Diff of the two buildlogs: -- --- b1/build.log 2021-06-20 15:49:03.141937677 +0000 +++ b2/build.log 2021-06-20 15:56:24.417282652 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 20 03:42:17 -12 2021 -I: pbuilder-time-stamp: 1624203737 +I: Current time: Sun Jul 24 12:12:06 +14 2022 +I: pbuilder-time-stamp: 1658614326 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Sep 4 01:22:38 2018 -12 +gpgv: Signature made Wed Sep 5 03:22:38 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -27,136 +27,170 @@ dpkg-source: info: unpacking garli_2.1-3.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/10763/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/36717/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/36717/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/36717/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='348e3f82219f4a45b2f58605ed52b52e' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - 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='10763' - PS1='# ' - PS2='> ' + INVOCATION_ID=52fb6727316f47e5b8e843663dfe6676 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=36717 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.XbqUEVu3Pr/pbuilderrc_TpY4 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.XbqUEVu3Pr/b1 --logfile b1/build.log garli_2.1-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.XbqUEVu3Pr/pbuilderrc_Rc61 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.XbqUEVu3Pr/b2 --logfile b2/build.log garli_2.1-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 6 20:23 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/10763/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 24 12:12 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 11 04:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/36717/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -276,7 +310,7 @@ Get: 74 http://deb.debian.org/debian buster/main amd64 openmpi-bin amd64 3.1.3-11 [200 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libopenmpi-dev amd64 3.1.3-11 [974 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 ncl-tools amd64 2.1.21+git20180827.c71b264-2 [197 kB] -Fetched 31.5 MB in 0s (75.2 MB/s) +Fetched 31.5 MB in 1s (59.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -607,7 +641,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-3 dpkg-buildpackage: info: source distribution unstable @@ -670,8 +704,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -750,7 +784,7 @@ config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build - make -j15 + make -j16 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' @@ -771,13 +805,13 @@ 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:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); ^~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:20: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(modName, "model%d", modelNum); @@ -801,6 +835,10 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': +datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf(inf, "%d %d", &num_taxa, &num_chars); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] @@ -863,42 +901,6 @@ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': -datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf(inf, "%d %d", &num_taxa, &num_chars); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from population.cpp:45: -reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': -reconnode.h:388:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&unique, scalarSize, 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In constructor 'Swap::Swap(FILE*&)': -reconnode.h:264:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&count, scalarSize, 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from treenode.h:30, - from tree.h:31, - from individual.h:21, - from population.h:31, - from population.cpp:45: -bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': -bipartition.h:518:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) rep, sizeof(unsigned int), nBlocks, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': -population.cpp:1880:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) &seed, sizeof(seed), 1, pin); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1887:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) &t, sizeof(t), 1, pin); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1896:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(this, scalarSize, 1, pin); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::__cxx11::string&)': configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(&ch, sizeof(char), 1, file); @@ -906,6 +908,7 @@ configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(&ch, sizeof(char), 1, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -941,6 +944,38 @@ model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(dummy, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from population.cpp:45: +reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': +reconnode.h:388:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&unique, scalarSize, 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +reconnode.h: In constructor 'Swap::Swap(FILE*&)': +reconnode.h:264:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&count, scalarSize, 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from treenode.h:30, + from tree.h:31, + from individual.h:21, + from population.h:31, + from population.cpp:45: +bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': +bipartition.h:518:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) rep, sizeof(unsigned int), nBlocks, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': +population.cpp:1880:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) &seed, sizeof(seed), 1, pin); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp:1887:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) &t, sizeof(t), 1, pin); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp:1896:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(this, scalarSize, 1, pin); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1008,7 +1043,6 @@ tree.cpp:6881:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:19: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] sprintf(oStr, "R(%d)", d + 1); @@ -1143,8 +1177,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -1221,7 +1255,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/garli-2.1' dh_auto_build - make -j15 + make -j16 make[1]: Entering directory '/build/garli-2.1' make all-recursive make[2]: Entering directory '/build/garli-2.1' @@ -1242,6 +1276,7 @@ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); ^~~~~~~~ @@ -1269,71 +1304,9 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': -adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) this, 