Diff of the two buildlogs: -- --- b1/build.log 2023-05-13 01:32:12.740066087 +0000 +++ b2/build.log 2023-05-13 01:42:41.536517843 +0000 @@ -1,6 +1,9 @@ -I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 13 19:49:49 -12 2024 -I: pbuilder-time-stamp: 1718351389 +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: Sat May 13 15:32:17 +14 2023 +I: pbuilder-time-stamp: 1683941537 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +20,7 @@ I: copying [./garli_2.1.orig.tar.gz] I: copying [./garli_2.1-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Feb 20 02:34:04 2022 -12 +gpgv: Signature made Mon Feb 21 04:34:04 2022 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./garli_2.1-7.dsc: no acceptable signature found @@ -26,137 +29,168 @@ dpkg-source: info: unpacking garli_2.1-7.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/29619/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1084/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 13 15:32 /bin/sh -> /bin/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/1084/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1084/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=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(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=7' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='faf349555d1540a1b57d11e07d3e8e53' - 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='29619' - 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=1084 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/r-b-build.hxGuNhDI/pbuilderrc_N8QG --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hxGuNhDI/b1 --logfile b1/build.log garli_2.1-7.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/r-b-build.hxGuNhDI/pbuilderrc_2Kv4 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hxGuNhDI/b2 --logfile b2/build.log --extrapackages usrmerge garli_2.1-7.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 ionos16-i386 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-686-pae #1 SMP Debian 5.10.178-3 (2023-04-22) i686 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 2023 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 2023 more - -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount - -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 2023 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/29619/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more + -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount + -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 13 15:32 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1084/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -286,7 +320,7 @@ Get: 84 http://deb.debian.org/debian bookworm/main i386 openmpi-bin i386 4.1.4-3+b1 [196 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 libopenmpi-dev i386 4.1.4-3+b1 [920 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 ncl-tools i386 2.1.21+git20210811.b1213a7-4 [216 kB] -Fetched 46.5 MB in 1s (40.3 MB/s) +Fetched 46.5 MB in 23s (2006 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19604 files and directories currently installed.) @@ -648,8 +682,18 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../garli_2.1-7_source.changes +I: user script /srv/workspace/pbuilder/1084/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/1084/tmp/hooks/A99_set_merged_usr finished +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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../garli_2.1-7_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-7 dpkg-buildpackage: info: source distribution unstable @@ -746,13 +790,13 @@ checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -783,8 +827,8 @@ checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for malloc.h... yes checking for stddef.h... yes @@ -821,7 +865,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j16 + make -j7 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' @@ -834,47 +878,6 @@ 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 configreader.o configreader.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 datamatr.o datamatr.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 funcs.o funcs.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 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 -garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); - | ^~~~~~~~ -garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] - 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); - | ^~~~~~~~ -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from configoptions.cpp:20: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -919,7 +922,28 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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 /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from configoptions.cpp:20: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); @@ -936,8 +960,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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 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 +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 +garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); + | ^~~~~~~~ +garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); + | ^~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -968,30 +998,50 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_function.h:1438: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': +reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from individual.cpp:21: + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from adaptation.cpp:18: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_function.h:1438: -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1004,13 +1054,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -1033,14 +1076,25 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from tree.h:24: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from configreader.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1056,13 +1110,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -1085,9 +1132,86 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1097,7 +1221,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from model.cpp:17: + from population.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1135,21 +1259,153 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from garlimain.cpp:46: +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from configreader.cpp:21: + from /usr/include/c++/12/iomanip:40, + from individual.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1187,11 +1443,13 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1201,7 +1459,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from adaptation.cpp:18: + from model.cpp:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1239,20 +1497,85 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +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 +garlimain.cpp: In function 'int SubGarliMain(int)': +garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] + 323 | else sprintf(temp, ".run%d", rank); + | ^~ +garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] + 323 | else sprintf(temp, ".run%d", rank); + | ^~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +garlimain.cpp: In function 'int SubGarliMain(int)': +garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] + 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); + | ^~ +garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] + 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': +model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from garlimain.cpp:40: + from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from population.h:23: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from tree.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1268,10 +1591,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -1287,6 +1606,36 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +In file included from optimization.cpp:21: +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); @@ -1334,11 +1676,6 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from optimization.cpp:21: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -1346,137 +1683,11 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/map:60, - from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, - from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2887, - from mpitrick.cpp:20: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_function.h:1438: -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/map:60, + from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, + from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2887, + from mpitrick.cpp:20: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_function.h:1438: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': +reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -2249,35 +2250,43 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': -configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] - 337 | sprintf(modName, "model%d", modelNum); - | ^~ -configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] - 337 | sprintf(modName, "model%d", modelNum); - | ^~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', - inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from individual.cpp:28: + from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from individual.cpp:21: + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from population.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2293,7 +2302,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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 reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -2309,9 +2317,38 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': +configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 337 | sprintf(modName, "model%d", modelNum); + | ^~ +configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2321,7 +2358,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from model.cpp:17: + from adaptation.cpp:18: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2337,13 +2374,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -2366,10 +2396,17 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2379,7 +2416,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from population.h:23: + from configreader.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2410,6 +2447,12 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); + | ^~~~~~~~ +garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); + | ^~~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -2421,16 +2464,85 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from population.cpp:23: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from population.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2468,21 +2580,145 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from garlimain.cpp:46: +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from configreader.cpp:21: + from /usr/include/c++/12/iomanip:40, + from individual.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2520,16 +2756,29 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2539,7 +2788,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from population.h:23: + from model.cpp:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2570,11 +2819,6 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from population.cpp:49: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -2582,29 +2826,49 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from adaptation.cpp:18: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from tree.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2642,14 +2906,40 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from optimization.cpp:21: +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from tree.h:24: + from population.cpp:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2687,124 +2977,30 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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 -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from model.h:25, - from clamanager.h:25, - from condlike.cpp:22: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from configreader.cpp:18: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from rng.h:36, - from tree.h:30: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53: + from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3111,46 +3206,12 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, - from /usr/include/ncl/ncl.h:27, - from garlireader.cpp:41: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from datamatr.cpp:20: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53: + from datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3162,23 +3223,22 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from population.cpp:25: +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~ +population.cpp:3066:47: note: directive argument in the range [1, 536870911] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, @@ -3220,22 +3280,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~ -population.cpp:3066:47: note: directive argument in the range [1, 536870911] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ g++ -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 -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[3]: Leaving directory '/build/garli-2.1/src' Making all in tests @@ -3252,7 +3296,7 @@ # 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\nbootstrapseed = 42/' \{\} \; dh_auto_test - make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 + make -j7 check "TESTSUITEFLAGS=-j7 --verbose" VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' @@ -5922,7 +5966,7 @@ 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 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6219,7 +6263,7 @@ 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 28 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6371,7 +6415,7 @@ 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 10 seconds +Time used = 0 hours, 0 minutes and 20 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6575,7 +6619,7 @@ pass 79: -3350.2337 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2338 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6783,7 +6827,7 @@ pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 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 ... ####################################################### @@ -6945,7 +6989,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7100,7 +7144,7 @@ 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 ... ####################################################### @@ -7265,7 +7309,7 @@ pass 12: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 14 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7519,7 +7563,7 @@ pass 37: -13306.2063 (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 = -13306.2063 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 8 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7944,7 +7988,7 @@ pass 15: -467.6787 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6786 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9371,58 +9415,58 @@ Improvement over last 500 gen = 0.03349 Current score = -210.5119 Performing final optimizations... -pass 1 : -210.1431 (branch= 0.0000 alpha= 0.0977 pinv= 0.2251 eq freqs= 0.0000 rel rates= 0.0461) -pass 2 : -209.5362 (branch= 0.0000 alpha= 0.3284 pinv= 0.2534 eq freqs= 0.0028 rel rates= 0.0223) -pass 3 : -209.3315 (branch= 0.0351 alpha= 0.1413 pinv= 0.0149 eq freqs= 0.0067 rel rates= 0.0067) -pass 4 : -209.2606 (branch= 0.0423 alpha= 0.0193 pinv= 0.0022 eq freqs= 0.0011 rel rates= 0.0060) -pass 5 : -209.2229 (branch= 0.0234 alpha= 0.0075 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0068) -pass 6 : -209.1998 (branch= 0.0108 alpha= 0.0028 pinv= 0.0010 eq freqs= 0.0002 rel rates= 0.0083) -pass 7 : -209.1788 (branch= 0.0076 alpha= 0.0023 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0104) -pass 8 : -209.1606 (branch= 0.0047 alpha= 0.0012 pinv= 0.0001 eq freqs= 0.0007 rel rates= 0.0115) -pass 9 : -209.1465 (branch= 0.0025 