 0.010 114 -1600 -477.2624 0.010 114 -1700 -477.2622 0.010 114 -1800 -477.2619 0.010 114 -1900 -477.2617 0.010 114 -2000 -477.2611 0.010 114 -2100 -477.2609 0.010 114 -2200 -477.2606 0.010 114 -2300 -477.2604 0.010 114 -2400 -477.2603 0.010 114 -2500 -477.2599 0.010 114 -2600 -477.2594 0.010 114 -2700 -477.2591 0.010 114 -2800 -477.2588 0.010 114 -2900 -477.2583 0.010 114 -3000 -477.2583 0.010 114 -3100 -477.2582 0.010 114 -3200 -477.2582 0.010 114 -Reached termination condition! -last topological improvement at gen 114 -Improvement over last 500 gen = 0.00096 -Current score = -477.2582 -Performing final optimizations... -pass 1 : -477.2455 (branch= 0.0002 subset rates= 0.0125) -pass 2 : -477.2271 (branch= 0.0098 subset rates= 0.0086) -pass 3 : -477.2165 (branch= 0.0096 subset rates= 0.0010) -pass 4 : -477.2165 (branch= 0.0000 subset rates= 0.0000) -pass 5 : -477.2151 (branch= 0.0014 subset rates= 0.0000) -pass 6 : -477.2141 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -477.2135 (branch= 0.0005 subset rates= 0.0000) -pass 8 : -477.2132 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -477.2130 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2122 (branch= 0.0001 subset rates= 0.0007) -pass 11: -477.2121 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.2121 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.2121 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.2121 -Time used so far = 0 hours, 0 minutes and 12 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: - 0.64 1.90 2.62 + 0.64 1.90 2.66 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 3 (of 5)<<< +>>>Completed Search rep 1 (of 5)<<< ->>>Search rep 4 (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 @@ -16457,43 +15742,62 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=1494796128 +Starting with seed=1868627139 -Initial ln Likelihood: -655.0726 +Initial ln Likelihood: -672.1746 optimizing: starting branch lengths, subset rates... -pass 1:+ 161.491 (branch= 151.48 scale= 0.39 subset rates= 9.63) -pass 2:+ 10.553 (branch= 6.85 scale= 0.02 subset rates= 3.69) -pass 3:+ 2.614 (branch= 1.41 scale= 0.00 subset rates= 1.20) -pass 4:+ 1.527 (branch= 1.24 scale= 0.00 subset rates= 0.28) -pass 5:+ 0.812 (branch= 0.80 scale= 0.00 subset rates= 0.01) -pass 6:+ 0.174 (branch= 0.16 scale= 0.02 subset rates= 0.00) -pass 7:+ 0.053 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass 1:+ 166.816 (branch= 153.64 scale= 2.81 subset rates= 10.36) +pass 2:+ 20.204 (branch= 16.12 scale= 0.00 subset rates= 4.08) +pass 3:+ 5.370 (branch= 4.00 scale= 0.00 subset rates= 1.37) +pass 4:+ 1.615 (branch= 1.32 scale= 0.00 subset rates= 0.29) +pass 5:+ 0.256 (branch= 0.24 scale= 0.00 subset rates= 0.02) +pass 6:+ 0.059 (branch= 0.04 scale= 0.01 subset rates= 0.00) +pass 7:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8502 +lnL after optimization: -477.8421 gen current_lnL precision last_tree_imp -0 -477.8502 0.010 0 +0 -477.8421 0.010 0 +100 -477.8029 0.010 0 +200 -477.5627 0.010 179 +300 -477.5493 0.010 179 +400 -477.5271 0.010 179 +500 -477.5135 0.010 179 +600 -477.5063 0.010 179 +700 -477.4980 0.010 179 +800 -477.4957 0.010 179 +900 -477.4945 0.010 179 +1000 -477.4934 0.010 179 +1100 -477.4898 0.010 179 +1200 -477.4865 0.010 179 +1300 -477.4826 0.010 179 +1400 -477.4823 0.010 179 +1500 -477.4812 0.010 179 +1600 -477.4806 0.010 179 +1700 -477.4796 0.010 179 +1800 -477.4785 0.010 179 +1900 -477.4781 0.010 179 +2000 -477.4779 0.010 179 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.8502 +Current score = -477.4773 Performing final optimizations... -pass 1 : -477.8238 (branch= 0.0248 subset rates= 0.0015) -pass 2 : -477.7372 (branch= 0.0854 subset rates= 0.0013) -pass 3 : -477.7145 (branch= 0.0227 subset rates= 0.0000) -pass 4 : -477.7000 (branch= 