Diff of the two buildlogs: -- --- b1/build.log 2022-01-21 01:24:25.093019456 +0000 +++ b2/build.log 2022-01-21 01:33:32.248106649 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 20 13:11:52 -12 2022 -I: pbuilder-time-stamp: 1642727512 +I: Current time: Thu Feb 23 21:47:28 +14 2023 +I: pbuilder-time-stamp: 1677138448 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./garli_2.1-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.9BmHg2qy/trustedkeys.kbx': General error -gpgv: Signature made Wed Nov 18 02:03:14 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.h4MeHfaq/trustedkeys.kbx': General error +gpgv: Signature made Thu Nov 19 04:03:14 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -27,135 +27,169 @@ dpkg-source: info: unpacking garli_2.1-4.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3681189/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2362957/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/2362957/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2362957/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,-fixfilepath 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]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath 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='616d2344d4c64bf4969133476ab6bb22' - 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='3681189' - PS1='# ' - PS2='> ' + INVOCATION_ID=bbdb09f5b1d1418ab939b45e17a4ae21 + 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=2362957 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.9YWcC3wOuC/pbuilderrc_MhIk --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9YWcC3wOuC/b1 --logfile b1/build.log garli_2.1-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.9YWcC3wOuC/pbuilderrc_hdrs --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9YWcC3wOuC/b2 --logfile b2/build.log garli_2.1-4.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 ionos11-amd64 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more - -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 6 21:24 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/3681189/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 2021 more + -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount + -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Feb 23 21:47 sh -> bash + lrwxrwxrwx 1 root root 4 Feb 10 05:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 2021 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/2362957/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -289,7 +323,7 @@ Get: 88 http://deb.debian.org/debian bullseye/main amd64 openmpi-bin amd64 4.1.0-10 [238 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libopenmpi-dev amd64 4.1.0-10 [1192 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 ncl-tools amd64 2.1.21+git20190531.feceb81-3 [200 kB] -Fetched 44.3 MB in 2s (27.9 MB/s) +Fetched 44.3 MB in 1s (60.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) @@ -669,7 +703,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../garli_2.1-4_source.changes +hostname: Name or service not known +I: Running cd /build/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../garli_2.1-4_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-4 dpkg-buildpackage: info: source distribution unstable @@ -731,8 +766,8 @@ 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 @@ -810,7 +845,7 @@ config.status: creating config.h config.status: executing depfiles commands 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' @@ -831,13 +866,15 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:26: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); @@ -861,76 +898,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': -model.cpp:3666:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3675:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3677:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3684:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3691:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3692:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3699:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3705:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3710:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3713:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': -configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 602 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 388 | 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] - 264 | 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] - 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); @@ -992,6 +966,69 @@ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': +model.cpp:3666:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3675:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3677:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3684:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3691:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3692:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3699:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3705:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3710:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3713:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 602 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 388 | 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] + 264 | 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] + 518 | 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] 1880 | fread((char *) &seed, sizeof(seed), 1, pin); @@ -1002,8 +1039,6 @@ population.cpp:1896:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1210,8 +1245,8 @@ 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 @@ -1287,7 +1322,7 @@ config.status: executing depfiles commands 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' @@ -1308,13 +1343,15 @@ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:26: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); @@ -1338,13 +1375,81 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 602 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': +adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 271 | fread((char *) this, 1, scalarSize, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 278 | 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] + 280 | 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] + 281 | 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] + 283 | 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] + 284 | 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] + 286 | 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] + 287 | 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] + 289 | 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] + 290 | 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] + 292 | 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] + 293 | 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] + 295 | 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] + 296 | 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] + 298 | 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] + 299 | 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] + 301 | 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] + 