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0110) -pass 10: -209.1351 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0100) -pass 11: -209.1253 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0090) -pass 12: -209.1166 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) -pass 13: -209.1088 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) -pass 14: -209.1016 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) -pass 15: -209.0949 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) -pass 16: -209.0887 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) -pass 17: -209.0828 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) -pass 18: -209.0773 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) -pass 19: -209.0720 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) -pass 20: -209.0672 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) - optimization up to ... -pass 30: -208.9999 (branch= 0.0075 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0583) - optimization up to ... -pass 40: -208.8391 (branch= 0.0298 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1220) +pass 1 : -210.1433 (branch= 0.0000 alpha= 0.0976 pinv= 0.2249 eq freqs= 0.0000 rel rates= 0.0461) +pass 2 : -209.5277 (branch= 0.0000 alpha= 0.3287 pinv= 0.2614 eq freqs= 0.0029 rel rates= 0.0226) +pass 3 : -209.3297 (branch= 0.0363 alpha= 0.1344 pinv= 0.0139 eq freqs= 0.0068 rel rates= 0.0066) +pass 4 : -209.2593 (branch= 0.0436 alpha= 0.0176 pinv= 0.0021 eq freqs= 0.0011 rel rates= 0.0061) +pass 5 : -209.2221 (branch= 0.0231 alpha= 0.0072 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) +pass 6 : -209.1992 (branch= 0.0108 alpha= 0.0026 pinv= 0.0009 eq freqs= 0.0002 rel rates= 0.0084) +pass 7 : -209.1782 (branch= 0.0076 alpha= 0.0022 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0105) +pass 8 : -209.1601 (branch= 0.0045 alpha= 0.0011 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0118) +pass 9 : -209.1459 (branch= 0.0023 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0112) +pass 10: -209.1347 (branch= 0.0010 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: -209.1164 (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= 0.0048) + optimization up to ... +pass 30: -208.9995 (branch= 0.0075 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0584) + optimization up to ... +pass 40: -208.8384 (branch= 0.0298 alpha= 0.0000 pinv= 0.0016 eq freqs= 0.0076 rel rates= 0.1222) optimization up to ... -pass 50: -208.6977 (branch= 0.0133 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1209) +pass 50: -208.6973 (branch= 0.0132 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1208) optimization up to ... -pass 60: -208.6234 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0723) +pass 60: -208.6230 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0722) optimization up to ... -pass 70: -208.5739 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0489) +pass 70: -208.5737 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0487) optimization up to ... -pass 80: -208.5379 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0356) +pass 80: -208.5379 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0354) optimization up to ... pass 90: -208.5108 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) optimization up to ... -pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) +pass 100: -208.4895 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0211) optimization up to ... -pass 110: -208.4726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) +pass 110: -208.4726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0168) optimization up to ... -pass 120: -208.4588 (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: -208.4473 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) +pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0113) optimization up to ... -pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) +pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) optimization up to ... -pass 150: -208.4293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) +pass 150: -208.4292 (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: -208.4161 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) +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= 0.0054) +pass 180: -208.4107 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) optimization up to ... pass 190: -208.4060 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... @@ -9430,11 +9474,11 @@ optimization up to ... pass 210: -208.3981 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) optimization up to ... -pass 220: -208.3948 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) +pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... pass 230: -208.3917 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... -pass 240: -208.3890 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) +pass 240: -208.3889 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3864 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... @@ -9442,21 +9486,21 @@ optimization up to ... pass 270: -208.3820 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 290: -208.3782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3765 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 310: -208.3750 (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= 0.0016) optimization up to ... -pass 320: -208.3735 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... -pass 330: -208.3722 (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= 0.0014) 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 ... -pass 350: -208.3697 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 350: -208.3696 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3685 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... @@ -9472,44 +9516,40 @@ 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) 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: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) - optimization up to ... -pass 490: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) - optimization up to ... -pass 500: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +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 510: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... -pass 513: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 497: -208.3584 (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 = -208.3584 +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 123.058, AG = 189.902, AT = 7.010, CG = 206.183, CT = 196.157, GT = 1.000 + AC = 122.553, AG = 189.115, AT = 6.992, CG = 205.327, CT = 195.368, 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 with an invariant (invariable) site category, proportion estimated - 0.2780 + 0.2781 Substitution rate categories under this model: rate proportion - 0.0000 0.2780 + 0.0000 0.2781 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 @@ -9523,11 +9563,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3583 +Replicate 1 : -208.3584 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: 123.1 189.9 7.01 206.2 196.2 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.6 189.1 6.992 205.3 195.4 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -9663,36 +9703,36 @@ Improvement over last 500 gen = 0.03747 Current score = -211.2888 Performing final optimizations... -pass 1 : -209.0783 (branch= 0.0000 alpha= 0.7564 pinv= 1.3685 eq freqs= 0.0051 rel rates= 0.0804) -pass 2 : -208.5904 (branch= 0.0486 alpha= 0.3875 pinv= 0.0099 eq freqs= 0.0123 rel rates= 0.0296) -pass 3 : -208.5208 (branch= 0.0388 alpha= 0.0022 pinv= 0.0021 eq freqs= 0.0019 rel rates= 0.0247) -pass 4 : -208.4907 (branch= 0.0067 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0020 rel rates= 0.0213) -pass 5 : -208.4692 (branch= 0.0009 alpha= 0.0010 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0193) -pass 6 : -208.4497 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0183) -pass 7 : -208.4325 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0168) -pass 8 : -208.4166 (branch= 0.0001 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0154) -pass 9 : -208.4024 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0140) -pass 10: -208.3889 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0132) -pass 11: -208.3768 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0120) -pass 12: -208.3660 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0108) -pass 13: -208.3558 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0101) -pass 14: -208.3465 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0092) -pass 15: -208.3380 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0085) -pass 16: -208.3301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0079) -pass 17: -208.3228 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0072) -pass 18: -208.3158 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) -pass 19: -208.3094 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) -pass 20: -208.3033 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) - optimization up to ... -pass 30: -208.2582 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0449) +pass 1 : -209.0464 (branch= 0.0000 alpha= 0.7596 pinv= 1.3961 eq freqs= 0.0053 rel rates= 0.0813) +pass 2 : -208.6439 (branch= 0.0509 alpha= 0.3036 pinv= 0.0089 eq freqs= 0.0115 rel rates= 0.0277) +pass 3 : -208.5246 (branch= 0.0332 alpha= 0.0571 pinv= 0.0020 eq freqs= 0.0020 rel rates= 0.0249) +pass 4 : -208.4904 (branch= 0.0069 alpha= 0.0045 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0218) +pass 5 : -208.4687 (branch= 0.0013 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0003 rel rates= 0.0197) +pass 6 : -208.4486 (branch= 0.0013 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0185) +pass 7 : -208.4317 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0164) +pass 8 : -208.4157 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0155) +pass 9 : -208.4011 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0144) +pass 10: -208.3881 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0129) +pass 11: -208.3761 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0118) +pass 12: -208.3653 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0108) +pass 13: -208.3553 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0099) +pass 14: -208.3462 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) +pass 15: -208.3377 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0084) +pass 16: -208.3297 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0079) +pass 17: -208.3224 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) +pass 18: -208.3156 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) +pass 19: -208.3090 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) +pass 20: -208.3031 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0059) + optimization up to ... +pass 30: -208.2581 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0449) optimization up to ... -pass 40: -208.2302 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0279) +pass 40: -208.2301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0279) optimization up to ... -pass 50: -208.2111 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0190) +pass 50: -208.2112 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) optimization up to ... -pass 60: -208.1972 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0139) +pass 60: -208.1973 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) optimization up to ... -pass 70: -208.1867 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 70: -208.1868 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... pass 80: -208.1785 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... @@ -9754,16 +9794,16 @@ optimization up to ... pass 370: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 373: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) +pass 372: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1244 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 22.224, AG = 32.293, AT = 0.001, CG = 36.377, CT = 80.250, GT = 1.000 + AC = 22.223, AG = 32.290, AT = 0.001, CG = 36.375, CT = 80.262, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: @@ -9791,7 +9831,7 @@ Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 22.22 32.29 0.001 36.38 80.25 1 0.221 0.344 0.216 0.218 999.900 0.338 +rep 1: 22.22 32.29 0.001 36.38 80.26 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL @@ -9922,150 +9962,161 @@ 2000 -210.9688 0.010 1502 2500 -210.8711 0.010 1502 3000 -210.7510 0.010 2883 -3500 -210.7006 0.010 2883 +3500 -210.7005 0.010 2883 4000 -210.6775 0.010 2883 -4500 -210.6277 0.010 2883 -5000 -210.5647 0.010 2883 -5500 -210.5012 0.010 2883 -6000 -210.3398 0.010 2883 +4500 -210.6526 0.010 2883 +5000 -210.5940 0.010 4692 +5500 -210.5367 0.010 5207 +6000 -210.4081 0.010 5812 +6500 -210.3701 0.010 5812 +7000 -210.3450 0.010 5812 +7500 -210.3290 0.010 5812 +8000 -210.1893 0.010 7789 +8500 -210.1401 0.010 8330 +9000 -210.0737 0.010 8330 +9500 -210.0359 0.010 8330 +10000 -210.0205 0.010 8330 + Optimizing parameters... improved 0.465 lnL + Optimizing branchlengths... improved 0.000 lnL +10500 -209.5308 0.010 8330 Reached termination condition! -last topological improvement at gen 2883 -Improvement over last 500 gen = 0.04654 -Current score = -210.3270 +last topological improvement at gen 8330 +Improvement over last 500 gen = 0.01768 +Current score = -209.5308 Performing final optimizations... -pass 1 : -209.7238 (branch= 0.0035 alpha= 0.1982 pinv= 0.3270 eq freqs= 0.0000 rel rates= 0.0745) -pass 2 : -209.3594 (branch= 0.0173 alpha= 0.2671 pinv= 0.0527 eq freqs= 0.0034 rel rates= 0.0241) -pass 3 : -209.2620 (branch= 0.0413 alpha= 0.0372 pinv= 0.0083 eq freqs= 0.0051 rel rates= 0.0055) -pass 4 : -209.2081 (branch= 0.0317 alpha= 0.0153 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0061) -pass 5 : -209.1621 (branch= 0.0277 alpha= 0.0101 pinv= 0.0000 eq freqs= 0.0015 rel rates= 0.0066) -pass 6 : -209.1365 (branch= 0.0109 alpha= 0.0036 pinv= 0.0006 eq freqs= 0.0010 rel rates= 0.0095) -pass 7 : -209.1173 (branch= 0.0067 alpha= 0.0019 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0100) -pass 8 : -209.1050 (branch= 0.0027 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0088) -pass 9 : -209.0958 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0077) -pass 10: -209.0881 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0070) -pass 11: -209.0815 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0062) -pass 12: -209.0756 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) -pass 13: -209.0702 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) -pass 14: -209.0652 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) -pass 15: -209.0603 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) -pass 16: -209.0555 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 17: -209.0503 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) -pass 18: -209.0447 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) -pass 19: -209.0386 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) -pass 20: -209.0319 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0058) +pass 1 : -209.3193 (branch= 0.0000 alpha= 0.1723 pinv= 0.0392 eq freqs= 0.0000 rel rates= 0.0000) +pass 2 : -209.2381 (branch= 0.0321 alpha= 0.0358 pinv= 0.0026 eq freqs= 0.0027 rel rates= 0.0080) +pass 3 : -209.1748 (branch= 0.0449 alpha= 0.0143 pinv= 0.0016 eq freqs= 0.0024 rel rates= 0.0000) +pass 4 : -209.1239 (branch= 0.0298 alpha= 0.0161 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 5 : -209.0951 (branch= 0.0145 alpha= 0.0042 pinv= 0.0010 eq freqs= 0.0036 rel rates= 0.0055) +pass 6 : -209.0778 (branch= 0.0076 alpha= 0.0014 pinv= 0.0002 eq freqs= 0.0003 rel rates= 0.0078) +pass 7 : -209.0686 (branch= 0.0022 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0063) +pass 8 : -209.0622 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0055) +pass 9 : -209.0562 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0052) +pass 10: -209.0504 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0050) +pass 11: -209.0441 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) +pass 