1, scalarSize, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:278:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:280:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:281:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) randNNInum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:283:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:284:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) exNNInum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:286:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:287:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) randSPRnum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:289:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:290:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) limSPRnum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:292:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:293:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:295:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:296:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) randRecomnum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:298:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:299:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:301:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:302:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:304:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] @@ -1374,13 +1347,6 @@ model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(dummy, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::__cxx11::string&)': -configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&ch, sizeof(char), 1, file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&ch, sizeof(char), 1, file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1412,6 +1378,75 @@ population.cpp:1896:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(this, scalarSize, 1, pin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': +adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) this, 1, scalarSize, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:278:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:280:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:281:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) randNNInum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:283:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:284:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) exNNInum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:286:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:287:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) randSPRnum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:289:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:290:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) limSPRnum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:292:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:293:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:295:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:296:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) randRecomnum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:298:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:299:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:301:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:302:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:304:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::__cxx11::string&)': +configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&ch, sizeof(char), 1, file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&ch, sizeof(char), 1, file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1479,7 +1514,6 @@ tree.cpp:6881:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:19: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] sprintf(oStr, "R(%d)", d + 1); @@ -1512,7 +1546,7 @@ # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1/' \{\} \; dh_auto_test - make -j15 check VERBOSE=1 + make -j16 check VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' @@ -4631,7 +4665,7 @@ 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 12 seconds +Time used = 0 hours, 0 minutes and 13 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4835,7 +4869,7 @@ pass 75: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2334 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5043,7 +5077,7 @@ pass 74: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5525,7 +5559,7 @@ pass 13: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -5779,7 +5813,7 @@ pass 36: -13306.2061 (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 = -13306.2061 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 12 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6204,7 +6238,7 @@ pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7052,7 +7086,7 @@ pass 16: -464.5473 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5473 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7755,7 +7789,7 @@ pass 498: -208.3583 (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 +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8019,7 +8053,7 @@ pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 5 seconds +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8313,7 +8347,7 @@ pass 491: -208.3584 (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 6 seconds +Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8604,7 +8638,7 @@ pass 490: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) Looking for minimum length branches... Final score = -208.3583 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -11318,11 +11352,6 @@ 800 -99.0437 0.500 783 900 -99.0045 0.500 783 1000 -98.8740 0.500 949 -1100 -98.8107 0.500 1029 -1200 -98.8004 0.500 1029 -1300 -98.7501 0.500 1029 -1400 -98.6926 0.500 1029 -1500 -98.6821 0.500 1029 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11419,9 +11448,9 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1562, seed 1876056423, best lnL -98.628 +Bootstrap rep 1 (of 1) generation 1001, seed 1264445715, best lnL -98.874 gen current_lnL precision last_tree_imp -1562 -98.6277 0.500 1029 +1001 -98.8740 0.500 949 MODEL REPORT - Parameter values are FINAL Model 1 @@ -11435,15 +11464,15 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.8820 + 0.6652 with an invariant (invariable) site category, proportion estimated - 0.0461 + 0.0626 Substitution rate categories under this model: rate proportion - 0.0000 0.0461 - 0.1614 0.3180 - 0.6785 0.3180 - 2.1601 0.3180 + 0.0000 0.0626 + 0.1054 0.3125 + 0.5916 0.3125 + 2.3030 0.3125 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -11453,15 +11482,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -98.6277 +Replicate 1 : -98.8740 Parameter estimates: alpha pinv -rep 1: 0.882 0.046 +rep 1: 0.665 0.063 Treelengths: TL -rep 1: 1.734 +rep 1: 1.521 Saving best tree to bootstrap file ch.a.G3.boot.tre @@ -11679,9 +11708,9 @@ STARTING RUN Restarting from checkpoint... - generation 779, seed 928785680, best lnL -110.585 + generation 794, seed 884972805, best lnL -110.569 gen current_lnL precision last_tree_imp -779 -110.5854 0.010 707 +794 -110.5688 0.010 707 800 -110.5642 0.010 707 900 -110.5555 0.010 707 1000 -110.5065 0.010 707 @@ -11873,6 +11902,12 @@ 2000 -111.6817 0.010 563 2100 -111.6817 0.010 563 2200 -111.6817 0.010 563 +2300 -111.6817 0.010 563 +2400 -111.6817 0.010 563 +2500 -111.6817 0.010 563 +2600 -111.6816 0.010 563 +2700 -111.6816 0.010 563 +2800 -111.6816 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11958,9 +11993,9 @@ STARTING RUN Restarting from checkpoint... - generation 2235, seed 1580706156, best lnL -111.682 + generation 2853, seed 532729490, best lnL -111.682 gen current_lnL precision last_tree_imp -2235 -111.6817 0.010 563 +2853 -111.6815 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -11984,14 +12019,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6817 +Replicate 1 : -111.6815 