302 | 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] + 304 | 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] + 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1407,79 +1512,10 @@ model.cpp:3713:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': -adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 271 | fread((char *) this, 1, scalarSize, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 278 | 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] - 280 | 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] - 281 | 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] - 283 | 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] - 284 | 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] - 286 | 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] - 287 | 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] - 289 | 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] - 290 | 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] - 292 | 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] - 293 | 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] - 295 | 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] - 296 | 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] - 298 | 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] - 299 | 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] - 301 | 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] - 302 | 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] - 304 | 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] - 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': -configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 602 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1547,7 +1583,6 @@ 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] 6881 | 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 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:22: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); @@ -1582,7 +1617,7 @@ # 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' @@ -4549,7 +4584,7 @@ pass 10: -12956.1235 (branch= 0.0000 omega= 0.0000) Looking for minimum length branches... Final score = -12956.1235 -Time used = 0 hours, 0 minutes and 42 seconds +Time used = 0 hours, 0 minutes and 18 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4701,7 +4736,7 @@ 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 21 seconds +Time used = 0 hours, 0 minutes and 12 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4907,7 +4942,7 @@ pass 82: -3350.2335 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2335 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5115,7 +5150,7 @@ pass 76: -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 ... ####################################################### @@ -5432,7 +5467,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5597,7 +5632,7 @@ 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 7 seconds +Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -5851,7 +5886,7 @@ pass 38: -13306.2062 (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 = -13306.2062 -Time used = 0 hours, 0 minutes and 8 seconds +Time used = 0 hours, 0 minutes and 6 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6703,7 +6738,7 @@ pass 22: -477.6852 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6852 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6914,7 +6949,7 @@ pass 14: -472.3906 (branch= 0.0000) Looking for minimum length branches... Final score = -472.3906 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7549,7 +7584,7 @@ pass 16: -474.6461 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.6461 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7826,7 +7861,7 @@ pass 494: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3584 -Time used = 0 hours, 0 minutes and 3 seconds +Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8090,7 +8125,7 @@ pass 372: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 5 seconds +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8671,7 +8706,7 @@ pass 490: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3585 -Time used = 0 hours, 0 minutes and 5 seconds +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -11380,6 +11415,12 @@ 300 -100.5813 0.500 183 400 -100.3300 0.500 183 500 -100.0135 0.500 183 +600 -99.2983 0.500 549 +700 -99.1955 0.500 549 +800 -99.0437 0.500 783 +900 -99.0045 0.500 783 +1000 -98.8740 0.500 949 +1100 -98.8107 0.500 1029 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11476,17 +11517,11 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 578, seed 1283700979, best lnL -99.346 +Bootstrap rep 1 (of 1) generation 1153, seed 1608446853, best lnL -98.806 gen current_lnL precision last_tree_imp -578 -99.3464 0.500 549 -600 -99.2983 0.500 549 -700 -99.1955 0.500 549 -800 -99.0437 0.500 783 -900 -99.0045 0.500 783 -1000 -98.8740 0.500 949 -NOTE: ****Specified generation limit (1000) reached... +1153 -98.8064 0.500 1029 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -11498,41 +11533,37 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.6652 + 0.6963 with an invariant (invariable) site category, proportion estimated - 0.0626 + 0.0608 Substitution rate categories under this model: rate proportion - 0.0000 0.0626 - 0.1054 0.3125 - 0.5916 0.3125 - 2.3030 0.3125 + 0.0000 0.0608 + 0.1138 0.3131 + 0.6067 0.3131 + 2.2795 0.3131 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -98.8740 +Replicate 1 : -98.8064 Parameter estimates: alpha pinv -rep 1: 0.665 0.063 +rep 1: 0.696 0.061 Treelengths: TL -rep 1: 1.521 +rep 1: 1.611 Saving best tree to bootstrap file ch.a.G3.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf @@ -11655,6 +11686,11 @@ 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 +600 -111.7788 0.500 84 +Optimization precision reduced + Optimizing parameters... improved 0.386 lnL + Optimizing branchlengths... improved 0.390 lnL +700 -110.8142 0.010 615 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11741,14 +11777,9 @@ STARTING RUN Restarting from checkpoint... - generation 598, seed 2088754582, best lnL -111.779 + generation 711, seed 1683349145, best lnL -110.621 gen current_lnL precision last_tree_imp -598 -111.7788 0.500 84 -600 -111.7788 0.500 84 -Optimization precision reduced - Optimizing parameters... improved 0.386 lnL - Optimizing branchlengths... improved 0.390 lnL -700 -110.8142 0.010 615 +711 -110.6213 0.010 707 800 -110.5642 0.010 707 900 -110.5555 0.010 707 1000 -110.5065 0.010 707 @@ -11938,6 +11969,8 @@ 1800 -111.6818 0.010 563 1900 -111.6818 0.010 563 2000 -111.6817 0.010 563 +2100 -111.6817 0.010 563 +2200 -111.6817 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12023,9 +12056,9 @@ STARTING RUN Restarting from checkpoint... - generation 2011, seed 2009137307, best lnL -111.682 + generation 2257, seed 813259455, best lnL -111.682 gen current_lnL precision last_tree_imp -2011 -111.6817 0.010 563 +2257 -111.6817 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -12041,7 +12074,7 @@ no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... @@ -12274,9 +12307,9 @@ STARTING RUN Restarting from checkpoint... - generation 54, seed 227725811, best lnL -205.599 + generation 56, seed 1686783873, best lnL -205.599 gen current_lnL precision