12: -209.0372 (branch= 0.0013 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0055) +pass 13: -209.0295 (branch= 0.0016 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0059) +pass 14: -209.0210 (branch= 0.0018 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0064) +pass 15: -209.0120 (branch= 0.0016 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0071) +pass 16: -209.0020 (branch= 0.0019 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0078) +pass 17: -208.9907 (branch= 0.0023 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0085) +pass 18: -208.9781 (branch= 0.0026 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0005 rel rates= 0.0094) +pass 19: -208.9643 (branch= 0.0029 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0006 rel rates= 0.0102) +pass 20: -208.9493 (branch= 0.0032 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0007 rel rates= 0.0110) optimization up to ... -pass 30: -208.9062 (branch= 0.0239 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0051 rel rates= 0.0958) +pass 30: -208.7712 (branch= 0.0290 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0090 rel rates= 0.1381) optimization up to ... -pass 40: -208.7363 (branch= 0.0228 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0081 rel rates= 0.1371) +pass 40: -208.6637 (branch= 0.0054 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0030 rel rates= 0.0985) optimization up to ... -pass 50: -208.6455 (branch= 0.0027 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0016 rel rates= 0.0861) +pass 50: -208.6016 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0610) optimization up to ... -pass 60: -208.5892 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0555) +pass 60: -208.5583 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0429) optimization up to ... -pass 70: -208.5493 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0001 rel rates= 0.0395) +pass 70: -208.5263 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0317) optimization up to ... -pass 80: -208.5195 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0296) +pass 80: -208.5017 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0245) optimization up to ... -pass 90: -208.4965 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0229) +pass 90: -208.4824 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0192) optimization up to ... -pass 100: -208.4782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0182) +pass 100: -208.4668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0155) optimization up to ... -pass 110: -208.4633 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0148) +pass 110: -208.4539 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0128) optimization up to ... -pass 120: -208.4511 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0122) +pass 120: -208.4432 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0106) optimization up to ... -pass 130: -208.4407 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0103) +pass 130: -208.4341 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) optimization up to ... -pass 140: -208.4320 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0087) +pass 140: -208.4263 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) optimization up to ... -pass 150: -208.4245 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) +pass 150: -208.4196 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... -pass 160: -208.4181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) +pass 160: -208.4138 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... -pass 170: -208.4125 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) +pass 170: -208.4087 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) optimization up to ... -pass 180: -208.4076 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) +pass 180: -208.4043 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) optimization up to ... -pass 190: -208.4032 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0043) +pass 190: -208.4003 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... -pass 200: -208.3994 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0038) +pass 200: -208.3967 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... -pass 210: -208.3959 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) +pass 210: -208.3934 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... -pass 220: -208.3927 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) +pass 220: -208.3905 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... -pass 230: -208.3898 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) +pass 230: -208.3878 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... -pass 240: -208.3872 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) +pass 240: -208.3854 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... -pass 250: -208.3848 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 250: -208.3832 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... -pass 260: -208.3826 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) +pass 260: -208.3811 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 270: -208.3806 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) +pass 270: -208.3792 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... -pass 280: -208.3788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +pass 280: -208.3775 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 290: -208.3770 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) +pass 290: -208.3758 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 300: -208.3754 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 300: -208.3743 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... -pass 310: -208.3739 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) +pass 310: -208.3729 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 320: -208.3726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 330: -208.3713 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) +pass 330: -208.3703 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 340: -208.3700 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 340: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 350: -208.3689 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 350: -208.3681 (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) +pass 360: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 370: -208.3668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 370: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 380: -208.3659 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 380: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 390: -208.3650 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 390: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 400: -208.3641 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 400: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 410: -208.3633 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 410: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 420: -208.3625 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 420: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 430: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 430: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 440: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 440: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 450: -208.3604 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 450: -208.3600 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 460: -208.3598 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 460: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 470: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 470: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) +pass 480: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 481: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... -Final score = -208.3584 -Time used = 0 hours, 0 minutes and 5 seconds +Final score = -208.3585 +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 = 122.423, AG = 188.915, AT = 6.984, CG = 205.110, CT = 195.167, GT = 1.000 + AC = 122.040, AG = 188.326, AT = 6.962, CG = 204.470, CT = 194.555, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2905 0.2035 0.2835 + (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated - 0.2780 + 0.2781 Substitution rate categories under this model: rate proportion - 0.0000 0.2780 + 0.0000 0.2781 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 @@ -10084,11 +10135,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3584 +Replicate 1 : -208.3585 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122.4 188.9 6.984 205.1 195.2 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122 188.3 6.962 204.5 194.6 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -10217,136 +10268,136 @@ Optimizing branchlengths... improved 0.350 lnL 1500 -210.9424 0.010 1230 2000 -210.7769 0.010 1230 -2500 -210.6534 0.010 1230 -3000 -210.6127 0.010 1230 +2500 -210.6535 0.010 1230 +3000 -210.6026 0.010 1230 Reached termination condition! last topological improvement at gen 1230 -Improvement over last 500 gen = 0.03866 -Current score = -210.5968 +Improvement over last 500 gen = 0.04157 +Current score = -210.5932 Performing final optimizations... -pass 1 : -210.1948 (branch= 0.0000 alpha= 0.1301 pinv= 0.2111 eq freqs= 0.0000 rel rates= 0.0608) -pass 2 : -209.5752 (branch= 0.0039 alpha= 0.3416 pinv= 0.2381 eq freqs= 0.0033 rel rates= 0.0326) -pass 3 : -209.3378 (branch= 0.0534 alpha= 0.1436 pinv= 0.0210 eq freqs= 0.0088 rel rates= 0.0107) -pass 4 : -209.2576 (branch= 0.0495 alpha= 0.0232 pinv= 0.0016 eq freqs= 0.0022 rel rates= 0.0037) -pass 5 : -209.2071 (branch= 0.0354 alpha= 0.0086 pinv= 0.0011 eq freqs= 0.0004 rel rates= 0.0049) -pass 6 : -209.1726 (branch= 0.0200 alpha= 0.0061 pinv= 0.0003 eq freqs= 0.0011 rel rates= 0.0070) -pass 7 : -209.1462 (branch= 0.0107 alpha= 0.0041 pinv= 0.0002 eq freqs= 0.0006 rel rates= 0.0108) -pass 8 : -209.1250 (branch= 0.0075 alpha= 0.0017 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0112) -pass 9 : -209.1114 (branch= 0.0031 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0097) -pass 10: -209.1014 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0084) -pass 11: -209.0931 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0074) -pass 12: -209.0861 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) -pass 13: -209.0798 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) -pass 14: -209.0742 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) -pass 15: -209.0689 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) -pass 16: -209.0640 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) -pass 17: -209.0592 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 18: -209.0543 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 19: -209.0491 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) -pass 20: -209.0435 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) +pass 1 : -210.1853 (branch= 0.0000 alpha= 0.1339 pinv= 0.2109 eq freqs= 0.0000 rel rates= 0.0632) +pass 2 : -209.5476 (branch= 0.0093 alpha= 0.3576 pinv= 0.2467 eq freqs= 0.0052 rel rates= 0.0189) +pass 3 : -209.3350 (branch= 0.0400 alpha= 0.1339 pinv= 0.0167 eq freqs= 0.0078 rel rates= 0.0143) +pass 4 : -209.2572 (branch= 0.0460 alpha= 0.0208 pinv= 0.0029 eq freqs= 0.0033 rel rates= 0.0048) +pass 5 : -209.2091 (branch= 0.0332 alpha= 0.0097 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0043) +pass 6 : -209.1768 (branch= 0.0181 alpha= 0.0054 pinv= 0.0005 eq freqs= 0.0013 rel rates= 0.0070) +pass 7 : -209.1510 (branch= 0.0101 alpha= 0.0036 pinv= 0.0002 eq freqs= 0.0008 rel rates= 0.0110) +pass 8 : -209.1301 (branch= 0.0070 alpha= 0.0017 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0114) +pass 9 : -209.1163 (branch= 0.0031 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0099) +pass 10: -209.1061 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0086) +pass 11: -209.0976 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0076) +pass 12: -209.0903 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0068) +pass 13: -209.0838 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0062) +pass 14: -209.0780 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) +pass 15: -209.0725 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) +pass 16: -209.0674 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) +pass 17: -209.0626 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 18: -209.0579 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) +pass 19: -209.0529 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 20: -209.0476 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... -pass 30: -208.9362 (branch= 0.0193 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0038 rel rates= 0.0835) +pass 30: -208.9477 (branch= 0.0173 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0032 rel rates= 0.0787) optimization up to ... -pass 40: -208.7603 (branch= 0.0269 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1383) +pass 40: -208.7714 (branch= 0.0282 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0088 rel rates= 0.1373) optimization up to ... -pass 50: -208.6585 (branch= 0.0044 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0024 rel rates= 0.0944) +pass 50: -208.6643 (branch= 0.0053 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0028 rel rates= 0.0983) optimization up to ... -pass 60: -208.5981 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0595) +pass 60: -208.6021 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0612) optimization up to ... -pass 70: -208.5558 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0419) +pass 70: -208.5586 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0431) optimization up to ... -pass 80: -208.5245 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0311) +pass 80: -208.5265 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0318) optimization up to ... -pass 90: -208.5003 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0240) +pass 90: -208.5019 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0244) optimization up to ... -pass 100: -208.4813 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) +pass 100: -208.4825 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0192) optimization up to ... -pass 110: -208.4658 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0153) +pass 110: -208.4669 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0155) optimization up to ... -pass 120: -208.4531 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0127) +pass 120: -208.4541 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0127) optimization up to ... -pass 130: -208.4425 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 130: -208.4433 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0108) optimization up to ... -pass 140: -208.4335 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) +pass 140: -208.4342 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) optimization up to ... -pass 150: -208.4258 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) +pass 150: -208.4264 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) optimization up to ... -pass 160: -208.4192 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 160: -208.4197 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... -pass 170: -208.4134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) +pass 170: -208.4139 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... -pass 180: -208.4084 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 180: -208.4088 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) optimization up to ... -pass 190: -208.4039 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) +pass 190: -208.4043 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... -pass 200: -208.4000 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) +pass 200: -208.4003 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... -pass 210: -208.3964 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) +pass 210: -208.3967 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... -pass 