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%
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(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