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.605 +rep 1: 2.606 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log @@ -12123,7 +12158,6 @@ 30 -205.6499 0.500 18 40 -205.6371 0.500 18 50 -205.6175 0.500 18 -60 -205.5990 0.500 53 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12210,9 +12244,10 @@ STARTING RUN Restarting from checkpoint... - generation 62, seed 2117091137, best lnL -205.594 + generation 51, seed 1784766670, best lnL -205.617 gen current_lnL precision last_tree_imp -62 -205.5939 0.500 53 +51 -205.6174 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 @@ -12401,14 +12436,6 @@ lnL after optimization: -203.1334 gen current_lnL precision last_tree_imp 0 -203.1334 0.500 0 -10 -201.4172 0.500 10 -20 -199.1396 0.500 20 -30 -199.1218 0.500 20 -40 -198.6458 0.500 33 -50 -198.5840 0.500 33 -60 -197.5336 0.500 55 -70 -197.4975 0.500 55 -80 -197.3836 0.500 55 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12496,9 +12523,17 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 86, seed 2060542775, best lnL -197.344 +Bootstrap rep 1 (of 1) generation 1, seed 1398556760, best lnL -203.124 gen current_lnL precision last_tree_imp -86 -197.3436 0.500 55 +1 -203.1237 0.500 0 +10 -201.4172 0.500 10 +20 -199.1396 0.500 20 +30 -199.1218 0.500 20 +40 -198.6458 0.500 33 +50 -198.5840 0.500 33 +60 -197.5336 0.500 55 +70 -197.4975 0.500 55 +80 -197.3836 0.500 55 90 -197.3175 0.500 55 100 -197.3149 0.500 55 NOTE: ****Specified generation limit (100) reached... @@ -12713,13 +12748,6 @@ Optimization precision reduced Optimizing parameters... improved 0.835 lnL Optimizing branchlengths... improved 0.087 lnL -1100 -3352.7094 0.010 0 -1200 -3352.6266 0.010 0 -1300 -3352.5046 0.010 0 -1400 -3352.3936 0.010 0 -1500 -3352.3890 0.010 0 -1600 -3352.2802 0.010 0 -1700 -3352.2723 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12823,78 +12851,74 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1723, seed 1797417136, best lnL -3352.207 +Search rep 1 (of 2) generation 1072, seed 1681054827, best lnL -3352.745 gen current_lnL precision last_tree_imp -1723 -3352.2068 0.010 0 -1800 -3352.1948 0.010 0 -1900 -3351.8390 0.010 0 -2000 -3351.7561 0.010 0 -2100 -3351.6082 0.010 0 -2200 -3351.3633 0.010 0 -2300 -3351.3388 0.010 0 -2400 -3351.3304 0.010 0 -2500 -3351.2272 0.010 0 -2600 -3351.1611 0.010 0 -2700 -3351.1609 0.010 0 -2800 -3351.1131 0.010 0 -2900 -3351.1124 0.010 0 -3000 -3351.1085 0.010 0 +1072 -3352.7446 0.010 0 +1100 -3352.7094 0.010 0 +1200 -3352.6266 0.010 0 +1300 -3352.5046 0.010 0 +1400 -3352.3936 0.010 0 +1500 -3352.3890 0.010 0 +1600 -3352.2802 0.010 0 +1700 -3352.2723 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.1085 +Current score = -3352.2068 Performing final optimizations... -pass 1 : -3351.0285 (branch= 0.0000 alpha= 0.0000 pinv= 0.0235 eq freqs= 0.0277 rel rates= 0.0287 subset rates= 0.0000) -pass 2 : -3350.9336 (branch= 0.0000 alpha= 0.0126 pinv= 0.0193 eq freqs= 0.0049 rel rates= 0.0582 subset rates= 0.0000) -pass 3 : -3350.8513 (branch= 0.0032 alpha= 0.0188 pinv= 0.0169 eq freqs= 0.0013 rel rates= 0.0421 subset rates= 0.0000) -pass 4 : -3350.7752 (branch= 0.0033 alpha= 0.0185 pinv= 0.0154 eq freqs= 0.0014 rel rates= 0.0361 subset rates= 0.0014) -pass 5 : -3350.7085 (branch= 0.0061 alpha= 0.0143 pinv= 0.0147 eq freqs= 0.0004 rel rates= 0.0296 subset rates= 0.0016) -pass 6 : -3350.6524 (branch= 0.0044 alpha= 0.0130 pinv= 0.0136 eq freqs= 0.0000 rel rates= 0.0251 subset rates= 0.0000) -pass 7 : -3350.6018 (branch= 0.0009 alpha= 0.0123 pinv= 0.0124 eq freqs= 0.0001 rel rates= 0.0229 subset rates= 0.0020) -pass 8 : -3350.5574 (branch= 0.0023 alpha= 0.0116 pinv= 0.0114 eq freqs= 0.0001 rel rates= 0.0190 subset rates= 0.0000) -pass 9 : -3350.5179 (branch= 0.0004 alpha= 0.0105 pinv= 0.0103 eq freqs= 0.0000 rel rates= 0.0170 subset rates= 0.0014) -pass 10: -3350.4826 (branch= 0.0013 alpha= 0.0097 pinv= 0.0100 eq freqs= 0.0001 rel rates= 0.0142 subset rates= 0.0000) -pass 11: -3350.4524 (branch= 0.0002 alpha= 0.0087 pinv= 0.0084 eq freqs= 0.0000 rel rates= 0.0128 subset rates= 0.0000) -pass 12: -3350.4241 (branch= 0.0000 alpha= 0.0083 pinv= 0.0076 eq freqs= 0.0000 rel rates= 0.0114 subset rates= 0.0009) -pass 13: -3350.4001 (branch= 0.0007 alpha= 0.0072 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0092 subset rates= 0.0000) -pass 14: -3350.3793 (branch= 0.0001 alpha= 0.0064 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0082 subset rates= 0.0000) -pass 15: -3350.3606 (branch= 0.0000 alpha= 0.0059 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0073 subset rates= 0.0000) -pass 16: -3350.3440 (branch= 0.0000 alpha= 0.0054 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0064 subset rates= 0.0000) -pass 17: -3350.3294 (branch= 0.0000 alpha= 0.0048 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0055 subset rates= 0.0000) -pass 18: -3350.3166 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0047 subset rates= 0.0000) -pass 19: -3350.3054 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) -pass 20: -3350.2957 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0035 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2469 (branch= 0.0000 alpha= 0.0167 pinv= 0.0150 eq freqs= 0.0001 rel rates= 0.0170 subset rates= 0.0000) +pass 1 : -3351.8914 (branch= 0.0052 alpha= 0.0189 pinv= 0.0207 eq freqs= 0.0290 rel rates= 0.2339 subset rates= 0.0077) +pass 2 : -3351.6340 (branch= 0.0148 alpha= 0.0107 pinv= 0.0183 eq freqs= 0.0058 rel rates= 0.2056 subset rates= 0.0021) +pass 3 : -3351.4225 (branch= 0.0112 alpha= 0.0156 pinv= 0.0162 eq freqs= 0.0024 rel rates= 0.1643 subset rates= 0.0018) +pass 4 : -3351.2457 (branch= 0.0111 alpha= 0.0139 pinv= 0.0155 eq freqs= 0.0009 rel rates= 0.1326 subset rates= 0.0028) +pass 5 : -3351.1013 (branch= 0.0073 alpha= 0.0121 pinv= 0.0145 eq freqs= 0.0004 rel rates= 0.1076 subset rates= 0.0025) +pass 6 : -3350.9803 (branch= 0.0055 alpha= 0.0117 pinv= 0.0134 eq freqs= 0.0005 rel rates= 0.0884 subset rates= 0.0015) +pass 7 : -3350.8778 (branch= 0.0039 alpha= 0.0110 pinv= 0.0124 eq freqs= 0.0002 rel rates= 0.0738 subset rates= 0.0013) +pass 8 : -3350.7905 (branch= 0.0026 alpha= 0.0103 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0628 subset rates= 0.0000) +pass 9 : -3350.7127 (branch= 0.0008 alpha= 0.0101 pinv= 0.0103 eq freqs= 0.0001 rel rates= 0.0552 subset rates= 0.0013) +pass 10: -3350.6456 (branch= 0.0015 alpha= 0.0095 pinv= 0.0100 eq freqs= 0.0002 rel rates= 0.0459 subset rates= 0.0000) +pass 11: -3350.5876 (branch= 0.0004 alpha= 0.0085 pinv= 0.0085 eq freqs= 0.0001 rel rates= 0.0395 subset rates= 0.0011) +pass 12: -3350.5389 (branch= 0.0008 alpha= 0.0079 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0321 subset rates= 0.0000) +pass 13: -3350.4978 (branch= 0.0002 alpha= 0.0073 pinv= 0.0069 eq freqs= 0.0001 rel rates= 0.0267 subset rates= 0.0000) +pass 14: -3350.4620 (branch= 0.0001 alpha= 0.0068 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0227 subset rates= 0.0000) +pass 15: -3350.4309 (branch= 0.0000 alpha= 0.0062 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0193 subset rates= 0.0000) +pass 16: -3350.4041 (branch= 0.0000 alpha= 0.0055 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0163 subset rates= 0.0000) +pass 17: -3350.3809 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0138 subset rates= 0.0000) +pass 18: -3350.3609 (branch= 0.0000 