last_tree_imp -54 -205.5990 0.500 53 +56 -205.5990 0.500 53 60 -205.5990 0.500 53 70 -205.5741 0.500 53 80 -205.4022 0.500 76 @@ -12471,6 +12504,7 @@ 30 -199.5474 0.500 20 40 -198.9134 0.500 39 50 -198.8194 0.500 39 +60 -198.0322 0.500 59 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12558,10 +12592,9 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 54, seed 1502463517, best lnL -198.784 +Bootstrap rep 1 (of 1) generation 64, seed 628128032, best lnL -198.007 gen current_lnL precision last_tree_imp -54 -198.7835 0.500 39 -60 -198.0322 0.500 59 +64 -198.0072 0.500 59 70 -198.0072 0.500 59 80 -197.9625 0.500 59 90 -197.8311 0.500 59 @@ -12785,7 +12818,6 @@ 1500 -3352.2764 0.010 0 1600 -3352.1737 0.010 0 1700 -3352.1613 0.010 0 -1800 -3352.0805 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12889,9 +12921,10 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1884, seed 102687786, best lnL -3351.733 +Search rep 1 (of 2) generation 1722, seed 1657585205, best lnL -3352.098 gen current_lnL precision last_tree_imp -1884 -3351.7327 0.010 0 +1722 -3352.0980 0.010 0 +1800 -3352.0805 0.010 0 1900 -3351.7327 0.010 0 2000 -3351.6677 0.010 0 2100 -3351.4852 0.010 0 @@ -12906,64 +12939,62 @@ 3000 -3351.0145 0.010 0 3100 -3351.0017 0.010 0 3200 -3350.9810 0.010 0 -3300 -3350.9785 0.010 0 -3400 -3350.9748 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.9748 +Current score = -3350.9785 Performing final optimizations... -pass 1 : -3350.9009 (branch= 0.0000 alpha= 0.0000 pinv= 0.0168 eq freqs= 0.0062 rel rates= 0.0509 subset rates= 0.0000) -pass 2 : -3350.8189 (branch= 0.0000 alpha= 0.0162 pinv= 0.0166 eq freqs= 0.0027 rel rates= 0.0465 subset rates= 0.0000) -pass 3 : -3350.7485 (branch= 0.0038 alpha= 0.0178 pinv= 0.0149 eq freqs= 0.0000 rel rates= 0.0326 subset rates= 0.0011) -pass 4 : -3350.6851 (branch= 0.0088 alpha= 0.0137 pinv= 0.0143 eq freqs= 0.0000 rel rates= 0.0254 subset rates= 0.0013) -pass 5 : -3350.6307 (branch= 0.0060 alpha= 0.0123 pinv= 0.0133 eq freqs= 0.0000 rel rates= 0.0213 subset rates= 0.0015) -pass 6 : -3350.5845 (branch= 0.0038 alpha= 0.0108 pinv= 0.0122 eq freqs= 0.0002 rel rates= 0.0192 subset rates= 0.0000) -pass 7 : -3350.5414 (branch= 0.0013 alpha= 0.0112 pinv= 0.0110 eq freqs= 0.0000 rel rates= 0.0181 subset rates= 0.0014) -pass 8 : -3350.5048 (branch= 0.0019 alpha= 0.0100 pinv= 0.0101 eq freqs= 0.0001 rel rates= 0.0146 subset rates= 0.0000) -pass 9 : -3350.4713 (branch= 0.0002 alpha= 0.0093 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0138 subset rates= 0.0011) -pass 10: -3350.4422 (branch= 0.0009 alpha= 0.0085 pinv= 0.0082 eq freqs= 0.0001 rel rates= 0.0114 subset rates= 0.0000) -pass 11: -3350.4166 (branch= 0.0001 alpha= 0.0077 pinv= 0.0074 eq freqs= 0.0000 rel rates= 0.0104 subset rates= 0.0000) -pass 12: -3350.3936 (branch= 0.0000 alpha= 0.0073 pinv= 0.0066 eq freqs= 0.0000 rel rates= 0.0091 subset rates= 0.0000) -pass 13: -3350.3731 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0079 subset rates= 0.0000) -pass 14: -3350.3550 (branch= 0.0000 alpha= 0.0059 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0069 subset rates= 0.0000) -pass 15: -3350.3391 (branch= 0.0000 alpha= 0.0053 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0059 subset rates= 0.0000) -pass 16: -3350.3252 (branch= 0.0000 alpha= 0.0047 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0050 subset rates= 0.0000) -pass 17: -3350.3131 (branch= 0.0000 alpha= 0.0041 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0044 subset rates= 0.0000) -pass 18: -3350.3024 (branch= 0.0000 alpha= 0.0036 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0037 subset rates= 0.0000) -pass 19: -3350.2932 (branch= 0.0000 alpha= 0.0032 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0032 subset rates= 0.0000) -pass 20: -3350.2850 (branch= 0.0000 alpha= 0.0028 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2448 (branch= 0.0000 alpha= 0.0140 pinv= 0.0127 eq freqs= 0.0000 rel rates= 0.0135 subset rates= 0.0000) +pass 1 : -3350.9072 (branch= 0.0000 alpha= 0.0000 pinv= 0.0111 eq freqs= 0.0072 rel rates= 0.0529 subset rates= 0.0000) +pass 2 : -3350.8274 (branch= 0.0000 alpha= 0.0163 pinv= 0.0168 eq freqs= 0.0000 rel rates= 0.0467 subset rates= 0.0000) +pass 3 : -3350.7544 (branch= 0.0038 alpha= 0.0175 pinv= 0.0154 eq freqs= 0.0029 rel rates= 0.0322 subset rates= 0.0011) +pass 4 : -3350.6917 (branch= 0.0080 alpha= 0.0137 pinv= 0.0145 eq freqs= 0.0000 rel rates= 0.0252 subset rates= 0.0014) +pass 5 : -3350.6366 (branch= 0.0061 alpha= 0.0129 pinv= 0.0134 eq freqs= 0.0004 rel rates= 0.0208 subset rates= 0.0014) +pass 6 : -3350.5879 (branch= 0.0039 alpha= 0.0113 pinv= 0.0124 eq freqs= 0.0003 rel rates= 0.0198 subset rates= 0.0011) +pass 7 : -3350.5460 (branch= 0.0025 alpha= 0.0107 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0171 subset rates= 0.0000) +pass 8 : -3350.5080 (branch= 0.0004 alpha= 0.0103 pinv= 0.0102 eq freqs= 0.0000 rel rates= 0.0158 subset rates= 0.0013) +pass 9 : -3350.4746 (branch= 0.0012 alpha= 0.0096 pinv= 0.0093 eq freqs= 0.0001 rel rates= 0.0132 subset rates= 0.0000) +pass 10: -3350.4456 (branch= 0.0002 alpha= 0.0086 pinv= 0.0083 eq freqs= 0.0000 rel rates= 0.0119 subset rates= 0.0000) +pass 11: -3350.4192 (branch= 0.0001 alpha= 0.0083 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0105 subset rates= 0.0000) +pass 12: -3350.3958 (branch= 0.0000 alpha= 0.0075 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0091 subset rates= 0.0000) +pass 13: -3350.3741 (branch= 0.0000 alpha= 0.0068 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0079 subset rates= 0.0011) +pass 14: -3350.3561 (branch= 0.0005 alpha= 0.0057 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0063 subset rates= 0.0000) +pass 15: -3350.3405 (branch= 0.0001 alpha= 0.0050 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) +pass 16: -3350.3266 (branch= 0.0000 alpha= 0.0046 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0051 subset rates= 0.0000) +pass 17: -3350.3142 (branch= 0.0000 alpha= 0.0042 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0044 subset rates= 0.0000) +pass 18: -3350.3034 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0038 subset rates= 0.0000) +pass 19: -3350.2940 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0033 subset rates= 0.0000) +pass 20: -3350.2857 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2446 (branch= 0.0000 alpha= 0.0143 pinv= 0.0129 eq freqs= 0.0000 rel rates= 0.0138 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2358 (branch= 0.0000 alpha= 0.0030 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0032 subset rates= 0.0000) +pass 40: -3350.2355 (branch= 0.0000 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0033 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2339 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) +pass 50: -3350.2336 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 62: -3350.2335 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 68: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2335 +Final score = -3350.2331 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.112, AG = 10.399, AT = 2.685, CG = 0.001, CT = 21.861, GT = 1.000 + AC = 3.116, AG = 10.421, AT = 2.692, CG = 0.001, CT = 