0.0144 subset rates= 0.0000) -pass 5 : -477.6937 (branch= 0.0054 subset rates= 0.0010) -pass 6 : -477.6897 (branch= 0.0040 subset rates= 0.0000) -pass 7 : -477.6878 (branch= 0.0019 subset rates= 0.0000) -pass 8 : -477.6866 (branch= 0.0012 subset rates= 0.0000) -pass 9 : -477.6857 (branch= 0.0009 subset rates= 0.0000) -pass 10: -477.6853 (branch= 0.0004 subset rates= 0.0000) -pass 11: -477.6851 (branch= 0.0002 subset rates= 0.0000) -pass 12: -477.6850 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.6849 (branch= 0.0001 subset rates= 0.0000) -pass 14: -477.6848 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.6848 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.6848 (branch= 0.0000 subset rates= 0.0000) -pass 17: -477.6848 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.4694 (branch= 0.0074 subset rates= 0.0005) +pass 2 : -477.4505 (branch= 0.0190 subset rates= 0.0000) +pass 3 : -477.4431 (branch= 0.0074 subset rates= 0.0000) +pass 4 : -477.4405 (branch= 0.0025 subset rates= 0.0000) +pass 5 : -477.4375 (branch= 0.0031 subset rates= 0.0000) +pass 6 : -477.4347 (branch= 0.0028 subset rates= 0.0000) +pass 7 : -477.4339 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -477.4335 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -477.4332 (branch= 0.0003 subset rates= 0.0000) +pass 10: -477.4330 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.4326 (branch= 0.0001 subset rates= 0.0004) +pass 12: -477.4322 (branch= 0.0004 subset rates= 0.0000) +pass 13: -477.4320 (branch= 0.0001 subset rates= 0.0000) +pass 14: -477.4320 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4320 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.4320 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.6848 +Final score = -477.4320 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16522,11 +15826,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.89 2.81 + 0.63 1.92 2.73 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. + 7 branches were collapsed. ->>>Terminated Search rep 4 (of 5)<<< +>>>Terminated Search rep 2 (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!*** @@ -16534,15 +15838,13 @@ ####################################################### -Completed 4 replicate search(es) (of 5). +Completed 2 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 : -477.2137 -Replicate 2 : -477.4319 -Replicate 3 : -477.2121 (best) (same topology as 1) -Replicate 4 : -477.6848 (TERMINATED PREMATURELY) +Replicate 1 : -477.2137 (best) +Replicate 2 : -477.4320 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16558,11 +15860,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.677 0.641 1.902 2.660 -rep 2: 4.927 0.632 1.920 2.722 -rep 3: 4.669 0.644 1.904 2.619 -rep 4: 4.912 0.631 1.895 2.809 +rep 2: 4.930 0.631 1.922 2.729 -Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf @@ -16758,102 +16058,6 @@ 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 : -484.5448 (branch= 0.0006 subset rates= 0.0000) -pass 7 : -484.5440 (branch= 0.0007 subset rates= 0.0001) -pass 8 : -484.5437 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -484.5436 (branch= 0.0001 subset rates= 0.0000) -pass 10: -484.5435 (branch= 0.0001 subset rates= 0.0000) -pass 11: -484.5435 (branch= 0.0000 subset rates= 0.0000) -pass 12: -484.5435 (branch= 0.0000 subset rates= 0.0000) -pass 13: -484.5435 (branch= 0.0000 subset rates= 0.0000) -pass 14: -484.5435 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -484.5435 -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 2.93 -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: -496.6418 -gen current_lnL precision last_tree_imp -0 -496.6418 0.010 0 -100 -495.7052 0.010 100 -200 -492.2646 0.010 104 -300 -491.3468 0.010 275 -400 -491.3377 0.010 275 -500 -484.6361 0.010 487 -600 -484.6296 0.010 