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0118 subset rates= 0.0000) +pass 19: -3350.3435 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0100 subset rates= 0.0000) +pass 20: -3350.3285 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0085 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2552 (branch= 0.0000 alpha= 0.0171 pinv= 0.0156 eq freqs= 0.0001 rel rates= 0.0406 subset rates= 0.0000) + optimization up to ... +pass 40: -3350.2384 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0094 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2359 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0040 subset rates= 0.0000) +pass 50: -3350.2347 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0024 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2336 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) +pass 60: -3350.2338 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2331 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 70: -3350.2337 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 65: -3350.2330 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 75: -3350.2336 (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 = -3350.2331 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -3350.2336 +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 = 3.113, AG = 10.416, AT = 2.690, CG = 0.001, CT = 21.929, GT = 1.000 + AC = 3.109, AG = 10.390, AT = 2.683, CG = 0.001, CT = 21.836, 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 - 0.5767 + 0.5796 with an invariant (invariable) site category, proportion estimated - 0.3654 + 0.3663 Substitution rate categories under this model: rate proportion - 0.0000 0.3654 - 0.0483 0.1586 - 0.2991 0.1586 - 0.8690 0.1586 - 2.7836 0.1586 + 0.0000 0.3663 + 0.0489 0.1584 + 0.3007 0.1584 + 0.8705 0.1584 + 2.7798 0.1584 Model 2 Number of states = 2 (binary data) @@ -12919,20 +12943,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2336 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.113 10.42 2.69 0.001 21.93 1 0.333 0.222 0.157 0.288 0.577 0.365 +rep 1: 3.109 10.39 2.683 0.001 21.84 1 0.333 0.222 0.157 0.288 0.580 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.790 1.821 0.179 +rep 1: 0.787 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -13080,14 +13104,6 @@ 0 -3332.4700 0.500 0 100 -3324.9856 0.500 1 200 -3324.7543 0.500 1 -300 -3324.3007 0.500 1 -400 -3323.9848 0.500 1 -500 -3323.6818 0.500 1 -600 -3323.3459 0.500 1 -Optimization precision reduced - Optimizing parameters... improved 1.812 lnL - Optimizing branchlengths... improved 0.023 lnL -700 -3321.3650 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13188,76 +13204,70 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 758, seed 833073602, best lnL -3321.339 +Search rep 1 (of 2) generation 249, seed 1128119220, best lnL -3324.638 gen current_lnL precision last_tree_imp -758 -3321.3394 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 0.580 lnL - Optimizing branchlengths... improved 0.060 lnL -1200 -3320.1439 0.010 1 -1300 -3320.0846 0.010 1 +249 -3324.6381 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... -Current score = -3320.0697 +Current score = -3323.4776 Performing final optimizations... -pass 1 : -3319.5622 (branch= 0.0234 alpha= 0.0000 pinv= 0.0176 eq freqs= 0.0001 rel rates= 0.4040 ins/del rates= 0.0625) -pass 2 : -3319.2666 (branch= 0.0372 alpha= 0.0230 pinv= 0.0148 eq freqs= 0.0037 rel rates= 0.2098 ins/del rates= 0.0071) -pass 3 : -3319.0430 (branch= 0.0234 alpha= 0.0111 pinv= 0.0149 eq freqs= 0.0000 rel rates= 0.1691 ins/del rates= 0.0051) -pass 4 : -3318.8541 (branch= 0.0187 alpha= 0.0115 pinv= 0.0147 eq freqs= 0.0024 rel rates= 0.1360 ins/del rates= 0.0056) -pass 5 : -3318.6960 (branch= 0.0117 alpha= 0.0112 pinv= 0.0139 eq freqs= 0.0011 rel rates= 0.1158 ins/del rates= 0.0044) -pass 6 : -3318.5692 (branch= 0.0077 alpha= 0.0112 pinv= 0.0130 eq freqs= 0.0002 rel rates= 0.0915 ins/del rates= 0.0031) -pass 7 : -3318.4620 (branch= 0.0051 alpha= 0.0103 pinv= 0.0122 eq freqs= 0.0004 rel rates= 0.0770 ins/del rates= 0.0022) -pass 8 : -3318.3680 (branch= 0.0038 alpha= 0.0100 pinv= 0.0113 eq freqs= 0.0003 rel rates= 0.0671 ins/del rates= 0.0016) -pass 9 : -3318.2873 (branch= 0.0026 alpha= 0.0092 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0573 ins/del rates= 0.0011) -pass 10: -3318.2187 (branch= 0.0018 alpha= 0.0089 pinv= 0.0095 eq freqs= 0.0001 rel rates= 0.0475 ins/del rates= 0.0008) -pass 11: -3318.1600 (branch= 0.0012 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0399 ins/del rates= 0.0005) -pass 12: -3318.1096 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0336 ins/del rates= 0.0003) -pass 13: -3318.0670 (branch= 0.0005 alpha= 0.0073 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0274 ins/del rates= 0.0002) -pass 14: -3318.0302 (branch= 0.0003 alpha= 0.0067 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0232 ins/del rates= 0.0001) -pass 15: -3317.9983 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0198 ins/del rates= 0.0001) -pass 16: -3317.9704 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0169 ins/del rates= 0.0000) -pass 17: -3317.9463 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0144 ins/del rates= 0.0000) -pass 18: -3317.9253 (branch= 0.0000 alpha= 0.0044 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0123 ins/del rates= 0.0000) -pass 19: -3317.9070 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0105 ins/del rates= 0.0000) -pass 20: -3317.8911 (branch= 0.0000 alpha= 0.0035 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0090 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8115 (branch= 0.0000 alpha= 0.0188 pinv= 0.0173 eq freqs= 0.0001 rel rates= 0.0433 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7926 (branch= 0.0001 alpha= 0.0046 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0100 ins/del rates= 0.0000) +pass 1 : -3321.2507 (branch= 0.1076 alpha= 0.0112 pinv= 0.0157 eq freqs= 0.0600 rel rates= 0.6818 ins/del rates= 1.3506) +pass 2 : -3320.4465 (branch= 0.1944 alpha= 0.0036 pinv= 0.0168 eq freqs= 0.0377 rel rates= 0.5157 ins/del rates= 0.0361) +pass 3 : -3319.9329 (branch= 0.0682 alpha= 0.0084 pinv= 0.0162 eq freqs= 0.0084 rel rates= 0.3917 ins/del rates= 0.0207) +pass 4 : -3319.5339 (branch= 0.0352 alpha= 0.0096 pinv= 0.0158 eq freqs= 0.0034 rel rates= 0.3208 ins/del rates= 0.0143) +pass 5 : -3319.2253 (branch= 0.0227 alpha= 0.0105 pinv= 0.0152 eq freqs= 0.0010 rel rates= 0.2500 ins/del rates= 0.0091) +pass 6 : -3318.9836 (branch= 0.0148 alpha= 0.0108 pinv= 0.0145 eq freqs= 0.0008 rel rates= 0.1946 ins/del rates= 0.0063) +pass 7 : -3318.7891 (branch= 0.0091 alpha= 0.0107 pinv= 0.0136 eq freqs= 0.0006 rel rates= 0.1565 ins/del rates= 0.0039) +pass 8 : -3318.6296 (branch= 0.0061 alpha= 0.0107 pinv= 0.0127 eq freqs= 0.0005 rel rates= 0.1269 ins/del rates= 0.0025) +pass 9 : -3318.5000 (branch= 0.0039 alpha= 0.0104 pinv= 0.0118 eq freqs= 0.0003 rel rates= 0.1014 ins/del rates= 0.0017) +pass 10: -3318.3927 (branch= 0.0026 alpha= 0.0100 pinv= 0.0116 eq freqs= 0.0003 rel rates= 0.0817 ins/del rates= 0.0011) +pass 11: -3318.3034 (branch= 0.0017 alpha= 0.0095 pinv= 0.0107 eq freqs= 0.0002 rel rates= 0.0664 ins/del rates= 0.0008) +pass 12: -3318.2304 (branch= 0.0012 alpha= 0.0089 pinv= 0.0092 eq freqs= 0.0002 rel rates= 0.0532 ins/del rates= 0.0005) +pass 13: -3318.1684 (branch= 0.0008 