21.931, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3329 0.2222 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5776 + 0.5773 with an invariant (invariable) site category, proportion estimated - 0.3655 + 0.3656 Substitution rate categories under this model: rate proportion - 0.0000 0.3655 + 0.0000 0.3656 0.0485 0.1586 - 0.2996 0.1586 - 0.8695 0.1586 - 2.7824 0.1586 + 0.2994 0.1586 + 0.8693 0.1586 + 2.7829 0.1586 Model 2 Number of states = 2 (binary data) @@ -12988,20 +13019,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2335 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2331 (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: 3.112 10.4 2.685 0.001 21.86 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.116 10.42 2.692 0.001 21.93 1 0.333 0.222 0.157 0.288 0.577 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.788 1.820 0.180 +rep 1: 0.789 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -13152,12 +13183,6 @@ 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 500 -3323.6818 0.500 1 -600 -3323.3459 0.500 1 -Optimization precision reduced - Optimizing parameters... improved 1.812 lnL - Optimizing branchlengths... improved 0.023 lnL -700 -3321.3650 0.255 1 -800 -3321.0294 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13258,77 +13283,79 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 873, seed 866366283, best lnL -3321.014 +Search rep 1 (of 2) generation 555, seed 1614051380, best lnL -3323.453 gen current_lnL precision last_tree_imp -873 -3321.0142 0.255 1 +555 -3323.4534 0.500 1 +600 -3323.3459 0.500 1 +Optimization precision reduced + Optimizing parameters... improved 1.812 lnL + Optimizing branchlengths... improved 0.023 lnL +700 -3321.3650 0.255 1 +800 -3321.0294 0.255 1 900 -3321.0142 0.255 1 1000 -3320.9667 0.255 1 1100 -3320.8654 0.255 1 Optimization precision reduced Optimizing parameters... improved 0.580 lnL Optimizing branchlengths... improved 0.061 lnL -1200 -3320.1395 0.010 1 -1300 -3320.0805 0.010 1 -1400 -3320.0729 0.010 1 -1500 -3320.0238 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.0197 +Current score = -3320.1522 Performing final optimizations... -pass 1 : -3319.5681 (branch= 0.0160 alpha= 0.0000 pinv= 0.0153 eq freqs= 0.0000 rel rates= 0.3622 ins/del rates= 0.0580) -pass 2 : -3319.2542 (branch= 0.0434 alpha= 0.0177 pinv= 0.0155 eq freqs= 0.0093 rel rates= 0.2152 ins/del rates= 0.0127) -pass 3 : -3319.0278 (branch= 0.0265 alpha= 0.0127 pinv= 0.0155 eq freqs= 0.0000 rel rates= 0.1641 ins/del rates= 0.0077) -pass 4 : -3318.8478 (branch= 0.0144 alpha= 0.0113 pinv= 0.0148 eq freqs= 0.0018 rel rates= 0.1338 ins/del rates= 0.0039) -pass 5 : -3318.6917 (branch= 0.0098 alpha= 0.0117 pinv= 0.0140 eq freqs= 0.0011 rel rates= 0.1161 ins/del rates= 0.0035) -pass 6 : -3318.5643 (branch= 0.0076 alpha= 0.0113 pinv= 0.0131 eq freqs= 0.0006 rel rates= 0.0921 ins/del rates= 0.0027) -pass 7 : -3318.4553 (branch= 0.0050 alpha= 0.0105 pinv= 0.0122 eq freqs= 0.0006 rel rates= 0.0788 ins/del rates= 0.0021) -pass 8 : -3318.3624 (branch= 0.0031 alpha= 0.0103 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0666 ins/del rates= 0.0014) -pass 9 : -3318.2830 (branch= 0.0024 alpha= 0.0093 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0562 ins/del rates= 0.0010) -pass 10: -3318.2150 (branch= 0.0016 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0001 rel rates= 0.0471 ins/del rates= 0.0007) -pass 11: -3318.1569 (branch= 0.0011 alpha= 0.0085 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0394 ins/del rates= 0.0005) -pass 12: -3318.1070 (branch= 0.0007 alpha= 0.0079 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0330 ins/del rates= 0.0003) -pass 13: -3318.0647 (branch= 0.0004 alpha= 0.0074 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0271 ins/del rates= 0.0002) -pass 14: -3318.0283 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0228 ins/del rates= 0.0001) -pass 15: -3317.9966 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0195 ins/del rates= 0.0001) -pass 16: -3317.9691 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0166 ins/del rates= 0.0000) -pass 17: -3317.9451 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0142 ins/del rates= 0.0000) -pass 18: -3317.9243 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0121 ins/del rates= 0.0000) -pass 19: -3317.9061 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0104 ins/del rates= 0.0000) -pass 20: -3317.8903 (branch= 0.0000 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0089 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8113 (branch= 0.0000 alpha= 0.0189 pinv= 0.0174 eq freqs= 0.0001 rel rates= 0.0425 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7925 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0098 ins/del rates= 0.0000) +pass 1 : -3319.7677 (branch= 0.0384 alpha= 0.0086 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.3005 ins/del rates= 0.0208) +pass 2 : -3319.4562 (branch= 0.0409 alpha= 0.0061 pinv= 0.0160 eq freqs= 0.0000 rel rates= 0.2365 ins/del rates= 0.0119) +pass 3 : -3319.1918 (branch= 0.0352 alpha= 0.0112 pinv= 0.0148 eq freqs= 0.0025 rel rates= 0.1933 ins/del rates= 0.0075) +pass 4 : -3318.9740 (branch= 0.0238 alpha= 0.0106 pinv= 0.0146 eq freqs= 0.0015 rel rates= 0.1583 ins/del rates= 0.0091) +pass 5 : -3318.7938 (branch= 0.0146 alpha= 0.0095 pinv= 0.0139 eq freqs= 0.0009 rel rates= 0.1345 ins/del rates= 0.0069) +pass 6 : -3318.6474 (branch= 0.0101 alpha= 0.0108 pinv= 0.0129 eq freqs= 0.0003 rel rates= 0.1079 ins/del rates= 0.0043) +pass 7 : -3318.5231 (branch= 0.0064 alpha= 0.0096 pinv= 0.0122 eq freqs= 0.0004 rel rates= 0.0930 ins/del rates= 0.0027) +pass 8 : -3318.4160 (branch= 0.0048 alpha= 0.0092 pinv= 0.0113 eq freqs= 0.0004 rel rates= 0.0794 ins/del rates= 0.0020) +pass 9 : -3318.3261 (branch= 0.0031 alpha= 0.0093 pinv= 0.0104 eq freqs= 0.0002 rel rates= 0.0656 ins/del rates= 0.0013) +pass 10: -3318.2498 (branch= 0.0020 alpha= 0.0089 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0548 ins/del rates= 0.0009) +pass 11: -3318.1856 (branch= 0.0013 alpha= 0.0083 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0452 ins/del rates= 0.0006) +pass 12: -3318.1308 (branch= 0.0009 alpha= 0.0077 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0378 ins/del rates= 0.0004) +pass 13: -3318.0840 (branch= 0.0006 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0316 ins/del rates= 0.0002) +pass 14: -3318.0444 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0259 ins/del rates= 0.0001) +pass 15: -3318.0104 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0218 ins/del rates= 0.0001) +pass 16: -3317.9807 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0187 ins/del rates= 0.0000) +pass 17: -3317.9551 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0159 ins/del rates= 0.0000) +pass 18: -3317.9328 (branch= 0.0001 alpha= 0.0044 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0136 ins/del rates= 0.0000) +pass 19: -3317.9134 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0116 ins/del rates= 0.0000) +pass 20: -3317.8966 (branch= 0.0000 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0099 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8127 (branch= 0.0001 alpha= 0.0189 pinv= 0.0174 eq freqs= 0.0001 rel rates= 0.0474 