487 -700 -484.6245 0.010 487 -800 -484.6137 0.010 487 -900 -484.6031 0.010 487 -1000 -484.5990 0.010 487 -1100 -484.5941 0.010 487 -1200 -484.5900 0.010 487 -1300 -484.5886 0.010 487 -1400 -484.5884 0.010 487 -1500 -484.5814 0.010 487 -1600 -484.5810 0.010 487 -1700 -484.5774 0.010 487 -1800 -484.5752 0.010 487 -1900 -484.5738 0.010 487 -2000 -484.5733 0.010 487 -2100 -484.5724 0.010 487 -2200 -484.5717 0.010 487 -2300 -484.5716 0.010 487 -2400 -484.5708 0.010 487 -2500 -484.5706 0.010 487 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16982,36 +16186,31 @@ Subset 3: Random seed for bootstrap reweighting: 585640194 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 2511, seed 1062915541, best lnL -484.570 +Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 2940, seed 480357301, best lnL -484.579 gen current_lnL precision last_tree_imp -2511 -484.5705 0.010 487 -2600 -484.5691 0.010 487 -2700 -484.5686 0.010 487 -2800 -484.5682 0.010 487 -2900 -484.5681 0.010 487 -3000 -484.5679 0.010 487 -3100 -484.5677 0.010 487 -3200 -484.5676 0.010 487 +2940 -484.5785 0.010 661 +3000 -484.5785 0.010 661 Reached termination condition! -last topological improvement at gen 487 -Improvement over last 500 gen = 0.00094 -Current score = -484.5676 +last topological improvement at gen 661 +Improvement over last 500 gen = 0.00096 +Current score = -484.5785 Performing final optimizations... -pass 1 : -484.5666 (branch= 0.0000 subset rates= 0.0010) -pass 2 : -484.5503 (branch= 0.0163 subset rates= 0.0000) -pass 3 : -484.5466 (branch= 0.0037 subset rates= 0.0000) -pass 4 : -484.5447 (branch= 0.0019 subset rates= 0.0000) -pass 5 : -484.5444 (branch= 0.0003 subset rates= 0.0000) -pass 6 : -484.5442 (branch= 0.0002 subset rates= 0.0000) -pass 7 : -484.5437 (branch= 0.0005 subset rates= 0.0000) -pass 8 : -484.5433 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -484.5432 (branch= 0.0001 subset rates= 0.0000) -pass 10: -484.5431 (branch= 0.0001 subset rates= 0.0000) -pass 11: -484.5430 (branch= 0.0001 subset rates= 0.0000) -pass 12: -484.5430 (branch= 0.0000 subset rates= 0.0000) -pass 13: -484.5430 (branch= 0.0000 subset rates= 0.0000) +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 : -484.5440 (branch= 0.0007 subset rates= 0.0001) +pass 8 : -484.5437 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -484.5436 (branch= 0.0001 subset rates= 0.0000) +pass 10: -484.5435 (branch= 0.0001 subset rates= 0.0000) +pass 11: -484.5435 (branch= 0.0000 subset rates= 0.0000) +pass 12: -484.5435 (branch= 0.0000 subset rates= 0.0000) +pass 13: -484.5435 (branch= 0.0000 subset rates= 0.0000) +pass 14: -484.5435 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -484.5430 +Final score = -484.5435 Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL @@ -17040,81 +16239,80 @@ no rate heterogeneity Subset rate multipliers: - 0.66 2.00 2.95 + 0.66 2.00 2.93 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< ->>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< +>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus -Starting with seed=1361618962 +Starting with seed=1313877241 -Initial ln Likelihood: -723.5838 +Initial ln Likelihood: -686.5027 optimizing: starting branch lengths, subset rates... -pass 1:+ 204.018 (branch= 193.68 scale= 0.81 subset rates= 9.52) -pass 2:+ 10.997 (branch= 7.80 scale= 0.03 subset rates= 3.18) -pass 3:+ 10.354 (branch= 9.14 scale= 0.05 subset rates= 1.16) -pass 4:+ 1.540 (branch= 1.43 scale= 0.00 subset rates= 0.11) -pass 5:+ 0.055 (branch= 0.05 scale= 0.00 subset rates= 0.00) +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: -496.6204 +lnL after optimization: -496.6418 gen current_lnL precision last_tree_imp -0 -496.6204 0.010 0 -100 -496.5408 0.010 63 -200 -496.2154 0.010 128 -300 -495.2900 0.010 214 -400 -495.0512 0.010 385 -500 -485.9967 0.010 462 -600 -484.6299 0.010 550 -700 -484.6242 0.010 550 -800 -484.6178 0.010 550 -900 -484.6069 0.010 550 -1000 -484.6049 0.010 550 -1100 -484.5995 0.010 550 -1200 -484.5938 0.010 550 -1300 -484.5913 0.010 550 -1400 -484.5901 0.010 550 -1500 -484.5894 0.010 550 -1600 -484.5866 0.010 550 -1700 -484.5819 0.010 550 -1800 -484.5813 0.010 550 -1900 -484.5811 0.010 550 -2000 -484.5804 0.010 550 -2100 -484.5793 0.010 550 -2200 -484.5781 0.010 550 -2300 -484.5780 0.010 550 -2400 -484.5768 0.010 550 -2500 -484.5752 0.010 550 -2600 -484.5742 0.010 550 -2700 -484.5739 0.010 550 -2800 -484.5735 0.010 550 -2900 -484.5735 0.010 550 -3000 -484.5732 0.010 550 -3100 -484.5729 0.010 550 -3200 -484.5727 0.010 550 -3300 -484.5727 0.010 550 +0 -496.6418 0.010 0 +100 -495.7052 0.010 100 +200 -492.2646 0.010 104 +300 -491.3468 0.010 275 +400 -491.3377 0.010 275 +500 -484.6361 0.010 487 +600 -484.6296 0.010 487 +700 -484.6245 0.010 487 +800 -484.6137 0.010 487 +900 -484.6031 0.010 487 +1000 -484.5990 0.010 487 +1100 -484.5941 0.010 487 +1200 -484.5900 0.010 487 +1300 -484.5886 0.010 487 +1400 -484.5884 0.010 487 +1500 -484.5814 0.010 487 +1600 -484.5810 0.010 487 +1700 -484.5774 0.010 487 +1800 -484.5752 0.010 487 +1900 -484.5738 0.010 487 +2000 -484.5733 0.010 487 +2100 -484.5724 0.010 487 +2200 -484.5717 0.010 487 +2300 -484.5716 0.010 487 +2400 -484.5708 0.010 487 +2500 -484.5706 0.010 487 +2600 -484.5691 0.010 487 +2700 -484.5686 0.010 487 +2800 -484.5682 0.010 487 +2900 -484.5681 0.010 487 +3000 -484.5679 0.010 487 +3100 -484.5677 0.010 487 +3200 -484.5676 0.010 487 Reached termination condition! -last topological improvement at gen 550 -Improvement over last 500 gen = 0.00083 -Current score = -484.5727 +last topological improvement at gen 487 +Improvement over last 500 gen = 0.00094 +Current score = -484.5676 Performing final optimizations... -pass 1 : -484.5680 (branch= 0.0047 subset rates= 0.0000) -pass 2 : -484.5526 (branch= 0.0155 subset rates= 0.0000) -pass 3 : -484.5502 (branch= 0.0023 subset rates= 0.0000) -pass 4 : -484.5462 (branch= 0.0041 subset rates= 0.0000) -pass 5 : -484.5446 (branch= 0.0016 subset rates= 0.0000) -pass 6 : -484.5435 (branch= 0.0010 subset rates= 0.0000) -pass 7 : -484.5432 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -484.5430 (branch= 0.0001 subset rates= 0.0000) -pass 9 : -484.5430 (branch= 0.0001 subset rates= 0.0000) -pass 10: -484.5429 (branch= 0.0001 subset rates= 0.0000) -pass 11: -484.5428 (branch= 0.0000 subset rates= 0.0000) -pass 12: -484.5428 (branch= 0.0000 subset rates= 0.0000) -pass 13: -484.5428 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -484.5666 (branch= 0.0000 subset rates= 0.0010) +pass 2 : -484.5503 (branch= 0.0163 subset rates= 0.0000) +pass 3 : -484.5466 (branch= 0.0037 subset rates= 0.0000) +pass 4 : -484.5447 (branch= 0.0019 subset rates= 0.0000) +pass 5 : -484.5444 (branch= 0.0003 subset rates= 0.0000) +pass 6 : -484.5442 (branch= 0.0002 subset rates= 0.0000) +pass 7 : -484.5437 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -484.5433 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -484.5432 (branch= 0.0001 subset rates= 0.0000) +pass 10: -484.5431 (branch= 0.0001 subset rates= 0.0000) +pass 11: -484.5430 (branch= 0.0001 subset rates= 0.0000) +pass 12: -484.5430 (branch= 0.0000 subset rates= 0.0000) +pass 13: -484.5430 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -484.5428 -Time used so far = 0 hours, 0 minutes and 10 seconds +Final score = -484.5430 +Time used so far = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17146,55 +16344,46 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< ->>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< +>>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus -Starting with