220: -208.3932 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) +pass 220: -208.3935 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... -pass 230: -208.3903 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) +pass 230: -208.3906 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... -pass 240: -208.3877 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) +pass 240: -208.3879 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... -pass 250: -208.3852 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 250: -208.3855 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... -pass 260: -208.3830 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) +pass 260: -208.3832 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... -pass 270: -208.3810 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) +pass 270: -208.3812 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 280: -208.3791 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3793 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... -pass 290: -208.3773 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) +pass 290: -208.3775 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 300: -208.3757 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 300: -208.3759 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 310: -208.3742 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) +pass 310: -208.3743 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... -pass 320: -208.3728 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3729 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 330: -208.3715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) +pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 340: -208.3703 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 340: -208.3704 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 350: -208.3691 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 360: -208.3680 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 370: -208.3670 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 380: -208.3660 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 390: -208.3651 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 400: -208.3642 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 400: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 410: -208.3634 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 410: -208.3635 (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: -208.3619 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 440: -208.3612 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 450: -208.3605 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 450: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 460: -208.3599 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 460: -208.3600 (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: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 480: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 489: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) Looking for minimum length branches... Final score = -208.3584 -Time used = 0 hours, 0 minutes and 5 seconds +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.418, AG = 189.366, AT = 6.970, CG = 205.267, CT = 195.223, GT = 1.000 + AC = 122.439, AG = 189.413, AT = 6.971, CG = 205.316, CT = 195.264, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2834 Rate Heterogeneity Model: @@ -10379,7 +10430,7 @@ 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: 122.4 189.4 6.97 205.3 195.2 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.4 189.4 6.971 205.3 195.3 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -13055,11 +13106,6 @@ Optimization precision reduced Optimizing parameters... improved 0.159 lnL Optimizing branchlengths... improved 0.317 lnL -900 -88.9507 0.010 879 -1000 -88.8871 0.010 879 -1100 -88.8475 0.010 879 -1200 -88.8463 0.010 879 -1300 -88.8312 0.010 879 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13156,11 +13202,14 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1303, seed 915404468, best lnL -88.831 +Bootstrap rep 1 (of 1) generation 821, seed 259743281, best lnL -89.675 gen current_lnL precision last_tree_imp -1303 -88.8312 0.010 879 +821 -89.6750 0.010 817 +900 -88.9507 0.010 879 +1000 -88.8871 0.010 879 +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 @@ -13172,37 +13221,41 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.9984 + 0.9045 with an invariant (invariable) site category, proportion estimated - 0.1371 + 0.1355 Substitution rate categories under this model: rate proportion - 0.0000 0.1371 - 0.1887 0.2876 - 0.7119 0.2876 - 2.0994 0.2876 + 0.0000 0.1355 + 0.1669 0.2882 + 0.6855 0.2882 + 2.1476 0.2882 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were 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 : -88.8312 +Replicate 1 : -88.8871 Parameter estimates: alpha pinv -rep 1: 0.998 0.137 +rep 1: 0.904 0.136 Treelengths: TL -rep 1: 2.337 +rep 1: 2.441 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 @@ -13325,12 +13378,6 @@ 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 -600 -111.7788 0.500 84 -Optimization precision reduced - Optimizing parameters... improved 0.386 lnL - Optimizing branchlengths... improved 0.390 lnL -700 -110.8142 0.010 615 -800 -110.5642 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13417,9 +13464,15 @@ STARTING RUN Restarting from checkpoint... - generation 861, seed 926088541, best lnL -110.559 + generation 583, seed 527417082, best lnL -111.781 gen current_lnL precision last_tree_imp -861 -110.5588 0.010 707 +583 -111.7809 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... @@ -13603,11 +13656,6 @@ 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13693,9 +13741,9 @@ STARTING RUN Restarting from checkpoint... - generation 2064, seed 1300830078, best lnL -111.682 + generation 1599, seed 1011840859, best lnL -111.682 gen current_lnL precision last_tree_imp -2064 -111.6817 0.010 563 +1599 -111.6818 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13711,7 +13759,7 @@ no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... @@ -13719,14 +13767,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6817 +Replicate 1 : -111.6818 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.605 +rep 1: 2.606 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log @@ -13857,10 +13905,6 @@ 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 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13947,9 +13991,13 @@ STARTING RUN Restarting from checkpoint... - generation 82, seed 823304040, best lnL -205.402 + generation 45, seed 1279743899, best lnL -205.637 gen current_lnL precision last_tree_imp -82 -205.4022 0.500 76 +45 -205.6368 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... @@ -14139,7 +14187,6 @@ 10 -195.3554 0.500 0 20 -195.3341 0.500 0 30 -195.2776 0.500 0 -40 -195.2555 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14227,9 +14274,10 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 44, seed 1785684024, best lnL -195.255 +Bootstrap rep 1 (of 1) generation 37, seed 910819821, best lnL -195.264 gen current_lnL precision last_tree_imp -44 -195.2555 0.500 0 +37 -195.2644 0.500 0 +40 -195.2555 0.500 0 50 -195.2138 0.500 0 60 -195.1630 0.500 0 70 -195.0043 0.500 0 @@ -14446,16 +14494,12 @@ 900 -3353.8938 0.255 0 1000 -3353.6942 0.255 0 Optimization precision reduced - Optimizing parameters... improved 0.828 lnL - Optimizing branchlengths... improved 0.083 lnL -1100 -3352.7293 0.010 0 -1200 -3352.6847 0.010 0 -1300 -3352.5625 0.010 0 -1400 -3352.3243 0.010 0 -1500 -3352.2847 0.010 0 -1600 -3352.1841 0.010 0 -1700 -3352.1749 0.010 0 -1800 -3352.1044 0.010 0 + Optimizing parameters... improved 0.823 lnL + Optimizing branchlengths... improved 0.081 lnL +1100 -3352.7370 0.010 0 +1200 -3352.7015 0.010 0 +1300 -3352.5782 0.010 0 +1400 -3352.3342 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14559,80 +14603,76 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1856, seed 92048020, best lnL -3351.957 +Search rep 1 (of 2) generation 1453, seed 1093109233, best lnL -3352.327 gen current_lnL precision last_tree_imp -1856 -3351.9570 0.010 0 -1900 -3351.7635 0.010 0 -2000 -3351.6902 0.010 0 -2100 -3351.5165 0.010 0 -2200 -3351.3150 0.010 0 -2300 -3351.2813 0.010 0 -2400 -3351.2752 0.010 0 -2500 -3351.1977 0.010 0 -2600 -3351.1876 0.010 0 -2700 -3351.1873 0.010 0 -2800 -3351.1300 0.010 0 -2900 -3351.1267 0.010 0 -3000 -3351.1241 0.010 0 -3100 -3351.1215 0.010 0 -3200 -3351.1135 0.010 0 -3300 -3351.1010 0.010 0 +1453 -3352.3270 0.010 0 +1500 -3352.2948 0.010 0 +1600 -3352.1988 0.010 0 +1700 -3352.1901 0.010 0 +1800 -3352.1156 0.010 0 +1900 -3351.7724 0.010 0 +2000 -3351.7029 0.010 0 +2100 -3351.5856 0.010 0 +2200 -3351.3395 0.010 0 +2300 -3351.3192 0.010 0 +2400 -3351.3108 0.010 0 +2500 -3351.2081 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.0891 +Current score = -3351.2048 Performing final optimizations... -pass 1 : -3351.0047 (branch= 0.0000 alpha= 0.0150 pinv= 0.0205 eq freqs= 0.0000 rel rates= 0.0489 subset rates= 0.0000) -pass 2 : -3350.9116 (branch= 0.0066 alpha= 0.0081 pinv= 0.0184 eq freqs= 0.0052 rel rates= 0.0549 subset rates= 0.0000) -pass 3 : -3350.8277 (branch= 0.0016 alpha= 0.0163 pinv= 0.0158 eq freqs= 0.0039 rel rates= 0.0450 subset rates= 0.0012) -pass 4 : -3350.7536 (branch= 0.0058 alpha= 0.0157 pinv= 0.0147 eq freqs= 0.0000 rel rates= 0.0367 subset rates= 0.0011) -pass 5 : -3350.6904 (branch= 0.0041 alpha= 0.0135 pinv= 0.0136 eq freqs= 0.0005 rel rates= 0.0305 subset rates= 0.0010) -pass 6 : -3350.6363 (branch= 0.0034 alpha= 0.0120 pinv= 0.0126 eq freqs= 0.0003 rel rates= 0.0258 subset rates= 0.0000) -pass 7 : -3350.5867 (branch= 0.0010 alpha= 0.0113 pinv= 0.0115 eq freqs= 0.0001 rel rates= 0.0244 subset rates= 0.0014) -pass 8 : -3350.5436 (branch= 0.0019 alpha= 0.0108 pinv= 0.0105 eq freqs= 0.0001 rel rates= 0.0198 subset rates= 0.0000) -pass 9 : -3350.5049 (branch= 0.0003 alpha= 0.0098 pinv= 0.0095 eq freqs= 0.0000 rel rates= 0.0180 subset rates= 0.0011) -pass 10: -3350.4714 (branch= 0.0010 alpha= 0.0089 pinv= 0.0086 eq freqs= 0.0000 rel rates= 0.0149 subset rates= 0.0000) -pass 11: -3350.4419 (branch= 0.0002 alpha= 0.0081 pinv= 0.0078 eq freqs= 0.0000 rel rates= 0.0134 subset rates= 0.0000) -pass 12: -3350.4154 (branch= 0.0001 alpha= 0.0077 pinv= 0.0070 eq freqs= 0.0000 rel rates= 0.0118 subset rates= 0.0000) -pass 13: -3350.3920 (branch= 0.0000 alpha= 0.0070 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0101 subset rates= 0.0000) -pass 14: -3350.3714 (branch= 0.0000 alpha= 0.0063 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0087 subset rates= 0.0000) -pass 15: -3350.3534 (branch= 0.0000 alpha= 0.0056 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0074 subset rates= 0.0000) -pass 16: -3350.3376 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0064 subset rates= 0.0000) -pass 17: -3350.3237 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0055 subset rates= 0.0000) -pass 18: -3350.3117 (branch= 0.0000 alpha= 0.0039 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0047 subset rates= 0.0000) -pass 19: -3350.3012 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0040 subset rates= 0.0000) -pass 20: -3350.2920 (branch= 0.0000 alpha= 0.0030 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0035 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2463 (branch= 0.0000 alpha= 0.0150 pinv= 0.0136 eq freqs= 0.0000 rel rates= 0.0170 subset rates= 0.0000) +pass 1 : -3351.0892 (branch= 0.0000 alpha= 0.0070 pinv= 0.0201 eq freqs= 0.0386 rel rates= 0.0485 subset rates= 0.0013) +pass 2 : -3350.9865 (branch= 0.0073 alpha= 0.0086 pinv= 0.0194 eq freqs= 0.0027 rel rates= 0.0637 subset rates= 0.0010) +pass 3 : -3350.8963 (branch= 0.0083 alpha= 0.0164 pinv= 0.0170 eq freqs= 0.0000 rel rates= 0.0485 subset rates= 0.0000) +pass 4 : -3350.8129 (branch= 0.0063 alpha= 0.0164 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.0408 subset rates= 0.0038) +pass 5 : -3350.7441 (branch= 0.0052 alpha= 0.0137 pinv= 0.0147 eq freqs= 0.0006 rel rates= 0.0330 subset rates= 0.0015) +pass 6 : -3350.6812 (branch= 0.0052 alpha= 0.0129 pinv= 0.0136 eq freqs= 0.0002 rel rates= 0.0296 subset rates= 0.0014) +pass 7 : -3350.6272 (branch= 0.0034 alpha= 0.0116 pinv= 0.0126 eq freqs= 0.0002 rel rates= 0.0262 subset rates= 0.0000) +pass 8 : -3350.5788 (branch= 0.0007 alpha= 0.0115 pinv= 0.0113 eq freqs= 0.0001 rel rates= 0.0233 subset rates= 0.0015) +pass 9 : -3350.5365 (branch= 0.0017 alpha= 0.0107 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0195 subset rates= 0.0000) +pass 10: -3350.4979 (branch= 0.0003 alpha= 0.0097 pinv= 0.0100 eq freqs= 0.0000 rel rates= 0.0176 subset rates= 0.0010) +pass 11: -3350.4652 (branch= 0.0009 alpha= 0.0088 pinv= 0.0085 eq freqs= 0.0000 rel rates= 0.0145 subset rates= 0.0000) +pass 12: -3350.4364 (branch= 0.0002 alpha= 0.0079 pinv= 0.0076 eq freqs= 0.0000 rel rates= 0.0131 subset rates= 0.0000) +pass 13: -3350.4106 (branch= 0.0000 alpha= 0.0075 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0115 subset rates= 0.0000) +pass 14: -3350.3877 (branch= 0.0000 alpha= 0.0068 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0099 subset rates= 0.0000) +pass 15: -3350.3676 (branch= 0.0000 alpha= 0.0061 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0085 subset rates= 0.0000) +pass 16: -3350.3500 (branch= 0.0000 alpha= 0.0055 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0073 subset rates= 0.0000) +pass 17: -3350.3345 (branch= 0.0000 alpha= 0.0048 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0063 subset rates= 0.0000) +pass 18: -3350.3211 (branch= 0.0000 alpha= 0.0043 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0054 subset rates= 0.0000) +pass 19: -3350.3093 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0046 subset rates= 0.0000) +pass 20: -3350.2990 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0040 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2478 (branch= 0.0000 alpha= 0.0168 pinv= 0.0152 eq freqs= 0.0000 rel rates= 0.0192 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2360 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0040 subset rates= 0.0000) +pass 40: -3350.2362 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0045 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2338 (branch= 0.0000 alpha= 0.0006 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) +pass 50: -3350.2337 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0011 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2334 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 68: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 69: -3350.2331 (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 = -3350.2333 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -3350.2332 +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 = 3.115, AG = 10.412, AT = 2.689, CG = 0.001, CT = 21.897, GT = 1.000 + AC = 3.116, AG = 10.420, AT = 2.691, CG = 0.001, CT = 21.927, 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 - 0.5778 + 0.5773 with an invariant (invariable) site category, proportion estimated - 0.3657 + 0.3656 Substitution rate categories under this model: rate proportion - 0.0000 0.3657 - 0.0486 0.1586 - 0.2997 0.1586 - 0.8696 0.1586 - 2.7822 0.1586 + 0.0000 0.3656 + 0.0485 0.1586 + 0.2994 0.1586 + 0.8693 0.1586 + 2.7829 0.1586 Model 2 Number of states = 2 (binary data) @@ -14657,20 +14697,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2333 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2332 (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: 3.115 10.41 2.689 0.001 21.9 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.116 10.42 2.691 0.001 21.93 1 0.333 0.222 0.157 0.288 0.577 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.788 1.820 0.180 +rep 1: 0.789 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -14820,7 +14860,6 @@ 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 -500 -3323.6818 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14921,77 +14960,75 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 514, seed 1439459639, best lnL -3323.659 +Search rep 1 (of 