alpha= 0.0083 pinv= 0.0084 eq freqs= 0.0001 rel rates= 0.0441 ins/del rates= 0.0003) +pass 14: -3318.1157 (branch= 0.0005 alpha= 0.0077 pinv= 0.0076 eq freqs= 0.0001 rel rates= 0.0366 ins/del rates= 0.0002) +pass 15: -3318.0705 (branch= 0.0003 alpha= 0.0071 pinv= 0.0069 eq freqs= 0.0001 rel rates= 0.0307 ins/del rates= 0.0001) +pass 16: -3318.0326 (branch= 0.0002 alpha= 0.0065 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0249 ins/del rates= 0.0001) +pass 17: -3317.9998 (branch= 0.0001 alpha= 0.0059 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0211 ins/del rates= 0.0000) +pass 18: -3317.9714 (branch= 0.0001 alpha= 0.0053 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0179 ins/del rates= 0.0000) +pass 19: -3317.9469 (branch= 0.0001 alpha= 0.0048 pinv= 0.0045 eq freqs= 0.0000 rel rates= 0.0152 ins/del rates= 0.0000) +pass 20: -3317.9256 (branch= 0.0000 alpha= 0.0043 pinv= 0.0040 eq freqs= 0.0000 rel rates= 0.0129 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8197 (branch= 0.0001 alpha= 0.0232 pinv= 0.0214 eq freqs= 0.0001 rel rates= 0.0611 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7945 (branch= 0.0001 alpha= 0.0058 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0139 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7882 (branch= 0.0000 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0024 ins/del rates= 0.0000) +pass 50: -3317.7887 (branch= 0.0000 alpha= 0.0013 pinv= 0.0011 eq freqs= 0.0000 rel rates= 0.0033 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0005 ins/del rates= 0.0000) +pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0008 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 74: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 76: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 13 seconds +Final score = -3317.7870 +Time used so far = 0 hours, 0 minutes and 15 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.065, AG = 10.263, AT = 2.656, CG = 0.001, CT = 21.532, GT = 1.000 + AC = 3.067, AG = 10.271, AT = 2.658, CG = 0.001, CT = 21.547, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5749 + 0.5753 with an invariant (invariable) site category, proportion estimated - 0.3613 + 0.3615 Substitution rate categories under this model: rate proportion - 0.0000 0.3613 - 0.0480 0.1597 - 0.2980 0.1597 - 0.8679 0.1597 - 2.7861 0.1597 + 0.0000 0.3615 + 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) @@ -13283,13 +13293,13 @@ 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: 3.065 10.26 2.656 0.001 21.53 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.067 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 @@ -13433,31 +13443,6 @@ 3600 -210.7287 0.010 1104 3800 -210.7083 0.010 1104 4000 -210.6947 0.010 1104 -4200 -210.6743 0.010 1104 -4400 -210.6493 0.010 1104 -4600 -210.6258 0.010 1104 -4800 -210.5948 0.010 1104 -5000 -210.5740 0.010 1104 -5200 -210.5695 0.010 1104 -5400 -210.5462 0.010 1104 -5600 -210.5153 0.010 1104 -5800 -210.4824 0.010 1104 -6000 -210.4635 0.010 1104 -6200 -210.4597 0.010 1104 -6400 -210.4469 0.010 1104 -6600 -210.4215 0.010 1104 -6800 -210.3966 0.010 1104 -7000 -210.3385 0.010 1104 -7200 -210.3219 0.010 1104 -7400 -210.2808 0.010 1104 -7600 -210.2625 0.010 1104 -7800 -210.1873 0.010 1104 -8000 -210.1733 0.010 1104 -8200 -210.1282 0.010 1104 -8400 -210.1102 0.010 1104 -8600 -210.0896 0.010 1104 -8800 -210.0543 0.010 1104 -9000 -210.0431 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13537,37 +13522,32 @@ STARTING RUN Restarting from checkpoint... - generation 9065, seed 402313860, best lnL -210.000 + generation 4020, seed 436380365, best lnL -210.695 gen current_lnL precision last_tree_imp -9065 -210.0002 0.010 1104 -9100 -209.9813 0.010 1104 -9200 -209.9790 0.010 1104 -9300 -209.9614 0.010 1104 -9400 -209.9599 0.010 1104 -9500 -209.9577 0.010 1104 -9600 -209.9458 0.010 1104 +4020 -210.6947 0.010 1104 +4100 -210.6828 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.03550 +Improvement over last 500 gen = 0.04585 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.196, AG = 8.947, AT = 0.234, CG = 9.299, CT = 14.388, GT = 1.000 + AC = 2.570, AG = 4.748, AT = 0.222, CG = 4.460, CT = 6.970, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2351 0.3311 0.2101 0.2237 + (ACGT) 0.2329 0.3364 0.2106 0.2201 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.9485 + 1.1902 with an invariant (invariable) site category, proportion estimated - 0.2068 + 0.1148 Substitution rate categories under this model: rate proportion - 0.0000 0.2068 - 0.3480 0.2644 - 0.8452 0.2644 - 1.8067 0.2644 + 0.0000 0.1148 + 0.2293 0.2951 + 0.7543 0.2951 + 2.0164 0.2951 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -13578,15 +13558,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.9458 +Replicate 1 : -210.6828 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 5.196 8.947 0.234 9.299 14.39 1 0.235 0.331 0.210 0.224 1.948 0.207 +rep 1: 2.57 4.748 0.2216 4.46 6.97 1 0.233 0.336 0.211 0.220 1.190 0.115 Treelengths: TL -rep 1: 2.329 +rep 1: 2.232 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 @@ -13740,15 +13720,6 @@ 6200 -190.5467 0.010 1979 6400 -190.5266 0.010 1979 6600 -190.5076 0.010 1979 -6800 -190.5070 0.010 1979 -7000 -190.5054 0.010 1979 -7200 -190.4919 0.010 1979 -7400 -190.4907 0.010 1979 -7600 -190.4693 0.010 1979 -7800 -190.4653 0.010 1979 -8000 -190.4467 0.010 1979 -8200 -190.4397 0.010 1979 -8400 -190.4343 0.010 1979 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13829,33 +13800,33 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 8511, seed 1311482652, best lnL -190.434 +Bootstrap rep 1 (of 1) generation 6679, seed 1536079585, best lnL -190.507 gen current_lnL precision last_tree_imp -8511 -190.4336 0.010 1979 -8600 -190.4331 0.010 1979 +6679 -190.5070 0.010 1979 +6700 -190.5070 0.010 1979 Reached termination condition! last topological improvement at gen 1979 -Improvement over last 500 gen = 0.01069 +Improvement over last 500 gen = 0.03968 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.712, AG = 1.431, AT = 0.008, CG = 3.200, CT = 16.482, GT = 1.000 + AC = 0.646, AG = 1.342, AT = 0.009, CG = 2.968, CT = 14.097, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3160 0.3204 0.2593 0.1043 + (ACGT) 0.3164 0.3195 0.2597 0.1045 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 7.0869 + 7.0956 with an invariant (invariable) site category, proportion estimated - 0.1419 + 0.1388 Substitution rate categories under this model: rate proportion - 0.0000 0.1419 - 0.5709 0.2145 - 0.8414 0.2145 - 1.0788 0.2145 - 1.5090 0.2145 + 0.0000 0.1388 + 0.5711 0.2153 + 0.8415 0.2153 + 1.0787 0.2153 + 1.5087 0.2153 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. @@ -13865,15 +13836,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -190.4331 +Replicate 1 : -190.5070 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: 0.712 1.431 0.008019 3.2 16.48 1 0.316 0.320 0.259 0.104 7.087 0.142 +rep 1: 0.6464 1.342 0.00943 2.968 14.1 1 0.316 0.320 0.260 0.104 7.096 0.139 Treelengths: TL -rep 1: 2.362 +rep 1: 2.289 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -14338,13 +14309,6 @@ 8000 -210.1813 0.010 2883 8200 -210.1599 0.010 2883 8400 -210.0780 0.010 2883 -8600 -210.0378 0.010 2883 -8800 -210.0091 0.010 2883 -9000 -209.9765 0.010 2883 -9200 -209.9496 0.010 2883 -9400 -209.9484 0.010 2883 -9600 -209.9457 0.010 2883 -9800 -209.8760 