seed=549645566 +Starting with seed=1361618962 -Initial ln Likelihood: -759.3695 +Initial ln Likelihood: -723.5838 optimizing: starting branch lengths, subset rates... -pass 1:+ 236.279 (branch= 226.18 scale= 0.28 subset rates= 9.82) -pass 2:+ 12.013 (branch= 8.39 scale= 0.00 subset rates= 3.62) -pass 3:+ 4.326 (branch= 2.75 scale= 0.07 subset rates= 1.50) -pass 4:+ 2.897 (branch= 2.31 scale= 0.00 subset rates= 0.59) -pass 5:+ 5.236 (branch= 5.18 scale= 0.00 subset rates= 0.06) -pass 6:+ 0.046 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -498.5723 +pass 1:+ 204.018 (branch= 193.68 scale= 0.81 subset rates= 9.52) +pass 2:+ 10.997 (branch= 7.80 scale= 0.03 subset rates= 3.18) +pass 3:+ 10.354 (branch= 9.14 scale= 0.05 subset rates= 1.16) +pass 4:+ 1.540 (branch= 1.43 scale= 0.00 subset rates= 0.11) +pass 5:+ 0.055 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -496.6204 gen current_lnL precision last_tree_imp -0 -498.5723 0.010 0 -100 -489.0933 0.010 69 -200 -487.4592 0.010 113 -300 -487.4022 0.010 296 -400 -485.8397 0.010 391 -500 -485.3968 0.010 427 -600 -484.7727 0.010 587 -700 -484.6737 0.010 699 -800 -484.6416 0.010 716 -900 -484.6326 0.010 716 -1000 -484.6228 0.010 716 -1100 -484.6169 0.010 716 -1200 -484.6119 0.010 716 -1300 -484.6059 0.010 716 +0 -496.6204 0.010 0 +100 -496.5408 0.010 63 +200 -496.2154 0.010 128 +300 -495.2900 0.010 214 +400 -495.0512 0.010 385 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -484.6007 +Current score = -486.0213 Performing final optimizations... -pass 1 : -484.5905 (branch= 0.0100 subset rates= 0.0001) -pass 2 : -484.5633 (branch= 0.0269 subset rates= 0.0003) -pass 3 : -484.5607 (branch= 0.0026 subset rates= 0.0000) -pass 4 : -484.5489 (branch= 0.0118 subset rates= 0.0000) -pass 5 : -484.5465 (branch= 0.0024 subset rates= 0.0000) -pass 6 : -484.5452 (branch= 0.0013 subset rates= 0.0000) -pass 7 : -484.5445 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -484.5439 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -484.5436 (branch= 0.0002 subset rates= 0.0001) -pass 10: -484.5434 (branch= 0.0002 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 1 : -485.4799 (branch= 0.5415 subset rates= 0.0000) +pass 2 : -485.4273 (branch= 0.0526 subset rates= 0.0000) +pass 3 : -485.4129 (branch= 0.0140 subset rates= 0.0003) +pass 4 : -485.4021 (branch= 0.0109 subset rates= 0.0000) +pass 5 : -485.3992 (branch= 0.0029 subset rates= 0.0000) +pass 6 : -485.3977 (branch= 0.0013 subset rates= 0.0002) +pass 7 : -485.3975 (branch= 0.0002 subset rates= 0.0000) +pass 8 : -485.3971 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -485.3969 (branch= 0.0002 subset rates= 0.0000) +pass 10: -485.3968 (branch= 0.0001 subset rates= 0.0000) +pass 11: -485.3968 (branch= 0.0000 subset rates= 0.0000) +pass 12: -485.3968 (branch= 0.0000 subset rates= 0.0000) +pass 13: -485.3968 (branch= 0.0000 subset rates= 0.0000) +pass 14: -485.3968 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -484.5434 +Final score = -485.3968 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17223,11 +16412,11 @@ no rate heterogeneity Subset rate multipliers: - 0.66 2.00 2.96 + 0.66 2.01 2.99 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 4 (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!