2) generation 465, seed 380121777, best lnL -3323.707 gen current_lnL precision last_tree_imp -514 -3323.6590 0.500 1 +465 -3323.7073 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 +800 -3321.0295 0.255 1 900 -3321.0142 0.255 1 -1000 -3320.9667 0.255 1 -1100 -3320.8654 0.255 1 -Optimization precision reduced - Optimizing parameters... improved 0.577 lnL - Optimizing branchlengths... improved 0.059 lnL NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.2289 +Current score = -3321.0117 Performing final optimizations... -pass 1 : -3319.8103 (branch= 0.0402 alpha= 0.0065 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.3364 ins/del rates= 0.0195) -pass 2 : -3319.4796 (branch= 0.0492 alpha= 0.0082 pinv= 0.0156 eq freqs= 0.0000 rel rates= 0.2388 ins/del rates= 0.0189) -pass 3 : -3319.2060 (branch= 0.0344 alpha= 0.0096 pinv= 0.0151 eq freqs= 0.0027 rel rates= 0.2017 ins/del rates= 0.0101) -pass 4 : -3318.9901 (branch= 0.0199 alpha= 0.0106 pinv= 0.0147 eq freqs= 0.0000 rel rates= 0.1627 ins/del rates= 0.0079) -pass 5 : -3318.8081 (branch= 0.0133 alpha= 0.0098 pinv= 0.0139 eq freqs= 0.0031 rel rates= 0.1366 ins/del rates= 0.0053) -pass 6 : -3318.6587 (branch= 0.0088 alpha= 0.0110 pinv= 0.0130 eq freqs= 0.0004 rel rates= 0.1127 ins/del rates= 0.0035) -pass 7 : -3318.5311 (branch= 0.0063 alpha= 0.0100 pinv= 0.0121 eq freqs= 0.0007 rel rates= 0.0960 ins/del rates= 0.0025) -pass 8 : -3318.4242 (branch= 0.0040 alpha= 0.0097 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0800 ins/del rates= 0.0017) -pass 9 : -3318.3335 (branch= 0.0029 alpha= 0.0091 pinv= 0.0104 eq freqs= 0.0002 rel rates= 0.0669 ins/del rates= 0.0013) -pass 10: -3318.2558 (branch= 0.0019 alpha= 0.0088 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0564 ins/del rates= 0.0008) -pass 11: -3318.1905 (branch= 0.0013 alpha= 0.0083 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0464 ins/del rates= 0.0006) -pass 12: -3318.1348 (branch= 0.0008 alpha= 0.0077 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0388 ins/del rates= 0.0004) -pass 13: -3318.0871 (branch= 0.0006 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0324 ins/del rates= 0.0002) -pass 14: -3318.0471 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0264 ins/del rates= 0.0001) -pass 15: -3318.0124 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0224 ins/del rates= 0.0001) -pass 16: -3317.9825 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0190 ins/del rates= 0.0000) -pass 17: -3317.9565 (branch= 0.0001 alpha= 0.0049 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0162 ins/del rates= 0.0000) -pass 18: -3317.9340 (branch= 0.0001 alpha= 0.0044 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0138 ins/del rates= 0.0000) -pass 19: -3317.9144 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0118 ins/del rates= 0.0000) -pass 20: -3317.8975 (branch= 0.0000 alpha= 0.0035 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0101 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8129 (branch= 0.0001 alpha= 0.0189 pinv= 0.0174 eq freqs= 0.0001 rel rates= 0.0481 ins/del rates= 0.0000) +pass 1 : -3320.3839 (branch= 0.0457 alpha= 0.0000 pinv= 0.0123 eq freqs= 0.0126 rel rates= 0.5388 ins/del rates= 0.0185) +pass 2 : -3319.9222 (branch= 0.0584 alpha= 0.0041 pinv= 0.0165 eq freqs= 0.0036 rel rates= 0.3621 ins/del rates= 0.0169) +pass 3 : -3319.5590 (branch= 0.0398 alpha= 0.0089 pinv= 0.0158 eq freqs= 0.0065 rel rates= 0.2723 ins/del rates= 0.0199) +pass 4 : -3319.2760 (branch= 0.0257 alpha= 0.0103 pinv= 0.0154 eq freqs= 0.0020 rel rates= 0.2197 ins/del rates= 0.0099) +pass 5 : -3319.0377 (branch= 0.0194 alpha= 0.0091 pinv= 0.0148 eq freqs= 0.0010 rel rates= 0.1860 ins/del rates= 0.0080) +pass 6 : -3318.8367 (branch= 0.0129 alpha= 0.0104 pinv= 0.0139 eq freqs= 0.0010 rel rates= 0.1575 ins/del rates= 0.0053) +pass 7 : -3318.6724 (branch= 0.0080 alpha= 0.0104 pinv= 0.0131 eq freqs= 0.0004 rel rates= 0.1289 ins/del rates= 0.0034) +pass 8 : -3318.5408 (branch= 0.0050 alpha= 0.0107 pinv= 0.0122 eq freqs= 0.0007 rel rates= 0.1008 ins/del rates= 0.0021) +pass 9 : -3318.4282 (branch= 0.0036 alpha= 0.0098 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0861 ins/del rates= 0.0015) +pass 10: -3318.3336 (branch= 0.0024 alpha= 0.0097 pinv= 0.0111 eq freqs= 0.0003 rel rates= 0.0702 ins/del rates= 0.0010) +pass 11: -3318.2550 (branch= 0.0016 alpha= 0.0091 pinv= 0.0101 eq freqs= 0.0002 rel rates= 0.0569 ins/del rates= 0.0007) +pass 12: -3318.1896 (branch= 0.0011 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0467 ins/del rates= 0.0005) +pass 13: -3318.1340 (branch= 0.0007 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0389 ins/del rates= 0.0003) +pass 14: -3318.0865 (branch= 0.0005 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0323 ins/del rates= 0.0002) +pass 15: -3318.0463 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0264 ins/del rates= 0.0001) +pass 16: -3318.0118 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0223 ins/del rates= 0.0001) +pass 17: -3317.9819 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0190 ins/del rates= 0.0000) +pass 18: -3317.9560 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0161 ins/del rates= 0.0000) +pass 19: -3317.9335 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0138 ins/del rates= 0.0000) +pass 20: -3317.9139 (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: -3317.8169 (branch= 0.0001 alpha= 0.0215 pinv= 0.0198 eq freqs= 0.0001 rel rates= 0.0556 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7938 (branch= 0.0001 alpha= 0.0053 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0127 ins/del rates= 0.0000) optimization up to ... -pass 40: -3317.7929 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0111 ins/del rates= 0.0000) +pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7883 (branch= 0.0000 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0027 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 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0006 ins/del rates= 0.0000) +pass 70: -3317.7872 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 69: -3317.7871 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) +pass 78: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 13 seconds +Final score = -3317.7870 +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 = 3.061, AG = 10.250, AT = 2.652, CG = 0.001, CT = 21.511, GT = 1.000 + AC = 3.069, AG = 10.273, AT = 2.658, CG = 0.001, CT = 21.555, 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 - 0.5746 + 0.5752 with an invariant (invariable) site category, proportion estimated - 0.3611 + 0.3614 Substitution rate categories under this model: rate proportion - 0.0000 0.3611 - 0.0479 0.1597 - 0.2978 0.1597 - 0.8678 0.1597 - 2.7865 0.1597 + 0.0000 0.3614 + 0.0480 0.1596 + 0.2982 0.1596 + 0.8681 0.1596 + 2.7856 0.1596 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15017,13 +15054,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7870 (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: 3.061 10.25 2.652 0.001 21.51 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.069 10.27 2.658 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -15152,10 +15189,10 @@ Optimization precision reduced Optimizing parameters... improved 1.264 lnL Optimizing branchlengths... improved 0.275 lnL -1200 -211.1652 0.010 1104 +1200 -211.1651 0.010 1104 1400 -211.1318 0.010 1104 1600 -211.0218 0.010 1104 -1800 -210.9997 0.010 1104 +1800 -210.9996 0.010 1104 2000 -210.9460 0.010 1104 2200 -210.8946 0.010 1104 2400 -210.8863 0.010 1104 @@ -15172,13 +15209,6 @@ 4600 -210.6257 0.010 1104 4800 -210.5948 0.010 1104 5000 -210.5740 0.010 1104 -5200 -210.5693 0.010 1104 -5400 -210.5461 0.010 1104 -5600 -210.5151 0.010 1104 -5800 -210.4822 0.010 1104 -6000 -210.4632 0.010 1104 -6200 -210.4596 0.010 1104 -6400 -210.4467 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15258,32 +15288,33 @@ STARTING RUN Restarting from checkpoint... - generation 6506, seed 879616660, best lnL -210.427 + generation 5034, seed 505781465, best lnL -210.572 gen current_lnL precision last_tree_imp -6506 -210.4275 0.010 1104 -6600 -210.4213 0.010 1104 +5034 -210.5715 0.010 1104 +5100 -210.5710 0.010 1104 +5200 -210.5693 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.03936 +Improvement over last 500 gen = 0.04048 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.196, AG = 5.751, AT = 0.203, CG = 5.763, CT = 9.298, GT = 1.000 + AC = 2.798, AG = 5.232, AT = 0.196, CG = 4.937, CT = 7.825, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2383 0.3335 0.2107 0.2175 + (ACGT) 0.2331 0.3366 0.2107 0.2196 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.3086 + 1.2338 with an invariant (invariable) site category, proportion estimated - 0.1640 + 0.1337 Substitution rate categories under this model: rate proportion - 0.0000 0.1640 - 0.2518 0.2787 - 0.7748 0.2787 - 1.9734 0.2787 + 0.0000 0.1337 + 0.2378 0.2888 + 0.7623 0.2888 + 1.9999 0.2888 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. @@ -15294,15 +15325,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.4213 +Replicate 1 : -210.5693 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: 3.196 5.751 0.2029 5.763 9.298 1 0.238 0.333 0.211 0.218 1.309 0.164 +rep 1: 2.798 5.232 0.1964 4.937 7.825 1 0.233 0.337 0.211 0.220 1.234 0.134 Treelengths: TL -rep 1: 2.296 +rep 1: 2.254 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 @@ -15426,39 +15457,33 @@ Optimization precision reduced Optimizing parameters... improved 2.192 lnL Optimizing branchlengths... improved 0.320 lnL -1000 -167.2068 0.010 843 -1200 -167.1475 0.010 843 -1400 -167.0486 0.010 843 -1600 -166.9640 0.010 843 -1800 -166.8222 0.010 843 -2000 -166.6787 0.010 843 -2200 -166.5886 0.010 843 -2400 -166.4578 0.010 843 -2600 -166.3862 0.010 843 -2800 -166.3657 0.010 843 -3000 -166.3069 0.010 843 -3200 -166.2786 0.010 843 -3400 -166.2098 0.010 843 -3600 -166.0618 0.010 843 -3800 -165.9520 0.010 843 -4000 -165.9339 0.010 843 -4200 -165.8875 0.010 843 -4400 -165.8799 0.010 843 -4600 -165.7808 0.010 843 -4800 -165.7681 0.010 843 -5000 -165.6806 0.010 843 -5200 -165.6628 0.010 843 -5400 -165.5965 0.010 843 -5600 -165.4766 0.010 843 -5800 -165.3753 0.010 843 -6000 -165.2855 0.010 843 -6200 -165.2441 0.010 6021 -6400 -165.1353 0.010 6021 -6600 -165.0479 0.010 6021 -6800 -165.0423 0.010 6021 -7000 -164.8276 0.010 6021 -7200 -164.5704 0.010 6021 -7400 -164.5072 0.010 6021 +1000 -167.2071 0.010 843 +1200 -167.1478 0.010 843 +1400 -167.0488 0.010 843 +1600 -166.9642 0.010 843 +1800 -166.8224 0.010 843 +2000 -166.6789 0.010 843 +2200 -166.5888 0.010 843 +2400 -166.4579 0.010 843 +2600 -166.3863 0.010 843 +2800 -166.3658 0.010 843 +3000 -166.3071 0.010 843 +3200 -166.2788 0.010 843 +3400 -166.2100 0.010 843 +3600 -166.0620 0.010 843 +3800 -165.9522 0.010 843 +4000 -165.9341 0.010 843 +4200 -165.8877 0.010 843 +4400 -165.8801 0.010 843 +4600 -165.7810 0.010 843 +4800 -165.7684 0.010 843 +5000 -165.6809 0.010 843 +5200 -165.6631 0.010 843 +5400 -165.5973 0.010 843 +5600 -165.4764 0.010 843 +5800 -165.3722 0.010 843 +6000 -165.3452 0.010 843 +6200 -165.2643 0.010 843 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15539,61 +15564,73 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 7465, seed 589001259, best lnL -164.504 +Bootstrap rep 1 (of 1) generation 6266, seed 810008325, best lnL -165.201 gen current_lnL precision last_tree_imp -7465 -164.5043 0.010 6021 -7500 -164.5038 0.010 6021 -7600 -164.4959 0.010 6021 -7700 -164.3943 0.010 6021 -7800 -164.3912 0.010 6021 -7900 -164.3626 0.010 6021 -8000 -164.2518 0.010 6021 -8100 -164.1851 0.010 6021 -8200 -164.1840 0.010 6021 -8300 -164.1280 0.010 6021 -8400 -164.0573 0.010 6021 -8500 -164.0428 0.010 6021 -8600 -163.9766 0.010 6021 -8700 -163.8239 0.010 6021 -8800 -163.7930 0.010 6021 -8900 -163.7850 0.010 6021 -9000 -163.6971 0.010 6021 -9100 -163.6921 0.010 6021 -9200 -163.6897 0.010 6021 -9300 -163.6419 0.010 6021 -9400 -163.6356 0.010 6021 -9500 -163.6037 0.010 6021 -9600 -163.5752 0.010 6021 -9700 -163.5414 0.010 9694 -9800 -163.5023 0.010 9694 -9900 -163.5019 0.010 9694 -10000 -163.4898 0.010 9694 - Optimizing parameters... improved 1.540 lnL - Optimizing branchlengths... improved 0.027 lnL +6266 -165.2013 0.010 843 +6300 -165.1570 0.010 843 +6400 -165.1349 0.010 843 +6500 -165.1041 0.010 843 +6600 -165.0585 0.010 843 +6700 -165.0568 0.010 843 +6800 -165.0558 0.010 843 +6900 -164.9355 0.010 843 +7000 -164.9210 0.010 843 +7100 -164.8350 0.010 843 +7200 -164.8001 0.010 843 +7300 -164.7629 0.010 843 +7400 -164.7203 0.010 7384 +7500 -164.6622 0.010 7384 +7600 -164.6620 0.010 7384 +7700 -164.5342 0.010 7384 +7800 -164.5211 0.010 7384 +7900 -164.4747 0.010 7384 +8000 -164.4383 0.010 7384 +8100 -164.3294 0.010 7384 +8200 -164.2991 0.010 7384 +8300 -164.1855 0.010 7384 +8400 -164.1761 0.010 7384 +8500 -164.1673 0.010 7384 +8600 -164.1244 0.010 7384 +8700 -163.9939 0.010 7384 +8800 -163.9563 0.010 7384 +8900 -163.9226 0.010 7384 +9000 -163.8541 0.010 7384 +9100 -163.8507 0.010 7384 +9200 -163.8478 0.010 7384 +9300 -163.7794 0.010 7384 +9400 -163.7483 0.010 7384 +9500 -163.7089 0.010 7384 +9600 -163.6370 0.010 7384 +9700 -163.6119 0.010 7384 +9800 -163.6000 0.010 7384 +9900 -163.5964 0.010 7384 +10000 -163.5760 0.010 7384 + Optimizing parameters... improved 1.427 lnL + Optimizing branchlengths... improved 0.023 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 = 0.772, AG = 11.343, AT = 2.501, CG = 4.475, CT = 41.744, GT = 1.000 + AC = 0.623, AG = 8.569, AT = 1.923, CG = 3.484, CT = 33.004, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1311 0.4150 0.2443 0.2096 + (ACGT) 0.1298 0.4236 0.2357 0.2109 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 591.2921 + 51.6954 with an invariant (invariable) site category, proportion estimated - 0.3422 + 0.3606 Substitution rate categories under this model: rate proportion - 0.0000 0.3422 - 0.9482 0.1644 - 0.9862 0.1644 - 1.0129 0.1644 - 1.0527 0.1644 + 0.0000 0.3606 + 0.8292 0.1599 + 0.9495 0.1599 + 1.0395 0.1599 + 1.1819 0.1599 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 2 branches were collapsed. + 3 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! @@ -15604,15 +15641,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -161.9232 +Replicate 1 : -162.1261 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: 0.7721 11.34 2.501 4.475 41.74 1 0.131 0.415 0.244 0.210 591.292 0.342 +rep 1: 0.6227 8.569 1.923 3.484 33 1 0.130 0.424 0.236 0.211 51.695 0.361 Treelengths: TL -rep 1: 3.108 +rep 1: 3.167 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -15722,18 +15759,18 @@ Optimization precision reduced Optimizing parameters... improved 0.223 lnL Optimizing branchlengths... improved 0.080 lnL -1200 -213.6190 0.010 530 -1400 -213.5800 0.010 530 -1600 -213.5576 0.010 530 -1800 -213.3951 0.010 530 +1200 -213.6191 0.010 530 +1400 -213.5801 0.010 530 +1600 -213.5577 0.010 530 +1800 -213.3952 0.010 530 2000 -213.3646 0.010 530 -2200 -213.3318 0.010 530 -2400 -213.2445 0.010 530 -2600 -213.2282 0.010 530 +2200 -213.3319 0.010 530 +2400 -213.2446 0.010 530 +2600 -213.2283 0.010 530 2800 -213.2194 0.010 530 3000 -213.2002 0.010 530 -3200 -213.1945 0.010 530 -3400 -213.1682 0.010 530 +3200 -213.1946 0.010 530 +3400 -213.1683 0.010 530 3600 -213.1580 0.010 530 3800 -213.0251 0.010 3769 4000 -212.9704 0.010 3769 @@ -15751,18 +15788,11 @@ 6400 -212.7244 0.010 3769 6600 -212.7154 0.010 3769 6800 -212.7057 0.010 3769 -7000 -212.7024 0.010 3769 +7000 -212.7025 0.010 3769 7200 -212.7024 0.010 3769 7400 -212.6754 0.010 3769 7600 -212.6692 0.010 3769 7800 -212.6655 0.010 3769 -8000 -212.6638 0.010 3769 -8200 -212.6580 0.010 3769 -8400 -212.6570 0.010 3769 -8600 -212.6362 0.010 3769 -8800 -212.5814 0.010 3769 -9000 -212.5438 0.010 3769 -9200 -212.5310 0.010 3769 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15842,21 +15872,21 @@ STARTING RUN Restarting from checkpoint... - generation 9334, seed 449077140, best lnL -212.529 + generation 7879, seed 1407081587, best lnL -212.665 gen current_lnL precision last_tree_imp -9334 -212.5293 0.010 3769 -9400 -212.5139 0.010 3769 +7879 -212.6654 0.010 3769 +7900 -212.6643 0.010 3769 Reached termination