0.010 2883 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14432,34 +14396,42 @@ STARTING RUN Restarting from checkpoint... - generation 9875, seed 1288553779, best lnL -209.871 + generation 8569, seed 125209927, best lnL -210.038 gen current_lnL precision last_tree_imp -9875 -209.8711 0.010 2883 -9900 -209.8697 0.010 2883 -10000 -209.8544 0.010 2883 - Optimizing parameters... improved 0.412 lnL - Optimizing branchlengths... improved 0.003 lnL -NOTE: ****Specified generation limit (10000) reached... +8569 -210.0378 0.010 2883 +8600 -210.0378 0.010 2883 +8700 -210.0274 0.010 2883 +8800 -210.0091 0.010 2883 +8900 -209.9986 0.010 2883 +9000 -209.9765 0.010 2883 +9100 -209.9557 0.010 2883 +9200 -209.9496 0.010 2883 +9300 -209.9496 0.010 2883 +9400 -209.9484 0.010 2883 +9500 -209.9478 0.010 2883 +Reached termination condition! +last topological improvement at gen 2883 +Improvement over last 500 gen = 0.02875 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.851, AG = 5.111, AT = 0.047, CG = 5.326, CT = 10.145, GT = 1.000 + AC = 2.797, AG = 5.161, AT = 0.238, CG = 5.326, CT = 9.312, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2408 0.3349 0.2137 0.2106 + (ACGT) 0.2398 0.3377 0.2128 0.2097 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 3.7818 + 2.2351 with an invariant (invariable) site category, proportion estimated - 0.2956 + 0.2162 Substitution rate categories under this model: rate proportion - 0.0000 0.2956 - 0.4420 0.1761 - 0.7673 0.1761 - 1.0844 0.1761 - 1.7064 0.1761 + 0.0000 0.2162 + 0.3198 0.1959 + 0.6779 0.1959 + 1.0749 0.1959 + 1.9274 0.1959 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -14470,31 +14442,24 @@ If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.4393 +Replicate 1 : -209.9478 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: 2.851 5.111 0.04734 5.326 10.15 1 0.241 0.335 0.214 0.211 3.782 0.296 +rep 1: 2.797 5.161 0.2379 5.326 9.312 1 0.240 0.338 0.213 0.210 2.235 0.216 Treelengths: TL -rep 1: 2.454 +rep 1: 2.446 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 @@ -14699,10 +14664,6 @@ 800 -13181.6899 0.402 1 900 -13181.6040 0.402 1 1000 -13181.4970 0.402 1 -1100 -13181.4426 0.402 1 -Optimization precision reduced - Optimizing parameters... improved 0.019 lnL - Optimizing branchlengths... improved 0.000 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14825,12 +14786,15 @@ Subset 3: Random seed for bootstrap reweighting: 1903425807 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1114, seed 1750375237, best lnL -13181.424 +Bootstrap rep 1 (of 1) generation 1043, seed 1272235012, best lnL -13181.473 gen current_lnL precision last_tree_imp -1114 -13181.4239 0.304 1 +1043 -13181.4732 0.402 1 +1100 -13181.4426 0.402 1 +Optimization precision reduced + Optimizing parameters... improved 0.019 lnL + Optimizing branchlengths... improved 0.000 lnL 1200 -13181.4112 0.304 1 1300 -13181.3755 0.304 1 -1400 -13181.3694 0.304 1 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -14838,7 +14802,7 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 2.042, AG = 3.173, AT = 1.172, CG = 1.172, CT = 2.631, GT = 1.000 + AC = 2.042, AG = 3.173, AT = 1.174, CG = 1.174, CT = 2.631, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3054 0.1867 0.2740 0.2339 Rate Heterogeneity Model: @@ -14855,7 +14819,7 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 3.841, AG = 4.640, AT = 0.735, CG = 4.640, CT = 3.841, GT = 1.000 + AC = 3.841, AG = 4.722, AT = 0.735, CG = 4.722, CT = 3.841, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2508 0.1558 0.1899 0.4036 Rate Heterogeneity Model: @@ -14903,17 +14867,17 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13181.3694 (TERMINATED PREMATURELY) +Replicate 1 : -13181.3706 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.042 3.173 1.172 1.172 2.631 1 0.305 0.187 0.274 0.234 0.388 +rep 1: 2.042 3.173 1.174 1.174 2.631 1 0.305 0.187 0.274 0.234 0.388 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 3.841 4.64 0.7354 4.64 3.841 1 0.251 0.156 0.190 0.404 0.449 +rep 1: 3.841 4.722 0.7354 4.722 3.841 1 0.251 0.156 0.190 0.404 0.449 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv @@ -15238,6 +15202,11 @@ 1000 -467.7433 0.010 60 1100 -467.7397 0.010 60 1200 -467.7384 0.010 60 +1300 -467.7344 0.010 60 +1400 -467.7344 0.010 60 +1500 -467.7326 0.010 60 +1600 -467.7302 0.010 60 +1700 -467.7284 0.010 60 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15363,14 +15332,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1217, seed 2059296472, best lnL -467.737 +Search rep 2 (of 5) generation 1701, seed 580292609, best lnL -467.728 gen current_lnL precision last_tree_imp -1217 -467.7371 0.010 60 -1300 -467.7344 0.010 60 -1400 -467.7344 0.010 60 -1500 -467.7326 0.010 60 -1600 -467.7302 0.010 60 -1700 -467.7284 0.010 60 +1701 -467.7284 0.010 60 1800 -467.7262 0.010 60 1900 -467.7245 0.010 60 2000 -467.7222 0.010 60 @@ -15427,7 +15391,7 @@ 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 +Time used so far = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -15518,26 +15482,33 @@ 1100 -467.7284 0.010 73 1200 -467.7269 0.010 73 1300 -467.7243 0.010 73 +1400 -467.7221 0.010 73 +1500 -467.7216 0.010 73 +1600 -467.7190 0.010 73 +1700 -467.7187 0.010 73 +1800 -467.7179 0.010 73 +1900 -467.7168 0.010 73 +2000 -467.7163 0.010 73 +2100 -467.7159 0.010 73 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7236 +Current score = -467.7157 Performing final optimizations... -pass 1 : -467.7229 (branch= 0.0000 subset rates= 0.0006) -pass 2 : -467.7043 (branch= 0.0186 subset rates= 0.0000) -pass 3 : -467.6955 (branch= 0.0088 subset rates= 0.0000) -pass 4 : -467.6876 (branch= 0.0074 subset rates= 0.0005) -pass 5 : -467.6827 (branch= 0.0050 subset rates= 0.0000) -pass 6 : -467.6806 (branch= 0.0021 subset rates= 0.0000) -pass 7 : -467.6796 (branch= 0.0010 subset rates= 0.0000) -pass 8 : -467.6793 (branch= 0.0003 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: -467.6787 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6786 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6786 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6786 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6786 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7157 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.6974 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -467.6937 (branch= 0.0037 subset rates= 0.0000) +pass 4 : -467.6873 (branch= 0.0064 subset rates= 0.0000) +pass 5 : -467.6831 (branch= 0.0031 subset rates= 0.0011) +pass 6 : -467.6815 (branch= 0.0016 subset rates= 0.0000) +pass 7 : -467.6802 (branch= 0.0013 subset rates= 0.0000) +pass 8 : -467.6796 (branch= 0.0005 subset rates= 0.0002) +pass 9 : -467.6792 (branch= 0.0004 subset rates= 0.0000) +pass 10: -467.6790 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6790 (branch= 0.0000 subset rates= 0.0000) +pass 12: -467.6790 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6790 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6786 +Final score = -467.6789 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15566,7 +15537,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.17 + 0.79 1.47 2.17 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -15585,7 +15556,7 @@ Results: Replicate 1 : -467.6782 (best) Replicate 2 : -467.6782 (same topology as 1) -Replicate 3 : -467.6786 