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7929 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0109 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: -3317.7883 (branch= 0.0000 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0026 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: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0006 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= 0.0002 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... -pass 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) +pass 73: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7870 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -3317.7871 +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.070, AG = 10.282, AT = 2.662, CG = 0.001, CT = 21.582, GT = 1.000 + AC = 3.066, AG = 10.265, AT = 2.656, CG = 0.001, CT = 21.541, 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 - 0.5747 + 0.5750 with an invariant (invariable) site category, proportion estimated - 0.3612 + 0.3613 Substitution rate categories under this model: rate proportion - 0.0000 0.3612 - 0.0479 0.1597 - 0.2979 0.1597 - 0.8678 0.1597 - 2.7863 0.1597 + 0.0000 0.3613 + 0.0480 0.1597 + 0.2981 0.1597 + 0.8680 0.1597 + 2.7859 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -13354,13 +13381,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7871 (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: 3.07 10.28 2.662 0.001 21.58 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.066 10.27 2.656 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -13519,10 +13546,6 @@ 6600 -210.4214 0.010 1104 6800 -210.3965 0.010 1104 7000 -210.3384 0.010 1104 -7200 -210.3218 0.010 1104 -7400 -210.2807 0.010 1104 -7600 -210.2625 0.010 1104 -7800 -210.1872 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13602,9 +13625,16 @@ STARTING RUN Restarting from checkpoint... - generation 7816, seed 904882037, best lnL -210.183 + generation 7141, seed 1671907641, best lnL -210.322 gen current_lnL precision last_tree_imp -7816 -210.1826 0.010 1104 +7141 -210.3219 0.010 1104 +7200 -210.3218 0.010 1104 +7300 -210.2908 0.010 1104 +7400 -210.2807 0.010 1104 +7500 -210.2794 0.010 1104 +7600 -210.2625 0.010 1104 +7700 -210.2314 0.010 1104 +7800 -210.1872 0.010 1104 7900 -210.1766 0.010 1104 8000 -210.1732 0.010 1104 8100 -210.1384 0.010 1104 @@ -13817,63 +13847,15 @@ 8200 -190.4371 0.010 1979 8400 -190.4300 0.010 1979 8600 -190.4289 0.010 1979 -8800 -190.3393 0.010 1979 -9000 -190.3166 0.010 1979 -9200 -190.3110 0.010 1979 -9400 -190.2750 0.010 1979 -9600 -190.2684 0.010 1979 -9800 -190.2636 0.010 1979 -10000 -190.2593 0.010 1979 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 1.002, AG = 1.854, AT = 0.010, CG = 4.558, CT = 23.421, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.3198 0.3138 0.2643 0.1021 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 5.1786 - with an invariant (invariable) site category, proportion estimated - 0.1416 - Substitution rate categories under this model: - rate proportion - 0.0000 0.1416 - 0.5093 0.2146 - 0.8081 0.2146 - 1.0830 0.2146 - 1.5996 0.2146 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. - - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -190.2593 - -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: 1.002 1.854 0.009585 4.558 23.42 1 0.320 0.314 0.264 0.102 5.179 0.142 - -Treelengths: - TL -rep 1: 2.422 +NOTE: ****Specified time limit (5 seconds) reached... -Saving best tree to bootstrap file ch.n.G4.boot.tre +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -WARNING: Tree from prematurely terminated search saved to bootstrap file -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -13945,47 +13927,56 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 10001, seed 421406060, best lnL -190.259 +Bootstrap rep 1 (of 1) generation 8678, seed 624207080, best lnL -190.361 gen current_lnL precision last_tree_imp -10001 -190.2593 0.010 1979 +8678 -190.3615 0.010 1979 +8700 -190.3576 0.010 1979 +8800 -190.3393 0.010 1979 +8900 -190.3201 0.010 1979 +9000 -190.3166 0.010 1979 +9100 -190.3125 0.010 1979 +9200 -190.3110 0.010 1979 +Reached termination condition! +last topological improvement at gen 1979 +Improvement over last 500 gen = 0.04661 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 1.002, AG = 1.854, AT = 0.010, CG = 4.558, CT = 23.421, GT = 1.000 + AC = 0.898, AG = 1.716, AT = 0.009, CG = 4.161, CT = 21.158, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3198 0.3138 0.2643 0.1021 + (ACGT) 0.3174 0.3194 0.2591 0.1040 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 5.1786 + 5.9622 with an invariant (invariable) site category, proportion estimated 0.1416 Substitution rate categories under this model: rate proportion 0.0000 0.1416 - 0.5093 0.2146 - 0.8081 0.2146 - 1.0830 0.2146 - 1.5996 0.2146 + 0.5377 0.2146 + 0.8239 0.2146 + 1.0813 0.2146 + 1.5570 0.2146 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -190.2593 +Replicate 1 : -190.3110 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: 1.002 1.854 0.009585 4.558 23.42 1 0.320 0.314 0.264 0.102 5.179 0.142 +rep 1: 0.8984 1.716 0.009166 4.161 21.16 1 0.317 0.319 0.259 0.104 5.962 0.142 Treelengths: TL -rep 1: 2.422 +rep 1: 2.415 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -14456,67 +14447,15 @@ 9200 -209.8943 0.010 5977 9400 -209.8851 0.010 5977 9600 -209.8753 0.010 5977 -9800 -209.8445 0.010 5977 -10000 -209.8443 0.010 5977 - Optimizing parameters... improved 0.460 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 2.783, AG = 4.985, AT = 0.048, CG = 5.037, CT = 9.645, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2414 0.3364 0.2130 0.2092 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 4.8228 - with an invariant (invariable) site category, proportion estimated - 0.3071 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3071 - 0.4945 0.1732 - 0.7996 0.1732 - 1.0836 0.1732 - 1.6223 0.1732 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. - - -NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with - a positive constraint, it is possible for a constrained branch itself to be collapsed. - If you care, be careful to check whether this has happened or turn off branch collapsing. - -Saving site likelihoods to file ch.n.const.