condition! last topological improvement at gen 3769 -Improvement over last 500 gen = 0.04679 +Improvement over last 500 gen = 0.01110 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 7.543, AG = 14.661, AT = 0.626, CG = 14.601, CT = 9.342, GT = 1.000 + AC = 5.522, AG = 10.376, AT = 0.431, CG = 10.683, CT = 7.001, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2193 0.2876 0.1818 0.3113 + (ACGT) 0.2215 0.2881 0.1827 0.3076 Rate Heterogeneity Model: no rate heterogeneity @@ -15869,15 +15899,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.5139 +Replicate 1 : -212.6643 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 7.543 14.66 0.6258 14.6 9.342 1 0.219 0.288 0.182 0.311 +rep 1: 5.522 10.38 0.4313 10.68 7.001 1 0.222 0.288 0.183 0.308 Treelengths: TL -rep 1: 1.731 +rep 1: 1.728 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 @@ -16007,46 +16037,37 @@ Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL -1600 -211.2008 0.010 1502 -1800 -211.0870 0.010 1502 +1600 -211.2007 0.010 1502 +1800 -211.0869 0.010 1502 2000 -210.9688 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 +2600 -210.8172 0.010 1502 +2800 -210.7847 0.010 1502 3000 -210.7510 0.010 2883 -3200 -210.7244 0.010 2883 -3400 -210.7006 0.010 2883 +3200 -210.7243 0.010 2883 +3400 -210.7005 0.010 2883 3600 -210.6993 0.010 2883 -3800 -210.6779 0.010 2883 +3800 -210.6778 0.010 2883 4000 -210.6775 0.010 2883 -4200 -210.6505 0.010 2883 -4400 -210.6306 0.010 2883 -4600 -210.6208 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 -210.3398 0.010 2883 -6200 -210.3306 0.010 2883 -6400 -210.3132 0.010 2883 -6600 -210.3006 0.010 2883 -6800 -210.2825 0.010 2883 -7000 -210.2751 0.010 2883 -7200 -210.2750 0.010 2883 -7400 -210.2439 0.010 2883 -7600 -210.2321 0.010 2883 -7800 -210.1861 0.010 2883 -8000 -210.1813 0.010 2883 -8200 -210.1598 0.010 2883 -8400 -210.0779 0.010 2883 -8600 -210.0377 0.010 2883 -8800 -210.0091 0.010 2883 -9000 -209.9765 0.010 2883 -9200 -209.9496 0.010 2883 -9400 -209.9483 0.010 2883 +4200 -210.6761 0.010 2883 +4400 -210.6526 0.010 2883 +4600 -210.6396 0.010 2883 +4800 -210.6026 0.010 4692 +5000 -210.5940 0.010 4692 +5200 -210.5720 0.010 4692 +5400 -210.5439 0.010 5207 +5600 -210.5367 0.010 5207 +5800 -210.4677 0.010 5207 +6000 -210.4081 0.010 5812 +6200 -210.4005 0.010 5812 +6400 -210.3714 0.010 5812 +6600 -210.3661 0.010 5812 +6800 -210.3533 0.010 5812 +7000 -210.3450 0.010 5812 +7200 -210.3444 0.010 5812 +7400 -210.3290 0.010 5812 +7600 -210.3233 0.010 5812 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16134,33 +16155,55 @@ STARTING RUN Restarting from checkpoint... - generation 9406, seed 485829224, best lnL -209.948 + generation 7782, seed 1712897138, best lnL -210.273 gen current_lnL precision last_tree_imp -9406 -209.9481 0.010 2883 -9500 -209.9477 0.010 2883 -Reached termination condition! -last topological improvement at gen 2883 -Improvement over last 500 gen = 0.02876 +7782 -210.2728 0.010 5812 +7800 -210.2350 0.010 7789 +7900 -210.2072 0.010 7789 +8000 -210.1893 0.010 7789 +8100 -210.1876 0.010 7789 +8200 -210.1873 0.010 7789 +8300 -210.1804 0.010 7789 +8400 -210.1410 0.010 8330 +8500 -210.1401 0.010 8330 +8600 -210.1399 0.010 8330 +8700 -210.1255 0.010 8330 +8800 -210.1095 0.010 8330 +8900 -210.0995 0.010 8330 +9000 -210.0737 0.010 8330 +9100 -210.0727 0.010 8330 +9200 -210.0700 0.010 8330 +9300 -210.0493 0.010 8330 +9400 -210.0490 0.010 8330 +9500 -210.0359 0.010 8330 +9600 -210.0283 0.010 8330 +9700 -210.0265 0.010 8330 +9800 -210.0220 0.010 8330 +9900 -210.0208 0.010 8330 +10000 -210.0205 0.010 8330 + Optimizing parameters... improved 0.465 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.797, AG = 5.162, AT = 0.238, CG = 5.326, CT = 9.312, GT = 1.000 + AC = 2.629, AG = 4.659, AT = 0.043, CG = 4.795, CT = 9.000, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2398 0.3377 0.2128 0.2097 + (ACGT) 0.2406 0.3346 0.2128 0.2120 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 2.2351 + 3.0601 with an invariant (invariable) site category, proportion estimated - 0.2163 + 0.2876 Substitution rate categories under this model: rate proportion - 0.0000 0.2163 - 0.3198 0.1959 - 0.6779 0.1959 - 1.0749 0.1959 - 1.9274 0.1959 + 0.0000 0.2876 + 0.3939 0.1781 + 0.7348 0.1781 + 1.0828 0.1781 + 1.7885 0.1781 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -16171,24 +16214,31 @@ 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 : -209.9477 +Replicate 1 : -209.5559 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: 2.797 5.162 0.2379 5.326 9.312 1 0.240 0.338 0.213 0.210 2.235 0.216 +rep 1: 2.629 4.659 0.04268 4.795 9 1 0.241 0.335 0.213 0.212 3.060 0.288 Treelengths: TL -rep 1: 2.446 +rep 1: 2.409 Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/p.3diff.conf @@ -16392,14 +16442,6 @@ Optimizing branchlengths... improved 0.000 lnL 600 -13371.2064 0.402 0 700 -13371.0755 0.402 0 -800 -13370.9489 0.402 0 -900 -13370.7802 0.402 0 -1000 -13370.6791 0.402 0 -Optimization precision reduced - Optimizing parameters... improved 0.037 lnL - Optimizing branchlengths... improved 0.000 lnL -1100 -13370.5869 0.304 0 -1200 -13370.5240 0.304 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16522,16 +16564,15 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1252, seed 260969474, best lnL -13370.510 +Bootstrap rep 1 (of 1) generation 793, seed 1274993739, best lnL -13370.949 gen current_lnL precision last_tree_imp -1252 -13370.5103 0.304 0 -1300 -13370.5103 0.304 0 -1400 -13370.5063 0.304 0 -1500 -13370.4967 0.304 0 +793 -13370.9490 0.402 0 +800 -13370.9489 0.402 0 +900 -13370.7802 0.402 0 +1000 -13370.6791 0.402 0 Optimization precision reduced - Optimizing parameters... improved 0.015 lnL + Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL -1600 -13370.4816 0.206 0 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16539,46 +16580,46 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.598, AG = 2.495, AT = 1.197, CG = 1.197, CT = 4.134, GT = 1.000 + AC = 1.545, AG = 2.495, AT = 1.160, CG = 1.160, CT = 4.035, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3082 0.1811 0.3085 0.2021 + (ACGT) 0.3110 0.1818 0.3061 0.2010 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3642 + 0.3640 Substitution rate categories under this model: rate proportion 0.0119 0.2500 - 0.1545 0.2500 - 0.6894 0.2500 - 3.1441 0.2500 + 0.1544 0.2500 + 0.6892 0.2500 + 3.1446 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 = 2.624, AG = 4.245, AT = 0.821, CG = 4.245, CT = 2.624, GT = 1.000 + AC = 2.627, AG = 4.239, AT = 0.821, CG = 4.239, CT = 2.627, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2815 0.1769 0.1594 0.3822 + (ACGT) 0.2791 0.1777 0.1601 0.3830 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2458 + 0.2460 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0637 0.2500 - 0.4925 0.2500 - 3.4419 0.2500 + 0.0638 0.2500 + 0.4929 0.2500 + 3.4413 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 = 5.332, AT = 4.291, CG = 0.633, CT = 5.332, GT = 1.000 + AC = 1.000, AG = 5.382, AT = 4.304, CG = 0.635, CT = 5.382, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1554 0.3462 0.2765 0.2219 + (ACGT) 0.1555 0.3460 0.2769 0.2216 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1103 + 4.1101 with an invariant (invariable) site category, proportion estimated 0.0486 Substitution rate categories under this model: @@ -16604,25 +16645,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.4777 (TERMINATED PREMATURELY) +Replicate 1 : -13370.5950 (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: 1.598 2.495 1.197 1.197 4.134 1 0.308 0.181 0.309 0.202 0.364 +rep 1: 1.545 2.495 1.16 1.16 4.035 1 0.311 0.182 0.306 0.201 0.364 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: 2.624 4.245 0.821 4.245 2.624 1 0.281 0.177 0.159 0.382 0.246 +rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.279 0.178 0.160 0.383 0.246 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 5.332 4.291 0.6327 5.332 1 0.155 0.346 0.276 0.222 4.110 0.049 +rep 1: 1 5.382 4.304 0.6346 5.382 1 0.156 0.346 0.277 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.762 0.530 0.287 2.183 +rep 1: 1.772 0.530 0.285 2.185 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -16921,9 +16962,6 @@ 0 -467.8365 0.010 0 100 -467.8012 0.010 0 200 -467.7834 0.010 0 -300 -467.7718 0.010 0 -400 -467.7465 0.010 0 -500 -467.7421 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17049,9 +17087,12 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 598, seed 132005112, best lnL -467.739 +Search rep 2 (of 5) generation 258, seed 1040889290, best lnL -467.772 gen current_lnL precision last_tree_imp -598 -467.7393 0.010 0 +258 -467.7725 0.010 0 +300 -467.7718 0.010 0 +400 -467.7465 0.010 0 +500 -467.7421 0.010 0 600 -467.7393 0.010 0 700 -467.7358 0.010 0 800 -467.7328 0.010 0 @@ -17083,146 +17124,22 @@ 3400 -467.7029 0.010 0 3500 -467.7024 0.010 0 3600 -467.7020 0.010 0 -3700 -467.7017 0.010 0 -3800 -467.7016 0.010 0 -3900 -467.7013 0.010 0 -4000 -467.7004 0.010 0 -4100 -467.7001 0.010 0 -4200 -467.7001 0.010 0 -4300 -467.6998 0.010 0 -4400 -467.6997 0.010 0 -4500 -467.6997 0.010 0 -Reached termination condition! -last topological improvement at gen 0 -Improvement over last 500 gen = 0.00073 -Current score = -467.6997 -Performing final optimizations... -pass 1 : -467.6997 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.6876 (branch= 0.0121 subset rates= 0.0000) -pass 3 : -467.6830 (branch= 0.0046 subset rates= 0.0000) -pass 4 : -467.6821 (branch= 0.0009 subset rates= 0.0000) -pass 5 : -467.6812 (branch= 0.0010 subset rates= 0.0000) -pass 6 : -467.6804 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -467.6795 (branch= 0.0010 subset rates= 0.0000) -pass 8 : -467.6791 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -467.6790 (branch= 0.0001 subset rates= 0.0000) -pass 10: -467.6786 (branch= 0.0002 subset rates= 0.0002) -pass 11: -467.6783 (branch= 0.0003 subset rates= 0.0000) -pass 12: -467.6783 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6782 (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 10 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 2.18 -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=1668858692 - -Initial ln Likelihood: -630.9240 -optimizing: starting branch lengths, subset rates... -pass 1:+ 146.355 (branch= 140.50 scale= 1.37 subset rates= 4.49) -pass 2:+ 13.169 (branch= 11.99 scale= 0.01 subset rates= 1.16) -pass 3:+ 3.305 (branch= 3.17 scale= 0.00 subset rates= 0.14) -pass 4:+ 0.250 (branch= 0.25 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.025 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8212 -gen current_lnL precision last_tree_imp -0 -467.8212 0.010 0 -100 -467.7945 0.010 0 -200 -467.7839 0.010 0 -300 -467.7682 0.010 0 -400 -467.7554 0.010 0 -500 -467.7485 0.010 0 -600 -467.7439 0.010 0 -700 -467.7412 0.010 0 -800 -467.7399 0.010 0 -900 -467.7389 0.010 0 -1000 -467.7339 0.010 0 -1100 -467.7305 0.010 0 -1200 -467.7272 0.010 0 -1300 -467.7265 0.010 0 -1400 -467.7225 0.010 0 -1500 -467.7188 0.010 0 -1600 -467.7177 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7173 +Current score = -467.7020 Performing final optimizations... -pass 1 : -467.7171 (branch= 0.0000 subset rates= 0.0003) -pass 2 : -467.7016 (branch= 0.0155 subset rates= 0.0000) -pass 3 : -467.6918 (branch= 0.0098 subset rates= 0.0000) -pass 4 : -467.6859 (branch= 0.0059 subset rates= 0.0000) -pass 5 : -467.6838 (branch= 0.0021 subset rates= 0.0000) -pass 6 : -467.6810 (branch= 0.0028 subset rates= 0.0000) -pass 7 : -467.6798 (branch= 0.0011 subset rates= 0.0001) -pass 8 : -467.6793 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -467.6789 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6787 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6786 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6786 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6785 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7020 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.6899 (branch= 0.0121 subset rates= 0.0000) +pass 3 : -467.6852 (branch= 0.0047 subset rates= 0.0000) +pass 4 : -467.6836 (branch= 0.0016 subset rates= 0.0000) +pass 5 : -467.6820 (branch= 0.0015 subset rates= 0.0000) +pass 6 : -467.6800 (branch= 0.0020 subset rates= 0.0000) +pass 7 : -467.6792 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -467.6788 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -467.6787 (branch= 0.0001 subset rates= 0.0000) +pass 10: -467.6786 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 12: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6785 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6785 Time used so far = 0 hours, 0 minutes and 12 seconds @@ -17253,11 +17170,11 @@ no rate heterogeneity Subset rate multipliers: - 0.78 1.48 2.19 + 0.79 1.48 2.17 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 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!*** @@ -17265,14 +17182,13 @@ ####################################################### -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 : -467.6789 -Replicate 2 : -467.6782 (best) (same topology as 1) -Replicate 3 : -467.6785 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -467.6785 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17288,8 +17204,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.842 0.787 1.483 2.162 -rep 2: 3.842 0.787 1.478 2.180 -rep 3: 3.845 0.785 1.484 2.188 +rep 2: 3.840 0.788 1.476 2.172 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -17483,125 +17398,6 @@ 2700 -477.2420 0.010 555 2800 -477.2417 0.010 555 2900 -477.2414 0.010 555 -3000 -477.2413 0.010 555 -3100 -477.2407 0.010 555 -3200 -477.2401 0.010 555 -3300 -477.2400 0.010 555 -3400 -477.2398 0.010 555 -3500 -477.2393 0.010 555 -3600 -477.2392 0.010 555 -3700 -477.2392 0.010 555 -Reached termination condition! -last topological improvement at gen 555 -Improvement over last 500 gen = 0.00083 -Current score = -477.2392 -Performing final optimizations... -pass 1 : -477.2355 (branch= 0.0000 subset rates= 0.0037) -pass 2 : -477.2214 (branch= 0.0125 subset rates= 0.0017) -pass 3 : -477.2168 (branch= 0.0045 subset rates= 0.0000) -pass 4 : -477.2152 (branch= 0.0016 subset rates= 0.0000) -pass 5 : -477.2143 (branch= 0.0009 subset rates= 0.0000) -pass 6 : -477.2136 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -477.2130 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -477.2126 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -477.2125 (branch= 0.0001 subset rates= 0.0000) -pass 10: -477.2124 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2123 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2123 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2123 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.2123 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.2123 -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 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 2.64 -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=1515469919 - -Initial ln Likelihood: -688.6863 -optimizing: starting branch lengths, subset rates... -pass 1:+ 189.280 (branch= 176.40 scale= 2.54 subset rates= 10.33) -pass 2:+ 14.395 (branch= 10.07 scale= 0.00 subset rates= 4.33) -pass 3:+ 6.235 (branch= 4.71 scale= 0.00 subset rates= 1.52) -pass 4:+ 0.885 (branch= 0.55 scale= 0.01 subset rates= 0.33) -pass 5:+ 0.013 (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: -477.8776 -gen current_lnL precision last_tree_imp -0 -477.8776 0.010 0 -100 -477.7704 0.010 60 -200 -477.7486 0.010 60 -300 -477.5965 0.010 283 -400 -477.5567 0.010 306 -500 -477.5376 0.010 306 -600 -477.5187 0.010 306 -700 -477.5124 0.010 306 -800 -477.5083 0.010 306 -900 -477.5025 0.010 306 -1000 -477.5003 0.010 306 -1100 -477.4983 0.010 306 -1200 -477.4974 0.010 306 -1300 -477.4938 0.010 306 -1400 -477.4894 0.010 306 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17727,79 +17523,39 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1493, seed 1075098630, best lnL -477.489 +Search rep 1 (of 5) generation 2927, seed 1115276762, best lnL -477.241 gen current_lnL precision last_tree_imp -1493 -477.4888 0.010 306 -1500 -477.4888 0.010 306 -1600 -477.4870 0.010 306 -1700 -477.4845 0.010 306 -1800 -477.4841 0.010 306 -1900 -477.4821 0.010 306 -2000 -477.4818 0.010 306 -2100 -477.4817 0.010 306 -2200 -477.4790 0.010 306 -2300 -477.4783 0.010 306 -2400 -477.4762 0.010 306 -2500 -477.4754 0.010 306 -2600 -477.4751 0.010 306 -2700 -477.4751 0.010 306 -2800 -477.4750 0.010 306 -2900 -477.4740 0.010 306 -3000 -477.4726 0.010 306 -3100 -477.4719 0.010 306 -3200 -477.4714 0.010 306 -3300 -477.4714 0.010 306 -3400 -477.4701 0.010 306 -3500 -477.4699 0.010 306 -3600 -477.4698 0.010 306 -3700 -477.4672 0.010 306 -3800 -477.4666 0.010 306 -3900 -477.4666 0.010 306 -4000 -477.4641 0.010 306 -4100 -477.4635 0.010 306 -4200 -477.4634 0.010 306 -4300 -477.4634 0.010 306 -4400 -477.4622 0.010 306 -4500 -477.4621 0.010 306 -4600 -477.4612 0.010 306 -4700 -477.4611 0.010 306 -4800 -477.4610 0.010 306 -4900 -477.4607 0.010 306 -5000 -477.4604 0.010 306 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -5100 -477.4596 0.010 306 -5200 -477.4590 0.010 306 -5300 -477.4587 0.010 306 -5400 -477.4583 0.010 306 -5500 -477.4582 0.010 306 -5600 -477.4578 0.010 306 -5700 -477.4578 0.010 306 -5800 -477.4576 0.010 306 -5900 -477.4576 0.010 306 +2927 -477.2413 0.010 555 +3000 -477.2413 0.010 555 +3100 -477.2407 0.010 555 +3200 -477.2401 0.010 555 +3300 -477.2400 0.010 555 +3400 -477.2398 0.010 555 +3500 -477.2393 0.010 555 +3600 -477.2392 0.010 555 +3700 -477.2392 0.010 555 Reached termination condition! -last topological improvement at gen 306 -Improvement over last 500 gen = 0.00072 -Current score = -477.4576 +last topological improvement at gen 555 +Improvement over last 500 gen = 0.00083 +Current score = -477.2392 Performing final optimizations... -pass 1 : -477.4576 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -477.4494 (branch= 0.0082 subset rates= 0.0000) -pass 3 : -477.4389 (branch= 0.0104 subset rates= 0.0000) -pass 4 : -477.4389 (branch= 0.0000 subset rates= 0.0000) -pass 5 : -477.4356 (branch= 0.0032 subset rates= 0.0002) -pass 6 : -477.4345 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -477.4339 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -477.4325 (branch= 0.0004 subset rates= 0.0010) -pass 9 : -477.4320 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.4318 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0001) -pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2355 (branch= 0.0000 subset rates= 0.0037) +pass 2 : -477.2214 (branch= 0.0125 subset rates= 0.0017) +pass 3 : -477.2168 (branch= 0.0045 subset rates= 0.0000) +pass 4 : -477.2152 (branch= 0.0016 subset rates= 0.0000) +pass 5 : -477.2143 (branch= 0.0009 subset rates= 0.0000) +pass 6 : -477.2136 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -477.2130 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -477.2126 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -477.2125 (branch= 0.0001 subset rates= 0.0000) +pass 10: -477.2124 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2123 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2123 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2123 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.2123 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4316 -Time used so far = 0 hours, 0 minutes and 10 seconds +Final score = -477.2123 +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17827,13 +17583,13 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.74 + 0.64 1.90 2.64 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 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 @@ -17862,53 +17618,68 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=1516973561 +Starting with seed=1515469919 -Initial ln Likelihood: -690.1205 +Initial ln Likelihood: -688.6863 optimizing: starting branch lengths, subset rates... -pass 1:+ 190.188 (branch= 179.64 scale= 0.85 subset rates= 9.70) -pass 2:+ 14.015 (branch= 10.19 scale= 0.00 subset rates= 3.83) -pass 3:+ 4.783 (branch= 3.43 scale= 0.02 subset rates= 1.34) -pass 4:+ 1.212 (branch= 0.86 scale= 0.00 subset rates= 0.36) -pass 5:+ 1.203 (branch= 1.18 scale= 0.00 subset rates= 0.02) -pass 6:+ 0.714 (branch= 0.71 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.163 (branch= 0.16 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8436 +pass 1:+ 189.280 (branch= 176.40 scale= 2.54 subset rates= 10.33) +pass 2:+ 14.395 (branch= 10.07 scale= 0.00 subset rates= 4.33) +pass 3:+ 6.235 (branch= 4.71 scale= 0.00 subset rates= 1.52) +pass 4:+ 0.885 (branch= 0.55 scale= 0.01 subset rates= 0.33) +pass 5:+ 0.013 (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: -477.8776 gen current_lnL precision last_tree_imp -0 -477.8436 0.010 0 -100 -477.8199 0.010 0 -200 -477.7455 0.010 166 -300 -477.7343 0.010 166 -400 -477.7206 0.010 166 -500 -477.7157 0.010 166 -600 -477.7086 0.010 166 -700 -477.7016 0.010 166 -800 -477.6991 0.010 166 -900 -477.6956 0.010 166 -1000 -477.5237 0.010 935 -1100 -477.5163 0.010 935 +0 -477.8776 0.010 0 +100 -477.7704 0.010 60 +200 -477.7486 0.010 60 +300 -477.5965 0.010 283 +400 -477.5567 0.010 306 +500 -477.5376 0.010 306 +600 -477.5187 0.010 306 +700 -477.5124 0.010 306 +800 -477.5083 0.010 306 +900 -477.5025 0.010 306 +1000 -477.5003 0.010 306 +1100 -477.4983 0.010 306 +1200 -477.4974 0.010 306 +1300 -477.4938 0.010 306 +1400 -477.4894 0.010 306 +1500 -477.4888 0.010 306 +1600 -477.4870 0.010 306 +1700 -477.4845 0.010 306 +1800 -477.4841 0.010 306 +1900 -477.4821 0.010 306 +2000 -477.4818 0.010 306 +2100 -477.4817 0.010 306 +2200 -477.4790 0.010 306 +2300 -477.4783 0.010 306 +2400 -477.4762 0.010 306 +2500 -477.4754 0.010 306 +2600 -477.4751 0.010 306 +2700 -477.4751 0.010 306 +2800 -477.4750 0.010 306 +2900 -477.4740 0.010 306 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.5160 +Current score = -477.4726 Performing final optimizations... -pass 1 : -477.5063 (branch= 0.0052 subset rates= 0.0045) -pass 2 : -477.4710 (branch= 0.0335 subset rates= 0.0018) -pass 3 : -477.4524 (branch= 0.0186 subset rates= 0.0000) -pass 4 : -477.4458 (branch= 0.0066 subset rates= 0.0000) -pass 5 : -477.4395 (branch= 0.0062 subset rates= 0.0000) -pass 6 : -477.4356 (branch= 0.0040 subset rates= 0.0000) -pass 7 : -477.4339 (branch= 0.0017 subset rates= 0.0000) -pass 8 : -477.4327 (branch= 0.0012 subset rates= 0.0000) -pass 9 : -477.4323 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.4320 (branch= 0.0003 subset rates= 0.0000) -pass 11: -477.4318 (branch= 0.0002 subset rates= 0.0000) -pass 12: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4317 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.4726 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.4585 (branch= 0.0128 subset rates= 0.0014) +pass 3 : -477.4471 (branch= 0.0113 subset rates= 0.0000) +pass 4 : -477.4397 (branch= 0.0074 subset rates= 0.0000) +pass 5 : -477.4373 (branch= 0.0024 subset rates= 0.0000) +pass 6 : -477.4349 (branch= 0.0023 subset rates= 0.0000) +pass 7 : -477.4339 (branch= 0.0011 subset rates= 0.0000) +pass 8 : -477.4329 (branch= 0.0009 subset rates= 0.0000) +pass 9 : -477.4323 (branch= 0.0004 subset rates= 0.0002) +pass 10: -477.4321 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.4320 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4320 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.4320 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4319 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4319 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4317 +Final score = -477.4319 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17937,11 +17708,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.75 + 0.63 1.91 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 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!*** @@ -17949,14 +17720,13 @@ ####################################################### -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 : -477.2123 (best) -Replicate 2 : -477.4316 -Replicate 3 : -477.4317 (same topology as 2) (TERMINATED PREMATURELY) +Replicate 2 : -477.4319 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17972,8 +17742,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.673 0.642 1.904 2.637 -rep 2: 4.928 0.632 1.913 2.742 -rep 3: 4.929 0.632 1.911 2.751 +rep 2: 4.925 0.633 1.907 2.740 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### @@ -18176,104 +17945,6 @@ 3300 -425.5849 0.010 365 3400 -425.5842 0.010 365 3500 -425.5842 0.010 365 -3600 -425.5840 0.010 365 -3700 -425.5839 0.010 365 -3800 -425.5838 0.010 365 -3900 -425.5838 0.010 365 -Reached termination condition! -last topological improvement at gen 365 -Improvement over last 500 gen = 0.00044 -Current score = -425.5838 -Performing final optimizations... -pass 1 : -425.5804 (branch= 0.0000 subset rates= 0.0033) -pass 2 : -425.5612 (branch= 0.0144 subset rates= 0.0048) -pass 3 : -425.5523 (branch= 0.0070 subset rates= 0.0019) -pass 4 : -425.5516 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -425.5509 (branch= 0.0007 subset rates= 0.0000) -pass 6 : -425.5505 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -425.5501 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5496 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -425.5495 (branch= 0.0002 subset rates= 0.0000) -pass 10: -425.5494 (branch= 0.0000 subset rates= 0.0000) -pass 11: -425.5494 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.5494 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5494 (branch= 0.0000 subset rates= 0.0000) -pass 14: -425.5494 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -425.5494 -Time used so far = 0 hours, 0 minutes and 4 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: - 0.87 1.53 1.14 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 10 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=222492842 - -Initial ln Likelihood: -586.0233 -optimizing: starting branch lengths, subset rates... -pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) -pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) -pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) -pass 4:+ 1.686 (branch= 1.66 scale= 0.02 subset rates= 0.01) -pass 5:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.031 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 9:+ 0.043 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass10:+ 0.052 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass11:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) -pass12:+ 0.042 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass13:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass14:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.2275 -gen current_lnL precision last_tree_imp -0 -439.2275 0.010 0 -100 -428.8676 0.010 98 -200 -428.0499 0.010 164 -300 -427.6003 0.010 249 -400 -427.5648 0.010 249 -500 -427.4911 0.010 499 -600 -427.3864 0.010 511 -700 -425.7188 0.010 668 -800 -425.6951 0.010 722 -900 -425.6795 0.010 722 -1000 -425.6689 0.010 722 -1100 -425.6640 0.010 722 -1200 -425.6430 0.010 722 -1300 -425.6381 0.010 722 -1400 -425.6345 0.010 722 -1500 -425.6341 0.010 722 -1600 -425.6274 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18402,50 +18073,35 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1695, seed 753238599, best lnL -425.624 +Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3581, seed 14260827, best lnL -425.584 gen current_lnL precision last_tree_imp -1695 -425.6239 0.010 722 -1700 -425.6239 0.010 722 -1800 -425.6235 0.010 722 -1900 -425.6225 0.010 722 -2000 -425.6202 0.010 722 -2100 -425.6196 0.010 722 -2200 -425.6174 0.010 722 -2300 -425.6146 0.010 722 -2400 -425.6135 0.010 722 -2500 -425.6104 0.010 722 -2600 -425.6099 0.010 722 -2700 -425.6088 0.010 722 -2800 -425.6077 0.010 722 -2900 -425.6073 0.010 722 -3000 -425.6059 0.010 722 -3100 -425.6056 0.010 722 -3200 -425.6055 0.010 722 -3300 -425.6051 0.010 722 -3400 -425.6049 0.010 722 -3500 -425.6048 0.010 722 -3600 -425.6048 0.010 722 +3581 -425.5840 0.010 365 +3600 -425.5840 0.010 365 +3700 -425.5839 0.010 365 +3800 -425.5838 0.010 365 +3900 -425.5838 0.010 365 Reached termination condition! -last topological improvement at gen 722 -Improvement over last 500 gen = 0.00084 -Current score = -425.6048 +last topological improvement at gen 365 +Improvement over last 500 gen = 0.00044 +Current score = -425.5838 Performing final optimizations... -pass 1 : -425.5796 (branch= 0.0000 subset rates= 0.0251) -pass 2 : -425.5577 (branch= 0.0188 subset rates= 0.0031) -pass 3 : -425.5535 (branch= 0.0041 subset rates= 0.0000) -pass 4 : -425.5523 (branch= 0.0012 subset rates= 0.0000) -pass 5 : -425.5511 (branch= 0.0012 subset rates= 0.0000) -pass 6 : -425.5504 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -425.5497 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -425.5496 (branch= 0.0001 subset rates= 0.0000) -pass 9 : -425.5493 (branch= 0.0002 subset rates= 0.0000) -pass 10: -425.5493 (branch= 0.0000 subset rates= 0.0000) -pass 11: -425.5490 (branch= 0.0000 subset rates= 0.0002) -pass 12: -425.5490 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0004) +pass 1 : -425.5773 (branch= 0.0000 subset rates= 0.0065) +pass 2 : -425.5604 (branch= 0.0144 subset rates= 0.0025) +pass 3 : -425.5534 (branch= 0.0070 subset rates= 0.0000) +pass 4 : -425.5508 (branch= 0.0007 subset rates= 0.0018) +pass 5 : -425.5505 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -425.5498 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -425.5493 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.5489 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0002 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 14: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5486 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18475,80 +18131,85 @@ Subset rate multipliers: 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. + 10 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=2129292874 +Starting with seed=222492842 -Initial ln Likelihood: -588.2493 +Initial ln Likelihood: -586.0233 optimizing: starting branch lengths, subset rates... -pass 1:+ 141.030 (branch= 140.49 scale= 0.38 subset rates= 0.17) -pass 2:+ 6.536 (branch= 6.52 scale= 0.00 subset rates= 0.02) -pass 3:+ 1.051 (branch= 1.03 scale= 0.00 subset rates= 0.02) -pass 4:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.5713 +pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) +pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) +pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) +pass 4:+ 1.686 (branch= 1.66 scale= 0.02 subset rates= 0.01) +pass 5:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.031 (branch= 0.03 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 9:+ 0.043 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass10:+ 0.052 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass11:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass12:+ 0.042 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass13:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass14:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.2275 gen current_lnL precision last_tree_imp -0 -439.5713 0.010 0 -100 -431.1390 0.010 95 -200 -428.6584 0.010 167 -300 -427.6515 0.010 295 -400 -427.2440 0.010 295 -500 -427.2139 0.010 295 -600 -427.1679 0.010 568 -700 -427.1487 0.010 568 -800 -425.4818 0.010 762 -900 -425.4264 0.010 803 -1000 -425.4085 0.010 803 -1100 -425.4058 0.010 803 -1200 -425.3915 0.010 803 -1300 -425.3912 0.010 803 -1400 -425.3886 0.010 803 -1500 -425.3865 0.010 803 -1600 -425.3820 0.010 803 -1700 -425.3760 0.010 803 -1800 -425.3758 0.010 803 -1900 -425.3750 0.010 803 -2000 -425.3712 0.010 803 -2100 -425.3702 0.010 803 -2200 -425.3666 0.010 803 -2300 -425.3654 0.010 803 -2400 -425.3635 0.010 803 -2500 -425.3629 0.010 803 -2600 -425.3622 0.010 803 -2700 -425.3619 0.010 803 -2800 -425.3613 0.010 803 -2900 -425.3592 0.010 803 -3000 -425.3583 0.010 803 -3100 -425.3581 0.010 803 -3200 -425.3571 0.010 803 -3300 -425.3567 0.010 803 -3400 -425.3566 0.010 803 -3500 -425.3562 0.010 803 -3600 -425.3554 0.010 803 -3700 -425.3549 0.010 803 -3800 -425.3546 0.010 803 +0 -439.2275 0.010 0 +100 -428.8676 0.010 98 +200 -428.0499 0.010 164 +300 -427.6003 0.010 249 +400 -427.5648 0.010 249 +500 -427.4911 0.010 499 +600 -427.3864 0.010 511 +700 -425.7188 