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 3 : -467.6789 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -15602,7 +15573,7 @@ TL R(1) R(2) R(3) rep 1: 3.843 0.786 1.478 2.186 rep 2: 3.843 0.786 1.480 2.182 -rep 3: 3.840 0.788 1.476 2.169 +rep 3: 3.839 0.789 1.473 2.167 Saving final tree from best search rep (#1) to ch.p.mk.ssr.best.tre ####################################################### @@ -15819,7 +15790,7 @@ pass 14: -477.2119 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2119 -Time used so far = 0 hours, 0 minutes and 3 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -15908,12 +15879,6 @@ 1000 -477.5017 0.010 860 1100 -477.4987 0.010 860 1200 -477.4962 0.010 860 -1300 -477.4923 0.010 860 -1400 -477.4850 0.010 860 -1500 -477.4823 0.010 860 -1600 -477.4819 0.010 860 -1700 -477.4785 0.010 860 -1800 -477.4778 0.010 860 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16039,9 +16004,15 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1891, seed 1782491223, best lnL -477.477 +Search rep 2 (of 5) generation 1246, seed 1634265149, best lnL -477.495 gen current_lnL precision last_tree_imp -1891 -477.4775 0.010 860 +1246 -477.4953 0.010 860 +1300 -477.4923 0.010 860 +1400 -477.4850 0.010 860 +1500 -477.4823 0.010 860 +1600 -477.4819 0.010 860 +1700 -477.4785 0.010 860 +1800 -477.4778 0.010 860 1900 -477.4774 0.010 860 2000 -477.4770 0.010 860 2100 -477.4770 0.010 860 @@ -16191,35 +16162,27 @@ 2700 -477.4645 0.010 129 2800 -477.4636 0.010 129 2900 -477.4629 0.010 129 -3000 -477.4628 0.010 129 -3100 -477.4616 0.010 129 -3200 -477.4616 0.010 129 -3300 -477.4615 0.010 129 -3400 -477.4608 0.010 129 -3500 -477.4607 0.010 129 -3600 -477.4601 0.010 129 -3700 -477.4601 0.010 129 -3800 -477.4598 0.010 129 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.4598 +Current score = -477.4629 Performing final optimizations... -pass 1 : -477.4593 (branch= 0.0000 subset rates= 0.0005) -pass 2 : -477.4467 (branch= 0.0126 subset rates= 0.0000) -pass 3 : -477.4390 (branch= 0.0077 subset rates= 0.0000) -pass 4 : -477.4366 (branch= 0.0024 subset rates= 0.0000) -pass 5 : -477.4358 (branch= 0.0008 subset rates= 0.0000) -pass 6 : -477.4340 (branch= 0.0016 subset rates= 0.0002) -pass 7 : -477.4332 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -477.4326 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -477.4321 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4317 (branch= 0.0000 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 1 : -477.4629 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.4470 (branch= 0.0159 subset rates= 0.0000) +pass 3 : -477.4423 (branch= 0.0038 subset rates= 0.0010) +pass 4 : -477.4394 (branch= 0.0028 subset rates= 0.0000) +pass 5 : -477.4376 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -477.4354 (branch= 0.0021 subset rates= 0.0001) +pass 7 : -477.4351 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -477.4339 (branch= 0.0011 subset rates= 0.0000) +pass 9 : -477.4332 (branch= 0.0007 subset rates= 0.0000) +pass 10: -477.4329 (branch= 0.0003 subset rates= 0.0000) +pass 11: -477.4327 (branch= 0.0002 subset rates= 0.0000) +pass 12: -477.4326 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.4325 (branch= 0.0001 subset rates= 0.0000) +pass 14: -477.4325 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4325 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.4320 (branch= 0.0000 subset rates= 0.0005) 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 @@ -16248,7 +16211,7 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.92 2.74 + 0.63 1.92 2.72 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. @@ -16267,7 +16230,7 @@ Results: Replicate 1 : -477.2119 (best) Replicate 2 : -477.4316 -Replicate 3 : -477.4317 (same topology as 2) (TERMINATED PREMATURELY) +Replicate 3 : -477.4319 (same topology as 2) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16284,7 +16247,7 @@ TL R(1) R(2) R(3) rep 1: 4.672 0.643 1.908 2.621 rep 2: 4.930 0.631 1.914 2.745 -rep 3: 4.931 0.631 1.917 2.743 +rep 3: 4.925 0.632 1.917 2.722 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### @@ -16575,11 +16538,6 @@ 1600 -484.5835 0.010 627 1700 -484.5832 0.010 627 1800 -484.5826 0.010 627 -1900 -484.5779 0.010 627 -2000 -484.5771 0.010 627 -2100 -484.5759 0.010 627 -2200 -484.5756 0.010 627 -2300 -484.5755 0.010 627 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16708,9 +16666,14 @@ Subset 3: Random seed for bootstrap reweighting: 585640194 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 2354, seed 586985660, best lnL -484.574 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1819, seed 2137317194, best lnL -484.583 gen current_lnL precision last_tree_imp -2354 -484.5742 0.010 627 +1819 -484.5826 0.010 627 +1900 -484.5779 0.010 627 +2000 -484.5771 0.010 627 +2100 -484.5759 0.010 627 +2200 -484.5756 0.010 627 +2300 -484.5755 0.010 627 2400 -484.5742 0.010 627 2500 -484.5725 0.010 627 2600 -484.5719 0.010 627 @@ -16835,41 +16798,35 @@ 3900 -485.6418 0.010 1226 4000 -485.6416 0.010 1226 4100 -485.6413 0.010 1226 -4200 -485.6403 0.010 1226 -4300 -485.6401 0.010 1226 -4400 -485.6388 0.010 1226 -4500 -485.6388 0.010 1226 -4600 -485.6381 0.010 1226 -4700 -485.6380 0.010 1226 -4800 -485.6378 0.010 1226 -4900 -485.6368 0.010 1226 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -485.6368 +Current score = -485.6404 Performing final optimizations... -pass 1 : -485.6238 (branch= 0.0048 subset rates= 0.0081) -pass 2 : -485.6067 (branch= 0.0171 subset rates= 0.0000) -pass 3 : -485.6034 (branch= 0.0033 subset rates= 0.0000) -pass 4 : -485.6027 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -485.6006 (branch= 0.0020 subset rates= 0.0000) -pass 6 : -485.5979 (branch= 0.0027 subset rates= 0.0000) -pass 7 : -485.5955 (branch= 0.0024 subset rates= 0.0000) -pass 8 : -485.5938 (branch= 0.0017 subset rates= 0.0000) -pass 9 : -485.5922 (branch= 0.0015 subset rates= 0.0000) -pass 10: -485.5911 (branch= 0.0011 subset rates= 0.0000) -pass 11: -485.5902 (branch= 0.0009 subset rates= 0.0000) -pass 12: -485.5895 (branch= 0.0007 subset rates= 0.0000) -pass 13: -485.5889 (branch= 0.0006 subset rates= 0.0000) -pass 14: -485.5870 (branch= 0.0005 subset rates= 0.0014) -pass 15: -485.5859 (branch= 0.0010 subset rates= 0.0000) -pass 16: -485.5850 (branch= 0.0009 subset rates= 0.0000) -pass 17: -485.5843 (branch= 0.0007 subset rates= 0.0000) -pass 18: -485.5837 (branch= 0.0006 subset rates= 0.0000) -pass 19: -485.5833 (branch= 0.0005 subset rates= 0.0000) -pass 20: -485.5829 (branch= 0.0004 subset rates= 0.0000) +pass 1 : -485.6318 (branch= 0.0049 subset rates= 0.0038) +pass 2 : -485.6110 (branch= 0.0180 subset rates= 0.0028) +pass 3 : -485.6076 (branch= 0.0034 subset rates= 0.0000) +pass 4 : -485.6048 (branch= 0.0028 subset rates= 0.0000) +pass 5 : -485.6041 (branch= 0.0007 subset rates= 0.0000) +pass 6 : -485.6024 (branch= 0.0017 subset rates= 0.0000) +pass 7 : -485.6004 (branch= 0.0019 subset rates= 0.0000) +pass 8 : -485.5990 (branch= 0.0014 subset rates= 0.0000) +pass 9 : -485.5958 (branch= 0.0012 subset rates= 0.0020) +pass 10: -485.5927 (branch= 0.0027 subset rates= 0.0004) +pass 11: -485.5907 (branch= 0.0017 subset rates= 0.0002) +pass 12: -485.5894 (branch= 0.0014 subset rates= 0.0000) +pass 13: -485.5882 (branch= 0.0012 subset rates= 0.0000) +pass 14: -485.5873 (branch= 0.0009 subset rates= 0.0000) +pass 15: -485.5865 (branch= 0.0008 subset rates= 0.0000) +pass 16: -485.5859 (branch= 0.0006 subset rates= 0.0000) +pass 17: -485.5854 (branch= 0.0005 subset rates= 0.0000) +pass 18: -485.5849 (branch= 0.0004 subset rates= 0.0000) +pass 19: -485.5836 (branch= 0.0004 subset rates= 0.0010) +pass 20: -485.5827 (branch= 0.0009 subset rates= 0.0000) optimization up to ... -pass 29: -485.5788 (branch= 0.0036 subset rates= 0.0004) +pass 30: -485.5793 (branch= 0.0034 subset rates= 0.0000) + optimization up to ... +pass 31: -485.5793 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -485.5788 +Final score = -485.5793 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16898,7 +16855,7 @@ no rate heterogeneity Subset rate multipliers: - 0.65 2.00 3.18 + 0.65 2.01 3.