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -209.3841 - -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: 2.783 4.985 0.04773 5.037 9.645 1 0.241 0.336 0.213 0.209 4.823 0.307 - -Treelengths: - TL -rep 1: 2.447 - -Saving final tree from best search rep (#1) to ch.n.const.best.tre -Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -14595,29 +14534,33 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 350190222, best lnL -209.384 + generation 9694, seed 1048476749, best lnL -209.875 gen current_lnL precision last_tree_imp -10001 -209.3841 0.010 5977 +9694 -209.8753 0.010 5977 +9700 -209.8753 0.010 5977 +Reached termination condition! +last topological improvement at gen 5977 +Improvement over last 500 gen = 0.01900 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.783, AG = 4.985, AT = 0.048, CG = 5.037, CT = 9.645, GT = 1.000 + AC = 2.782, AG = 4.985, AT = 0.240, CG = 5.035, CT = 9.645, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2414 0.3364 0.2130 0.2092 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.8228 + 2.1082 with an invariant (invariable) site category, proportion estimated - 0.3071 + 0.2459 Substitution rate categories under this model: rate proportion - 0.0000 0.3071 - 0.4945 0.1732 - 0.7996 0.1732 - 1.0836 0.1732 - 1.6223 0.1732 + 0.0000 0.2459 + 0.3059 0.1885 + 0.6660 0.1885 + 1.0725 0.1885 + 1.9556 0.1885 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. @@ -14633,15 +14576,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.3841 +Replicate 1 : -209.8753 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: 2.783 4.985 0.04773 5.037 9.645 1 0.241 0.336 0.213 0.209 4.823 0.307 +rep 1: 2.782 4.985 0.2399 5.035 9.645 1 0.241 0.336 0.213 0.209 2.108 0.246 Treelengths: TL -rep 1: 2.447 +rep 1: 2.444 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 @@ -14855,7 +14798,6 @@ Optimizing parameters... improved 0.019 lnL Optimizing branchlengths... improved 0.000 lnL 1200 -13181.4112 0.304 1 -1300 -13181.3755 0.304 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14978,16 +14920,12 @@ Subset 3: Random seed for bootstrap reweighting: 1903425807 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1387, seed 1036027850, best lnL -13181.370 +Bootstrap rep 1 (of 1) generation 1221, seed 1863568284, best lnL -13181.411 gen current_lnL precision last_tree_imp -1387 -13181.3705 0.304 1 +1221 -13181.4112 0.304 1 +1300 -13181.3755 0.304 1 1400 -13181.3694 0.304 1 1500 -13181.3534 0.304 1 -1600 -13181.3306 0.304 1 -Optimization precision reduced - Optimizing parameters... improved 0.011 lnL - Optimizing branchlengths... improved 0.000 lnL -1700 -13181.3200 0.206 1 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -14995,55 +14933,55 @@ 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 = 1.173, CG = 1.173, CT = 2.656, GT = 1.000 + AC = 2.042, AG = 3.173, AT = 1.172, CG = 1.172, CT = 2.656, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3051 0.1870 0.2737 0.2342 + (ACGT) 0.3054 0.1867 0.2740 0.2339 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3878 + 0.3876 Substitution rate categories under this model: rate proportion 0.0150 0.2500 - 0.1726 0.2500 - 0.7177 0.2500 - 3.0948 0.2500 + 0.1724 0.2500 + 0.7175 0.2500 + 3.0952 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 3.839, AG = 4.640, AT = 0.735, CG = 4.640, CT = 3.839, GT = 1.000 + AC = 3.841, AG = 4.640, AT = 0.735, CG = 4.640, CT = 3.841, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2505 0.1555 0.1902 0.4037 + (ACGT) 0.2508 0.1558 0.1899 0.4036 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.4489 + 0.4487 Substitution rate categories under this model: rate proportion 0.0243 0.2500 - 0.2172 0.2500 - 0.7792 0.2500 - 2.9793 0.2500 + 0.2171 0.2500 + 0.7790 0.2500 + 2.9796 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 7.121, AT = 5.573, CG = 1.050, CT = 7.121, GT = 1.000 + AC = 1.000, AG = 7.157, AT = 5.572, CG = 1.050, CT = 7.157, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1612 0.3394 0.2965 0.2029 + (ACGT) 0.1611 0.3397 0.2961 0.2031 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.9040 + 4.9042 with an invariant (invariable) site category, proportion estimated - 0.0123 + 0.0116 Substitution rate categories under this model: rate proportion - 0.0000 0.0123 - 0.4980 0.2469 - 0.8016 0.2469 - 1.0835 0.2469 - 1.6169 0.2469 + 0.0000 0.0116 + 0.4980 0.2471 + 0.8016 0.2471 + 1.0835 0.2471 + 1.6169 0.2471 Subset rate multipliers: 0.53 0.28 2.20 @@ -15060,25 +14998,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13181.3031 (TERMINATED PREMATURELY) +Replicate 1 : -13181.3306 (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 1.173 1.173 2.656 1 0.305 0.187 0.274 0.234 0.388 +rep 1: 2.042 3.173 1.172 1.172 2.656 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: 3.839 4.64 0.7352 4.64 3.839 1 0.251 0.156 0.190 0.404 0.449 +rep 1: 3.841 4.64 0.7354 4.64 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 -rep 1: 1 7.121 5.573 1.05 7.121 1 0.161 0.339 0.296 0.203 4.904 0.012 +rep 1: 1 7.157 5.572 1.05 7.157 1 0.161 0.340 0.296 0.203 4.904 0.012 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.667 0.526 0.278 2.196 +rep 1: 1.670 0.526 0.278 2.196 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -15402,111 +15340,6 @@ 3000 -467.7065 0.010 62 3100 -467.7064 0.010 62 3200 -467.7062 0.010 62 -3300 -467.7053 0.010 62 -3400 -467.7052 0.010 62 -3500 -467.7047 0.010 62 -3600 -467.7047 0.010 62 -3700 -467.7045 0.010 62 -3800 -467.7044 0.010 62 -Reached termination condition! -last topological improvement at gen 62 -Improvement over last 500 gen = 0.00094 -Current score = -467.7044 -Performing final optimizations... -pass 1 : -467.6992 (branch= 0.0052 subset rates= 0.0000) -pass 2 : -467.6899 (branch= 0.0093 subset rates= 0.0000) -pass 3 : -467.6855 (branch= 0.0044 subset rates= 0.0000) -pass 4 : -467.6826 (branch= 0.0029 subset rates= 0.0000) -pass 5 : -467.6811 (branch= 0.0015 subset rates= 0.0000) -pass 6 : -467.6802 (branch= 0.0010 subset rates= 0.0000) -pass 7 : -467.6798 (branch= 0.0003 subset rates= 0.0000) -pass 8 : -467.6791 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -467.6788 (branch= 0.0003 subset rates= 0.0000) -pass 10: -467.6787 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6786 (branch= 0.0000 subset rates= 0.0000) -pass 12: -467.6786 (branch= 0.0000 subset rates= 0.0001) -pass 13: -467.6784 (branch= 0.0002 subset rates= 0.0000) -pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6784 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -467.6784 -Time used so far = 0 hours, 0 minutes and 5 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.79 1.47 2.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 2 (of 5)<<< - ->>>Search rep 3 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=92129707 - -Initial ln Likelihood: -601.8419 -optimizing: starting branch lengths, subset rates... -pass 1:+ 124.353 (branch= 119.72 scale= 0.23 subset rates= 4.41) -pass 2:+ 7.962 (branch= 7.00 scale= 0.00 subset rates= 0.96) -pass 3:+ 1.474 (branch= 1.29 scale= 0.02 subset rates= 0.17) -pass 4:+ 0.142 (branch= 0.14 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8958 -gen current_lnL precision last_tree_imp -0 -467.8958 0.010 0 -100 -467.8477 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15632,9 +15465,114 @@ STARTING RUN Restarting from checkpoint... -Search rep 3 (of 5) generation 181, seed 233782413, best lnL -467.828 +Search rep 2 (of 5) generation 3256, seed 1609860196, best lnL -467.706 +gen current_lnL precision last_tree_imp +3256 -467.7060 0.010 62 +3300 -467.7053 0.010 62 +3400 -467.7052 0.010 62 +3500 -467.7047 0.010 62 +3600 -467.7047 0.010 62 +3700 -467.7045 0.010 62 +3800 -467.7044 0.010 62 +Reached termination condition! +last topological improvement at gen 62 +Improvement over last 500 gen = 0.00094 +Current score = -467.7044 +Performing final optimizations... +pass 1 : -467.6992 (branch= 0.0052 subset rates= 0.0000) +pass 2 : -467.6899 (branch= 0.0093 subset rates= 0.0000) +pass 3 : -467.6855 (branch= 0.0044 subset rates= 0.0000) +pass 4 : -467.6826 (branch= 0.0029 subset rates= 0.0000) +pass 5 : -467.6811 (branch= 0.0015 subset rates= 0.0000) +pass 6 : -467.6802 (branch= 0.0010 subset rates= 0.0000) +pass 7 : -467.6798 (branch= 0.0003 