0.010 668 +800 -425.6951 0.010 722 +900 -425.6795 0.010 722 +1000 -425.6689 0.010 722 +1100 -425.6640 0.010 722 +1200 -425.6430 0.010 722 +1300 -425.6381 0.010 722 +1400 -425.6345 0.010 722 +1500 -425.6341 0.010 722 +1600 -425.6274 0.010 722 +1700 -425.6239 0.010 722 +1800 -425.6235 0.010 722 +1900 -425.6225 0.010 722 +2000 -425.6202 0.010 722 +2100 -425.6196 0.010 722 +2200 -425.6174 0.010 722 +2300 -425.6146 0.010 722 +2400 -425.6135 0.010 722 +2500 -425.6104 0.010 722 +2600 -425.6099 0.010 722 +2700 -425.6088 0.010 722 +2800 -425.6077 0.010 722 +2900 -425.6073 0.010 722 +3000 -425.6059 0.010 722 +3100 -425.6056 0.010 722 +3200 -425.6055 0.010 722 +3300 -425.6051 0.010 722 +3400 -425.6049 0.010 722 +3500 -425.6048 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.3537 +Current score = -425.6048 Performing final optimizations... -pass 1 : -425.3488 (branch= 0.0000 subset rates= 0.0049) -pass 2 : -425.3319 (branch= 0.0164 subset rates= 0.0005) -pass 3 : -425.3251 (branch= 0.0069 subset rates= 0.0000) -pass 4 : -425.3224 (branch= 0.0026 subset rates= 0.0000) -pass 5 : -425.3224 (branch= 0.0000 subset rates= 0.0000) -pass 6 : -425.3224 (branch= 0.0000 subset rates= 0.0000) -pass 7 : -425.3210 (branch= 0.0014 subset rates= 0.0000) -pass 8 : -425.3204 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -425.3203 (branch= 0.0000 subset rates= 0.0000) -pass 10: -425.3202 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.3202 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.3202 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.3202 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.5914 (branch= 0.0000 subset rates= 0.0135) +pass 2 : -425.5583 (branch= 0.0188 subset rates= 0.0143) +pass 3 : -425.5530 (branch= 0.0053 subset rates= 0.0000) +pass 4 : -425.5530 (branch= 0.0000 subset rates= 0.0000) +pass 5 : -425.5506 (branch= 0.0014 subset rates= 0.0009) +pass 6 : -425.5499 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -425.5492 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -425.5491 (branch= 0.0001 subset rates= 0.0000) +pass 9 : -425.5488 (branch= 0.0003 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.3202 +Final score = -425.5486 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18577,11 +18238,11 @@ no rate heterogeneity Subset rate multipliers: - 0.86 1.54 1.15 + 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) 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!*** @@ -18589,14 +18250,13 @@ ####################################################### -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 : -425.5494 -Replicate 2 : -425.5486 -Replicate 3 : -425.3202 (best) (TERMINATED PREMATURELY) +Replicate 1 : -425.5486 (best) +Replicate 2 : -425.5486 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18611,13 +18271,11 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.037 0.868 1.525 1.137 -rep 2: 3.039 0.869 1.528 1.121 -rep 3: 2.979 0.865 1.537 1.152 +rep 1: 3.038 0.868 1.532 1.122 +rep 2: 3.037 0.867 1.534 1.122 -Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf @@ -18810,123 +18468,6 @@ 2700 -473.9787 0.010 653 2800 -473.9776 0.010 653 2900 -473.9773 0.010 653 -3000 -473.9772 0.010 653 -3100 -473.9768 0.010 653 -3200 -473.9766 0.010 653 -3300 -473.9763 0.010 653 -3400 -473.9759 0.010 653 -3500 -473.9758 0.010 653 -3600 -473.9758 0.010 653 -3700 -473.9756 0.010 653 -Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00096 -Current score = -473.9756 -Performing final optimizations... -pass 1 : -473.9739 (branch= 0.0001 subset rates= 0.0015) -pass 2 : -473.9556 (branch= 0.0183 subset rates= 0.0000) -pass 3 : -473.9556 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9537 (branch= 0.0009 subset rates= 0.0011) -pass 5 : -473.9533 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -473.9523 (branch= 0.0004 subset rates= 0.0006) -pass 7 : -473.9517 (branch= 0.0005 subset rates= 0.0000) -pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0001) -pass 9 : -473.9509 (branch= 0.0003 subset rates= 0.0000) -pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -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 2.06 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=74284197 - -Initial ln Likelihood: -646.1143 -optimizing: starting branch lengths, subset rates... -pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) -pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) -pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) -pass 4:+ 2.491 (branch= 1.89 scale= 0.00 subset rates= 0.60) -pass 5:+ 0.683 (branch= 0.62 scale= 0.02 subset rates= 0.05) -pass 6:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8187 -gen current_lnL precision last_tree_imp -0 -474.8187 0.010 0 -100 -474.7244 0.010 55 -200 -474.7116 0.010 55 -300 -474.6999 0.010 55 -400 -474.5534 0.010 345 -500 -474.2023 0.010 476 -600 -474.1846 0.010 476 -700 -474.1656 0.010 476 -800 -474.0668 0.010 780 -900 -474.0383 0.010 814 -1000 -474.0330 0.010 814 -1100 -474.0261 0.010 814 -1200 -474.0208 0.010 814 -1300 -474.0176 0.010 814 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -19052,178 +18593,37 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1352, seed 1326616724, best lnL -474.015 +Search rep 1 (of 5) generation 2978, seed 517645293, best lnL -473.977 gen current_lnL precision last_tree_imp -1352 -474.0149 0.010 814 -1400 -474.0122 0.010 814 -1500 -474.0099 0.010 814 -1600 -474.0090 0.010 814 -1700 -474.0057 0.010 814 -1800 -474.0047 0.010 814 -1900 -474.0042 0.010 814 -2000 -474.0038 0.010 814 -2100 -474.0027 0.010 814 -2200 -474.0019 0.010 814 -2300 -474.0014 0.010 814 -2400 -474.0003 0.010 814 -2500 -473.9997 0.010 814 -2600 -473.9994 0.010 814 -2700 -473.9994 0.010 814 -2800 -473.9992 0.010 814 -2900 -473.9990 0.010 814 -3000 -473.9990 0.010 814 -Reached termination condition! -last topological improvement at gen 814 -Improvement over last 500 gen = 0.00071 -Current score = -473.9990 -Performing final optimizations... -pass 1 : -473.9820 (branch= 0.0079 subset rates= 0.0091) -pass 2 : -473.9629 (branch= 0.0160 subset rates= 0.0031) -pass 3 : -473.9577 (branch= 0.0048 subset rates= 0.0005) -pass 4 : -473.9551 (branch= 0.0026 subset rates= 0.0000) -pass 5 : -473.9547 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -473.9534 (branch= 0.0013 subset rates= 0.0000) -pass 7 : -473.9518 (branch= 0.0010 subset rates= 0.0006) -pass 8 : -473.9512 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -473.9511 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9510 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9509 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9509 -Time used so far = 0 hours, 0 minutes and 7 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.59 2.07 2.79 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 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 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=286368817 - -Initial ln Likelihood: -652.0823 -optimizing: starting branch lengths, subset rates... -pass 1:+ 160.614 (branch= 149.48 scale= 0.59 subset rates= 10.55) -pass 2:+ 10.707 (branch= 5.57 scale= 0.00 subset rates= 5.13) -pass 3:+ 4.869 (branch= 2.96 scale= 0.01 subset rates= 1.89) -pass 4:+ 0.897 (branch= 0.26 scale= 0.00 subset rates= 0.64) -pass 5:+ 0.114 (branch= 0.06 scale= 0.01 subset rates= 0.04) -pass 6:+ 0.020 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.021 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8400 -gen current_lnL precision last_tree_imp -0 -474.8400 0.010 0 -100 -474.7992 0.010 0 -200 -474.7684 0.010 0 -300 -474.6840 0.010 284 -400 -474.6659 0.010 284 -500 -474.6476 0.010 404 -600 -474.0462 0.010 593 -700 -474.0347 0.010 593 -800 -474.0228 0.010 593 -900 -474.0207 0.010 593 -1000 -474.0128 0.010 593 -1100 -474.0062 0.010 593 -1200 -474.0051 0.010 593 -1300 -474.0033 0.010 593 -1400 -473.9980 0.010 593 -1500 -473.9948 0.010 593 -1600 -473.9930 0.010 593 -1700 -473.9919 0.010 593 -1800 -473.9910 0.010 593 -1900 -473.9903 0.010 593 -2000 -473.9899 0.010 593 -2100 -473.9897 0.010 593 -2200 -473.9887 0.010 593 -2300 -473.9848 0.010 593 -2400 -473.9845 0.010 593 -2500 -473.9842 0.010 593 -2600 -473.9836 0.010 593 -2700 -473.9836 0.010 593 -2800 -473.9836 0.010 593 -2900 -473.9832 0.010 593 -3000 -473.9831 0.010 593 -3100 -473.9830 0.010 593 +2978 -473.9772 0.010 653 +3000 -473.9772 0.010 653 +3100 -473.9768 0.010 653 +3200 -473.9766 0.010 653 +3300 -473.9763 0.010 653 +3400 -473.9759 0.010 653 +3500 -473.9758 0.010 653 +3600 -473.9758 0.010 653 +3700 -473.9756 0.010 653 Reached termination condition! -last topological improvement at gen 593 -Improvement over last 500 gen = 0.00063 -Current score = -473.9830 +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00096 +Current score = -473.9756 Performing final optimizations... -pass 1 : -473.9821 (branch= 0.0000 subset rates= 0.0009) -pass 2 : -473.9625 (branch= 0.0167 subset rates= 0.0028) -pass 3 : -473.9599 (branch= 0.0027 subset rates= 0.0000) -pass 4 : -473.9566 (branch= 0.0033 subset rates= 0.0000) -pass 5 : -473.9539 (branch= 0.0027 subset rates= 0.0000) -pass 6 : -473.9525 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -473.9520 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -473.9512 (branch= 0.0002 subset rates= 0.0006) +pass 1 : -473.9739 (branch= 0.0001 subset rates= 0.0015) +pass 2 : -473.9556 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -473.9556 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9537 (branch= 0.0009 subset rates= 0.0011) +pass 5 : -473.9533 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -473.9523 (branch= 0.0004 subset rates= 0.0006) +pass 7 : -473.9517 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0001) pass 9 : -473.9509 (branch= 0.0003 subset rates= 0.0000) -pass 10: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9507 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9507 -Time used so far = 0 hours, 0 minutes and 11 seconds +Final score = -473.9508 +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19251,13 +18651,13 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.80 + 0.59 2.06 2.80 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 @@ -19286,42 +18686,62 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=2070583773 +Starting with seed=74284197 -Initial ln Likelihood: -607.1918 +Initial ln Likelihood: -646.1143 optimizing: starting branch lengths, subset rates... -pass 1:+ 114.195 (branch= 103.79 scale= 0.33 subset rates= 10.08) -pass 2:+ 12.135 (branch= 7.64 scale= 0.00 subset rates= 4.49) -pass 3:+ 4.696 (branch= 3.09 scale= 0.00 subset rates= 1.61) -pass 4:+ 1.072 (branch= 0.48 scale= 0.02 subset rates= 0.57) -pass 5:+ 0.184 (branch= 0.15 scale= 0.00 subset rates= 0.04) -pass 6:+ 0.054 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.014 (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: -474.8415 +pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) +pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) +pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) +pass 4:+ 2.491 (branch= 1.89 scale= 0.00 subset rates= 0.60) +pass 5:+ 0.683 (branch= 0.62 scale= 0.02 subset rates= 0.05) +pass 6:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8187 gen current_lnL precision last_tree_imp -0 -474.8415 0.010 0 -100 -474.1305 0.010 82 -200 -474.1118 0.010 82 +0 -474.8187 0.010 0 +100 -474.7244 0.010 55 +200 -474.7116 0.010 55 +300 -474.6999 0.010 55 +400 -474.5534 0.010 345 +500 -474.2023 0.010 476 +600 -474.1846 0.010 476 +700 -474.1656 0.010 476 +800 -474.0668 0.010 780 +900 -474.0383 0.010 814 +1000 -474.0330 0.010 814 +1100 -474.0261 0.010 814 +1200 -474.0208 0.010 814 +1300 -474.0176 0.010 814 +1400 -474.0122 0.010 814 +1500 -474.0099 0.010 814 +1600 -474.0090 0.010 814 +1700 -474.0057 0.010 814 +1800 -474.0047 0.010 814 +1900 -474.0042 0.010 814 +2000 -474.0038 0.010 814 +2100 -474.0027 0.010 814 +2200 -474.0019 0.010 814 +2300 -474.0014 0.010 814 +2400 -474.0003 0.010 814 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.0337 +Current score = -473.9998 Performing final optimizations... -pass 1 : -474.0127 (branch= 0.0187 subset rates= 0.0023) -pass 2 : -473.9833 (branch= 0.0294 subset rates= 0.0000) -pass 3 : -473.9670 (branch= 0.0162 subset rates= 0.0000) -pass 4 : -473.9567 (branch= 0.0100 subset rates= 0.0003) -pass 5 : -473.9516 (branch= 0.0052 subset rates= 0.0000) -pass 6 : -473.9498 (branch= 0.0017 subset rates= 0.0000) -pass 7 : -473.9492 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -473.9487 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -473.9485 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9484 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9484 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9484 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9483 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9483 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9869 (branch= 0.0079 subset rates= 0.0051) +pass 2 : -473.9626 (branch= 0.0189 subset rates= 0.0054) +pass 3 : -473.9578 (branch= 0.0025 subset rates= 0.0024) +pass 4 : -473.9552 (branch= 0.0025 subset rates= 0.0000) +pass 5 : -473.9542 (branch= 0.0011 subset rates= 0.0000) +pass 6 : -473.9532 (branch= 0.0009 subset rates= 0.0000) +pass 7 : -473.9518 (branch= 0.0011 subset rates= 0.0004) +pass 8 : -473.9512 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9483 +Final score = -473.9509 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -19350,11 +18770,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.80 + 0.59 2.06 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 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!*** @@ -19362,15 +18782,13 @@ ####################################################### -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 : -473.9508 -Replicate 2 : -473.9509 (same topology as 1) -Replicate 3 : -473.9507 (same topology as 1) -Replicate 4 : -473.9483 (best) (TERMINATED PREMATURELY) +Replicate 1 : -473.9508 (best) +Replicate 2 : -473.9509 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19386,11 +18804,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.349 0.589 2.064 2.801 -rep 2: 4.350 0.587 2.071 2.794 -rep 3: 4.349 0.588 2.065 2.804 -rep 4: 4.349 0.587 2.071 2.797 +rep 2: 4.350 0.587 2.065 2.815 -Saving final tree from best search rep (#4) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -19406,13 +18822,13 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j16 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j7 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/garli-2.1' Making install in src make[2]: Entering directory '/build/garli-2.1/src' make[3]: Entering directory '/build/garli-2.1/src' make[3]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/garli-2.1/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/garli-2.1/debian/tmp/usr/bin' /usr/bin/install -c Garli '/build/garli-2.1/debian/tmp/usr/bin' make install-exec-hook make[4]: Entering directory '/build/garli-2.1/src' @@ -19455,24 +18871,25 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-7_i386.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-7_all.deb'. -dpkg-deb: building package 'garli' in '../garli_2.1-7_i386.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_i386.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-7_i386.deb'. +dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-7_i386.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_i386.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-7_i386.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-7_i386.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-7_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) dpkg-genchanges: info: not including original source code in upload -I: copying local configuration +I: user script /srv/workspace/pbuilder/1084/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1084/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/29619 and its subdirectories -I: Current time: Thu Jun 13 19:55:12 -12 2024 -I: pbuilder-time-stamp: 1718351712 +I: removing directory /srv/workspace/pbuilder/1084 and its subdirectories +I: Current time: Sat May 13 15:42:40 +14 2023 +I: pbuilder-time-stamp: 1683942160