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -16917,7 +16874,7 @@ Results: Replicate 1 : -484.5428 Replicate 2 : -484.5428 (best) (same topology as 1) -Replicate 3 : -485.5788 (TERMINATED PREMATURELY) +Replicate 3 : -485.5793 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16934,7 +16891,7 @@ TL R(1) R(2) R(3) rep 1: 3.519 0.661 2.000 2.947 rep 2: 3.519 0.661 2.000 2.948 -rep 3: 3.673 0.648 2.000 3.183 +rep 3: 3.675 0.646 2.007 3.191 Saving tree from best search rep (#2) to bootstrap file ch.p.mkv.ssr.boot.tre @@ -17246,6 +17203,10 @@ 800 -474.0675 0.010 780 900 -474.0389 0.010 814 1000 -474.0337 0.010 814 +1100 -474.0268 0.010 814 +1200 -474.0215 0.010 814 +1300 -474.0182 0.010 814 +1400 -474.0128 0.010 814 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17371,13 +17332,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1052, seed 1667380914, best lnL -474.029 +Search rep 2 (of 5) generation 1442, seed 512244277, best lnL -474.011 gen current_lnL precision last_tree_imp -1052 -474.0293 0.010 814 -1100 -474.0268 0.010 814 -1200 -474.0215 0.010 814 -1300 -474.0182 0.010 814 -1400 -474.0128 0.010 814 +1442 -474.0114 0.010 814 1500 -474.0105 0.010 814 1600 -474.0097 0.010 814 1700 -474.0063 0.010 814 @@ -17414,7 +17371,7 @@ pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 8 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17515,24 +17472,138 @@ 2100 -473.9896 0.010 593 2200 -473.9886 0.010 593 2300 -473.9847 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 -473.9835 0.010 593 +2900 -473.9832 0.010 593 +3000 -473.9831 0.010 593 +3100 -473.9829 0.010 593 +Reached termination condition! +last topological improvement at gen 593 +Improvement over last 500 gen = 0.00065 +Current score = -473.9829 +Performing final optimizations... +pass 1 : -473.9813 (branch= 0.0000 subset rates= 0.0017) +pass 2 : -473.9645 (branch= 0.0167 subset rates= 0.0000) +pass 3 : -473.9634 (branch= 0.0012 subset rates= 0.0000) +pass 4 : -473.9591 (branch= 0.0042 subset rates= 0.0000) +pass 5 : -473.9566 (branch= 0.0026 subset rates= 0.0000) +pass 6 : -473.9557 (branch= 0.0009 subset rates= 0.0000) +pass 7 : -473.9531 (branch= 0.0008 subset rates= 0.0017) +pass 8 : -473.9529 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -473.9513 (branch= 0.0002 subset rates= 0.0014) +pass 10: -473.9511 (branch= 0.0002 subset rates= 0.0000) +pass 11: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9510 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0001) +pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 15: -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 11 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 3 (of 5)<<< + +>>>Search rep 4 (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=2070583773 + +Initial ln Likelihood: -607.1918 +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:+ 4.697 (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:+ 0.053 (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: -474.8419 +gen current_lnL precision last_tree_imp +0 -474.8419 0.010 0 +100 -474.1552 0.010 66 +200 -474.1375 0.010 66 +300 -474.0726 0.010 227 +400 -474.0527 0.010 227 +500 -474.0405 0.010 227 +600 -474.0290 0.010 227 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -473.9847 +Current score = -474.0245 Performing final optimizations... -pass 1 : -473.9814 (branch= 0.0000 subset rates= 0.0033) -pass 2 : -473.9642 (branch= 0.0171 subset rates= 0.0000) -pass 3 : -473.9589 (branch= 0.0053 subset rates= 0.0000) -pass 4 : -473.9570 (branch= 0.0020 subset rates= 0.0000) -pass 5 : -473.9546 (branch= 0.0024 subset rates= 0.0000) -pass 6 : -473.9535 (branch= 0.0009 subset rates= 0.0002) -pass 7 : -473.9522 (branch= 0.0009 subset rates= 0.0004) -pass 8 : -473.9517 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -473.9515 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0004) -pass 11: -473.9509 (branch= 0.0000 subset rates= 0.0001) -pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.0067 (branch= 0.0155 subset rates= 0.0023) +pass 2 : -473.9696 (branch= 0.0360 subset rates= 0.0011) +pass 3 : -473.9636 (branch= 0.0060 subset rates= 0.0000) +pass 4 : -473.9599 (branch= 0.0036 subset rates= 0.0000) +pass 5 : -473.9543 (branch= 0.0056 subset rates= 0.0000) +pass 6 : -473.9521 (branch= 0.0022 subset rates= 0.0000) +pass 7 : -473.9515 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -473.9511 (branch= 0.0002 subset rates= 0.0002) +pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9509 +Final score = -473.9508 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17565,7 +17636,7 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 4 (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!*** @@ -17573,14 +17644,15 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 4 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 : -473.9509 -Replicate 2 : -473.9508 (best) (same topology as 1) -Replicate 3 : -473.9509 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -473.9508 (same topology as 1) +Replicate 3 : -473.9508 (best) (same topology as 1) +Replicate 4 : -473.9508 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17597,9 +17669,10 @@ TL R(1) R(2) R(3) rep 1: 4.349 0.588 2.061 2.812 rep 2: 4.350 0.587 2.066 2.811 -rep 3: 4.351 0.587 2.067 2.814 +rep 3: 4.349 0.588 2.065 2.803 +rep 4: 4.349 0.588 2.065 2.808 -Saving final tree from best search rep (#2) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#3) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -17618,7 +17691,7 @@ dh_testroot dh_prep dh_auto_install - make -j15 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j16 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' @@ -17666,23 +17739,25 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-3_all.deb'. +dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-3_amd64.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-3_amd64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-3_amd64.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-3_amd64.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-3_amd64.deb'. -dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-3_amd64.deb'. +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../garli_2.1-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/36717/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/36717/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/10763 and its subdirectories -I: Current time: Sun Jun 20 03:49:02 -12 2021 -I: pbuilder-time-stamp: 1624204142 +I: removing directory /srv/workspace/pbuilder/36717 and its subdirectories +I: Current time: Sun Jul 24 12:19:24 +14 2022 +I: pbuilder-time-stamp: 1658614764