*** @@ -17235,15 +16424,14 @@ ####################################################### -Completed 4 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 : -484.5435 -Replicate 2 : -484.5430 -Replicate 3 : -484.5428 (best) (same topology as 2) -Replicate 4 : -484.5434 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -484.5430 (best) +Replicate 3 : -485.3968 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17260,10 +16448,9 @@ TL R(1) R(2) R(3) rep 1: 3.518 0.662 1.998 2.934 rep 2: 3.521 0.659 2.004 2.955 -rep 3: 3.519 0.661 1.997 2.954 -rep 4: 3.519 0.661 1.995 2.957 +rep 3: 3.698 0.657 2.007 2.990 -Saving tree from best search rep (#3) 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 @@ -17457,122 +16644,6 @@ 2700 -473.9795 0.010 653 2800 -473.9781 0.010 653 2900 -473.9779 0.010 653 -3000 -473.9779 0.010 653 -3100 -473.9775 0.010 653 -3200 -473.9773 0.010 653 -3300 -473.9771 0.010 653 -3400 -473.9771 0.010 653 -Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00084 -Current score = -473.9771 -Performing final optimizations... -pass 1 : -473.9758 (branch= 0.0000 subset rates= 0.0013) -pass 2 : -473.9557 (branch= 0.0183 subset rates= 0.0018) -pass 3 : -473.9557 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9546 (branch= 0.0011 subset rates= 0.0000) -pass 5 : -473.9534 (branch= 0.0012 subset rates= 0.0000) -pass 6 : -473.9521 (branch= 0.0013 subset rates= 0.0000) -pass 7 : -473.9515 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -473.9511 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9508 -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=1200027012 - -Initial ln Likelihood: -652.6239 -optimizing: starting branch lengths, subset rates... -pass 1:+ 158.853 (branch= 147.31 scale= 1.35 subset rates= 10.19) -pass 2:+ 14.269 (branch= 9.40 scale= 0.00 subset rates= 4.87) -pass 3:+ 3.602 (branch= 1.88 scale= 0.02 subset rates= 1.70) -pass 4:+ 0.888 (branch= 0.31 scale= 0.00 subset rates= 0.58) -pass 5:+ 0.131 (branch= 0.10 scale= 0.00 subset rates= 0.03) -pass 6:+ 0.065 (branch= 0.06 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8058 -gen current_lnL precision last_tree_imp -0 -474.8058 0.010 0 -100 -474.6960 0.010 23 -200 -474.6864 0.010 23 -300 -474.6806 0.010 23 -400 -474.6682 0.010 23 -500 -474.6292 0.010 468 -600 -474.1053 0.010 600 -700 -474.0357 0.010 646 -800 -474.0296 0.010 646 -900 -474.0225 0.010 646 -1000 -474.0203 0.010 646 -1100 -474.0157 0.010 646 -1200 -474.0152 0.010 646 -1300 -474.0120 0.010 646 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17698,57 +16769,34 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1329, seed 760395465, best lnL -474.012 +Search rep 1 (of 5) generation 2989, seed 928552504, best lnL -473.978 gen current_lnL precision last_tree_imp -1329 -474.0117 0.010 646 -1400 -474.0089 0.010 646 -1500 -474.0071 0.010 646 -1600 -474.0058 0.010 646 -1700 -474.0014 0.010 646 -1800 -473.9999 0.010 646 -1900 -473.9988 0.010 646 -2000 -473.9972 0.010 646 -2100 -473.9954 0.010 646 -2200 -473.9950 0.010 646 -2300 -473.9947 0.010 646 -2400 -473.9942 0.010 646 -2500 -473.9936 0.010 646 -2600 -473.9928 0.010 646 -2700 -473.9915 0.010 646 -2800 -473.9913 0.010 646 -2900 -473.9911 0.010 646 -3000 -473.9897 0.010 646 -3100 -473.9892 0.010 646 -3200 -473.9873 0.010 646 -3300 -473.9859 0.010 646 -3400 -473.9854 0.010 646 -3500 -473.9851 0.010 646 -3600 -473.9850 0.010 646 -3700 -473.9845 0.010 646 -3800 -473.9845 0.010 646 -3900 -473.9845 0.010 646 +2989 -473.9779 0.010 653 +3000 -473.9779 0.010 653 +3100 -473.9775 0.010 653 +3200 -473.9773 0.010 653 +3300 -473.9771 0.010 653 +3400 -473.9771 0.010 653 Reached termination condition! -last topological improvement at gen 646 -Improvement over last 500 gen = 0.00092 -Current score = -473.9845 +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00084 +Current score = -473.9771 Performing final optimizations... -pass 1 : -473.9779 (branch= 0.0066 subset rates= 0.0000) -pass 2 : -473.9614 (branch= 0.0164 subset rates= 0.0000) -pass 3 : -473.9562 (branch= 0.0025 subset rates= 0.0027) -pass 4 : -473.9562 (branch= 0.0000 subset rates= 0.0000) -pass 5 : -473.9534 (branch= 0.0028 subset rates= 0.0000) -pass 6 : -473.9521 (branch= 0.0013 subset rates= 0.0000) -pass 7 : -473.9519 (branch= 0.0002 subset rates= 0.0000) -pass 8 : -473.9518 (branch= 0.0002 subset rates= 0.0000) -pass 9 : -473.9516 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9515 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9514 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9514 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9514 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9514 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9743 (branch= 0.0000 subset rates= 0.0028) +pass 2 : -473.9560 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -473.9560 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9549 (branch= 0.0011 subset rates= 0.0000) +pass 5 : -473.9533 (branch= 0.0016 subset rates= 0.0000) +pass 6 : -473.9526 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -473.9519 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -473.9515 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -473.9513 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9512 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9512 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9512 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9514 -Time used so far = 0 hours, 0 minutes and 9 seconds +Final score = -473.9512 +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17776,13 +16824,13 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.82 + 0.59 2.07 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 2 (of 5)<<< +>>>Completed Search rep 1 (of 5)<<< ->>>Search rep 3 (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 @@ -17811,59 +16859,66 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=734845441 +Starting with seed=1200027012 -Initial ln Likelihood: -633.6976 +Initial ln Likelihood: -652.6239 optimizing: starting branch lengths, subset rates... -pass 1:+ 142.642 (branch= 131.15 scale= 1.12 subset rates= 10.37) -pass 2:+ 12.793 (branch= 7.73 scale= 0.03 subset rates= 5.04) -pass 3:+ 2.317 (branch= 0.63 scale= 0.02 subset rates= 1.67) -pass 4:+ 0.912 (branch= 0.32 scale= 0.00 subset rates= 0.59) -pass 5:+ 0.168 (branch= 0.14 scale= 0.00 subset rates= 0.03) -pass 6:+ 0.014 (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: -474.8524 +pass 1:+ 158.853 (branch= 147.31 scale= 1.35 subset rates= 10.19) +pass 2:+ 14.269 (branch= 9.40 scale= 0.00 subset rates= 4.87) +pass 3:+ 3.602 (branch= 1.88 scale= 0.02 subset rates= 1.70) +pass 4:+ 0.888 (branch= 0.31 scale= 0.00 subset rates= 0.58) +pass 5:+ 0.131 (branch= 0.10 scale= 0.00 subset rates= 0.03) +pass 6:+ 0.065 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8058 gen current_lnL precision last_tree_imp -0 -474.8524 0.010 0 -100 -474.6197 0.010 55 -200 -474.5821 0.010 132 -300 -474.5759 0.010 132 -400 -474.5490 0.010 358 -500 -474.5257 0.010 358 -600 -474.5159 0.010 358 -700 -474.5106 0.010 358 -800 -474.5018 0.010 358 -900 -474.4998 0.010 358 -1000 -474.4931 0.010 358 -1100 -474.4885 0.010 358 -1200 -474.4863 0.010 358 -1300 -474.4833 0.010 358 -1400 -474.4806 0.010 358 -1500 -474.4788 0.010 358 -1600 -474.4748 0.010 358 -1700 -474.4746 0.010 358 +0 -474.8058 0.010 0 +100 -474.6960 0.010 23 +200 -474.6864 0.010 23 +300 -474.6806 0.010 23 +400 -474.6682 0.010 23 +500 -474.6292 0.010 468 +600 -474.1053 0.010 600 +700 -474.0357 0.010 646 +800 -474.0296 0.010 646 +900 -474.0225 0.010 646 +1000 -474.0203 0.010 646 +1100 -474.0157 0.010 646 +1200 -474.0152 0.010 646 +1300 -474.0120 0.010 646 +1400 -474.0089 0.010 646 +1500 -474.0071 0.010 646 +1600 -474.0058 0.010 646 +1700 -474.0014 0.010 646 +1800 -473.9999 0.010 646 +1900 -473.9988 0.010 646 +2000 -473.9972 0.010 646 +2100 -473.9954 0.010 646 +2200 -473.9950 0.010 646 +2300 -473.9947 0.010 646 +2400 -473.9942 0.010 646 +2500 -473.9936 0.010 646 +2600 -473.9928 0.010 646 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4746 +Current score = -473.9915 Performing final optimizations... -pass 1 : -474.4746 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -474.4526 (branch= 0.0220 subset rates= 0.0000) -pass 3 : -474.4485 (branch= 0.0041 subset rates= 0.0000) -pass 4 : -474.4419 (branch= 0.0066 subset rates= 0.0000) -pass 5 : -474.4359 (branch= 0.0059 subset rates= 0.0000) -pass 6 : -474.4332 (branch= 0.0028 subset rates= 0.0000) -pass 7 : -474.4317 (branch= 0.0015 subset rates= 0.0000) -pass 8 : -474.4305 (branch= 0.0012 subset rates= 0.0000) -pass 9 : -474.4300 (branch= 0.0005 subset rates= 0.0000) -pass 10: -474.4298 (branch= 0.0002 subset rates= 0.0000) -pass 11: -474.4287 (branch= 0.0001 subset rates= 0.0010) -pass 12: -474.4285 (branch= 0.0002 subset rates= 0.0000) -pass 13: -474.4284 (branch= 0.0001 subset rates= 0.0000) -pass 14: -474.4283 (branch= 0.0000 subset rates= 0.0000) -pass 15: -474.4283 (branch= 0.0000 subset rates= 0.0000) -pass 16: -474.4283 (branch= 0.0000 subset rates= 0.0000) -pass 17: -474.4283 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9788 (branch= 0.0127 subset rates= 0.0000) +pass 2 : -473.9679 (branch= 0.0109 subset rates= 0.0000) +pass 3 : -473.9609 (branch= 0.0062 subset rates= 0.0007) +pass 4 : -473.9575 (branch= 0.0014 subset rates= 0.0020) +pass 5 : -473.9547 (branch= 0.0028 subset rates= 0.0000) +pass 6 : -473.9528 (branch= 0.0020 subset rates= 0.0000) +pass 7 : -473.9517 (branch= 0.0006 subset rates= 0.0005) +pass 8 : -473.9514 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -473.9512 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9511 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 13: -473.9510 (branch= 0.0000 subset rates= 0.0000) +pass 14: -473.9510 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -474.4283 +Final score = -473.9510 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17892,11 +16947,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.04 2.91 + 0.59 2.06 2.80 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 2 (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!*** @@ -17904,14 +16959,13 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 2 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 : -473.9508 (best) -Replicate 2 : -473.9514 (same topology as 1) -Replicate 3 : -474.4283 (TERMINATED PREMATURELY) +Replicate 1 : -473.9512 +Replicate 2 : -473.9510 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17926,11 +16980,10 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.350 0.587 2.069 2.802 -rep 2: 4.353 0.585 2.069 2.824 -rep 3: 4.600 0.588 2.036 2.908 +rep 1: 4.352 0.586 2.071 2.814 +rep 2: 4.348 0.589 2.063 2.796 -Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#2) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -17949,7 +17002,7 @@ dh_testroot dh_prep dh_auto_install - make -j18 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j10 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' @@ -17998,22 +17051,23 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-3_i386.deb'. +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-3_all.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-3_i386.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-3_i386.deb'. -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-3_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-3_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../garli_2.1-3_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/30017/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30017/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/44624 and its subdirectories -I: Current time: Wed Aug 11 20:07:45 -12 2021 -I: pbuilder-time-stamp: 1628755665 +I: removing directory /srv/workspace/pbuilder/30017 and its subdirectories +I: Current time: Fri Jul 10 15:58:09 +14 2020 +I: pbuilder-time-stamp: 1594346289