subset rates= 0.0000) +pass 8 : -467.6791 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -467.6788 (branch= 0.0003 subset rates= 0.0000) +pass 10: -467.6787 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6786 (branch= 0.0000 subset rates= 0.0000) +pass 12: -467.6786 (branch= 0.0000 subset rates= 0.0001) +pass 13: -467.6784 (branch= 0.0002 subset rates= 0.0000) +pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6784 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -467.6784 +Time used so far = 0 hours, 0 minutes and 6 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.79 1.47 2.18 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 2 (of 5)<<< + +>>>Search rep 3 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=92129707 + +Initial ln Likelihood: -601.8419 +optimizing: starting branch lengths, subset rates... +pass 1:+ 124.353 (branch= 119.72 scale= 0.23 subset rates= 4.41) +pass 2:+ 7.962 (branch= 7.00 scale= 0.00 subset rates= 0.96) +pass 3:+ 1.474 (branch= 1.29 scale= 0.02 subset rates= 0.17) +pass 4:+ 0.142 (branch= 0.14 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -467.8958 gen current_lnL precision last_tree_imp -181 -467.8282 0.010 0 +0 -467.8958 0.010 0 +100 -467.8477 0.010 0 200 -467.8279 0.010 0 300 -467.8200 0.010 0 400 -467.7980 0.010 315 @@ -15701,7 +15639,7 @@ pass 14: -467.6785 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6785 -Time used so far = 0 hours, 0 minutes and 9 seconds +Time used so far = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -15783,49 +15721,27 @@ 400 -467.7918 0.010 0 500 -467.7788 0.010 0 600 -467.7703 0.010 0 -700 -467.7600 0.010 0 -800 -467.7481 0.010 0 -900 -467.7413 0.010 0 -1000 -467.7337 0.010 0 -1100 -467.7296 0.010 0 -1200 -467.7258 0.010 0 -1300 -467.7227 0.010 0 -1400 -467.7214 0.010 0 -1500 -467.7206 0.010 0 -1600 -467.7201 0.010 0 -1700 -467.7188 0.010 0 -1800 -467.7150 0.010 0 -1900 -467.7143 0.010 0 -2000 -467.7142 0.010 0 -2100 -467.7123 0.010 0 -2200 -467.7123 0.010 0 -2300 -467.7091 0.010 0 -2400 -467.7068 0.010 0 -2500 -467.7062 0.010 0 -2600 -467.7057 0.010 0 -2700 -467.7057 0.010 0 -2800 -467.7056 0.010 0 -2900 -467.7055 0.010 0 -3000 -467.7043 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7043 +Current score = -467.7658 Performing final optimizations... -pass 1 : -467.7043 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.6916 (branch= 0.0127 subset rates= 0.0000) -pass 3 : -467.6883 (branch= 0.0033 subset rates= 0.0000) -pass 4 : -467.6841 (branch= 0.0041 subset rates= 0.0001) -pass 5 : -467.6824 (branch= 0.0018 subset rates= 0.0000) -pass 6 : -467.6804 (branch= 0.0019 subset rates= 0.0000) -pass 7 : -467.6801 (branch= 0.0003 subset rates= 0.0000) -pass 8 : -467.6792 (branch= 0.0009 subset rates= 0.0000) -pass 9 : -467.6786 (branch= 0.0006 subset rates= 0.0000) -pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6783 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6782 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6782 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7538 (branch= 0.0120 subset rates= 0.0000) +pass 2 : -467.7217 (branch= 0.0321 subset rates= 0.0000) +pass 3 : -467.6998 (branch= 0.0218 subset rates= 0.0000) +pass 4 : -467.6893 (branch= 0.0105 subset rates= 0.0000) +pass 5 : -467.6838 (branch= 0.0054 subset rates= 0.0001) +pass 6 : -467.6810 (branch= 0.0028 subset rates= 0.0000) +pass 7 : -467.6801 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -467.6795 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -467.6793 (branch= 0.0002 subset rates= 0.0000) +pass 10: -467.6792 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6788 (branch= 0.0004 subset rates= 0.0000) +pass 12: -467.6786 (branch= 0.0002 subset rates= 0.0000) +pass 13: -467.6785 (branch= 0.0001 subset rates= 0.0000) +pass 14: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 16: -467.6785 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6782 +Final score = -467.6785 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15854,7 +15770,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.19 + 0.79 1.47 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -15872,9 +15788,9 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -467.6784 -Replicate 2 : -467.6784 (same topology as 1) +Replicate 2 : -467.6784 (best) (same topology as 1) Replicate 3 : -467.6785 (same topology as 1) -Replicate 4 : -467.6782 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 4 : -467.6785 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -15892,9 +15808,9 @@ rep 1: 3.841 0.788 1.474 2.180 rep 2: 3.841 0.788 1.475 2.180 rep 3: 3.841 0.788 1.473 2.184 -rep 4: 3.844 0.786 1.479 2.185 +rep 4: 3.841 0.788 1.473 2.183 -Saving final tree from best search rep (#4) to ch.p.mk.ssr.best.tre +Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf @@ -16112,7 +16028,7 @@ pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4315 -Time used so far = 0 hours, 0 minutes and 2 seconds +Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16213,21 +16129,6 @@ 2200 -477.6758 0.010 102 2300 -477.6746 0.010 102 2400 -477.6746 0.010 102 -2500 -477.6741 0.010 102 -2600 -477.6729 0.010 102 -2700 -477.6723 0.010 102 -2800 -477.6705 0.010 102 -2900 -477.6701 0.010 102 -3000 -477.6699 0.010 102 -3100 -477.4305 0.010 3085 -3200 -477.3274 0.010 3181 -3300 -477.3173 0.010 3181 -3400 -477.3101 0.010 3181 -3500 -477.3067 0.010 3181 -3600 -477.2948 0.010 3181 -3700 -477.2947 0.010 3181 -3800 -477.2911 0.010 3181 -3900 -477.2903 0.010 3181 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16353,9 +16254,24 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 3921, seed 1992867316, best lnL -477.288 +Search rep 2 (of 5) generation 2427, seed 304237525, best lnL -477.674 gen current_lnL precision last_tree_imp -3921 -477.2884 0.010 3181 +2427 -477.6744 0.010 102 +2500 -477.6741 0.010 102 +2600 -477.6729 0.010 102 +2700 -477.6723 0.010 102 +2800 -477.6705 0.010 102 +2900 -477.6701 0.010 102 +3000 -477.6699 0.010 102 +3100 -477.4305 0.010 3085 +3200 -477.3274 0.010 3181 +3300 -477.3173 0.010 3181 +3400 -477.3101 0.010 3181 +3500 -477.3067 0.010 3181 +3600 -477.2948 0.010 3181 +3700 -477.2947 0.010 3181 +3800 -477.2911 0.010 3181 +3900 -477.2903 0.010 3181 4000 -477.2861 0.010 3181 4100 -477.2860 0.010 3181 4200 -477.2851 0.010 3181 @@ -16406,7 +16322,7 @@ pass 12: -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 8 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16496,159 +16412,26 @@ 1100 -477.5001 0.010 575 1200 -477.4987 0.010 575 1300 -477.4975 0.010 575 -1400 -477.4955 0.010 575 -1500 -477.4928 0.010 575 -1600 -477.4914 0.010 575 -1700 -477.4849 0.010 575 -1800 -477.4816 0.010 575 -1900 -477.4810 0.010 575 -2000 -477.4807 0.010 575 -2100 -477.4796 0.010 575 -2200 -477.4795 0.010 575 -2300 -477.4793 0.010 575 -2400 -477.4788 0.010 575 -2500 -477.4781 0.010 575 -2600 -477.4772 0.010 575 -2700 -477.4771 0.010 575 -2800 -477.4771 0.010 575 -2900 -477.4769 0.010 575 -3000 -477.4765 0.010 575 -3100 -477.4763 0.010 575 -Reached termination condition! -last topological improvement at gen 575 -Improvement over last 500 gen = 0.00090 -Current score = -477.4763 -Performing final optimizations... -pass 1 : -477.4762 (branch= 0.0000 subset rates= 0.0001) -pass 2 : -477.4560 (branch= 0.0162 subset rates= 0.0041) -pass 3 : -477.4429 (branch= 0.0131 subset rates= 0.0000) -pass 4 : -477.4401 (branch= 0.0028 subset rates= 0.0000) -pass 5 : -477.4374 (branch= 0.0026 subset rates= 0.0000) -pass 6 : -477.4347 (branch= 0.0027 subset rates= 0.0000) -pass 7 : -477.4336 (branch= 0.0009 subset rates= 0.0002) -pass 8 : -477.4326 (branch= 0.0010 subset rates= 0.0000) -pass 9 : -477.4321 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.4318 (branch= 0.0003 subset rates= 0.0000) -pass 11: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4316 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.4315 -Time used so far = 0 hours, 0 minutes and 10 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.63 1.91 2.74 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 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 Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=1950894339 - -Initial ln Likelihood: -634.4408 -optimizing: starting branch lengths, subset rates... -pass 1:+ 135.613 (branch= 124.55 scale= 1.40 subset rates= 9.66) -pass 2:+ 14.768 (branch= 10.98 scale= 0.00 subset rates= 3.79) -pass 3:+ 3.403 (branch= 2.12 scale= 0.00 subset rates= 1.28) -pass 4:+ 1.499 (branch= 1.15 scale= 0.00 subset rates= 0.35) -pass 5:+ 1.092 (branch= 1.05 scale= 0.01 subset rates= 0.03) -pass 6:+ 0.205 (branch= 0.21 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8600 -gen current_lnL precision last_tree_imp -0 -477.8600 0.010 0 -100 -477.7950 0.010 7 -200 -477.7708 0.010 7 -300 -477.7456 0.010 7 -400 -477.7339 0.010 7 -500 -477.7239 0.010 7 -600 -477.5387 0.010 566 -700 -477.5313 0.010 566 -800 -477.5308 0.010 566 -900 -477.5274 0.010 566 -1000 -477.5225 0.010 566 -1100 -477.5192 0.010 566 -1200 -477.5185 0.010 566 -1300 -477.5163 0.010 566 -1400 -477.5152 0.010 566 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.5123 +Current score = -477.4970 Performing final optimizations... -pass 1 : -477.4813 (branch= 0.0222 subset rates= 0.0088) -pass 2 : -477.4554 (branch= 0.0226 subset rates= 0.0033) -pass 3 : -477.4463 (branch= 0.0091 subset rates= 0.0000) -pass 4 : -477.4411 (branch= 0.0052 subset rates= 0.0000) -pass 5 : -477.4394 (branch= 0.0017 subset rates= 0.0000) -pass 6 : -477.4355 (branch= 0.0038 subset rates= 0.0000) -pass 7 : -477.4341 (branch= 0.0014 subset rates= 0.0000) -pass 8 : -477.4332 (branch= 0.0009 subset rates= 0.0000) -pass 9 : -477.4327 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.4323 (branch= 0.0003 subset rates= 0.0000) -pass 11: -477.4319 (branch= 0.0002 subset rates= 0.0002) +pass 1 : -477.4894 (branch= 0.0053 subset rates= 0.0023) +pass 2 : -477.4538 (branch= 0.0341 subset rates= 0.0015) +pass 3 : -477.4460 (branch= 0.0078 subset rates= 0.0000) +pass 4 : -477.4417 (branch= 0.0043 subset rates= 0.0000) +pass 5 : -477.4388 (branch= 0.0024 subset rates= 0.0005) +pass 6 : -477.4358 (branch= 0.0025 subset rates= 0.0005) +pass 7 : -477.4337 (branch= 0.0021 subset rates= 0.0000) +pass 8 : -477.4327 (branch= 0.0010 subset rates= 0.0000) +pass 9 : -477.4322 (branch= 0.0004 subset rates= 0.0000) +pass 10: -477.4320 (branch= 0.0003 subset rates= 0.0000) +pass 11: -477.4319 (branch= 0.0001 subset rates= 0.0000) pass 12: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4318 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 15: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4317 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4317 +Final score = -477.4316 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16677,11 +16460,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.92 2.74 + 0.63 1.91 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Terminated Search rep 4 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -16689,15 +16472,14 @@ ####################################################### -Completed 4 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -477.4315 Replicate 2 : -477.2119 (best) -Replicate 3 : -477.4315 (same topology as 1) -Replicate 4 : -477.4317 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 3 : -477.4316 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16714,8 +16496,7 @@ TL R(1) R(2) R(3) rep 1: 4.929 0.632 1.914 2.742 rep 2: 4.670 0.643 1.908 2.615 -rep 3: 4.929 0.632 1.914 2.743 -rep 4: 4.931 0.631 1.919 2.738 +rep 3: 4.928 0.632 1.914 2.735 Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre ####################################################### @@ -17007,95 +16788,6 @@ 1700 -484.5874 0.010 1054 1800 -484.5858 0.010 1054 1900 -484.5840 0.010 1054 -2000 -484.5836 0.010 1054 -2100 -484.5821 0.010 1054 -2200 -484.5818 0.010 1054 -2300 -484.5816 0.010 1054 -2400 -484.5813 0.010 1054 -2500 -484.5812 0.010 1054 -2600 -484.5812 0.010 1054 -Reached termination condition! -last topological improvement at gen 1054 -Improvement over last 500 gen = 0.00091 -Current score = -484.5812 -Performing final optimizations... -pass 1 : -484.5811 (branch= 0.0000 subset rates= 0.0001) -pass 2 : -484.5512 (branch= 0.0299 subset rates= 0.0000) -pass 3 : -484.5512 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -484.5479 (branch= 0.0033 subset rates= 0.0000) -pass 5 : -484.5464 (branch= 0.0016 subset rates= 0.0000) -pass 6 : -484.5449 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -484.5446 (branch= 0.0003 subset rates= 0.0000) -pass 8 : -484.5441 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -484.5440 (branch= 0.0001 subset rates= 0.0000) -pass 10: -484.5436 (branch= 0.0001 subset rates= 0.0003) -pass 11: -484.5435 (branch= 0.0001 subset rates= 0.0000) -pass 12: -484.5435 (branch= 0.0000 subset rates= 0.0000) -pass 13: -484.5434 (branch= 0.0000 subset rates= 0.0000) -pass 14: -484.5434 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -484.5434 -Time used so far = 0 hours, 0 minutes and 5 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.66 2.00 2.94 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. - ->>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< - ->>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< -Obtained starting tree 1 from Nexus -Starting with seed=1576203752 - -Initial ln Likelihood: -678.8220 -optimizing: starting branch lengths, subset rates... -pass 1:+ 160.281 (branch= 150.61 scale= 0.11 subset rates= 9.56) -pass 2:+ 7.789 (branch= 4.20 scale= 0.01 subset rates= 3.58) -pass 3:+ 7.313 (branch= 5.59 scale= 0.03 subset rates= 1.70) -pass 4:+ 4.548 (branch= 4.28 scale= 0.00 subset rates= 0.27) -pass 5:+ 0.362 (branch= 0.36 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.372 (branch= 0.37 scale= 0.00 subset rates= 0.00) -pass 7:+ 1.243 (branch= 1.22 scale= 0.02 subset rates= 0.00) -pass 8:+ 0.334 (branch= 0.31 scale= 0.00 subset rates= 0.02) -pass 9:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -496.5797 -gen current_lnL precision last_tree_imp -0 -496.5797 0.010 0 -100 -492.2457 0.010 96 -200 -486.0384 0.010 168 -300 -485.4244 0.010 267 -400 -485.3902 0.010 267 -500 -485.3043 0.010 480 -600 -485.2846 0.010 480 -700 -485.2751 0.010 480 -800 -485.2723 0.010 480 -900 -485.2643 0.010 480 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17224,9 +16916,98 @@ Subset 3: Random seed for bootstrap reweighting: 585640194 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 3 (of 5) generation 962, seed 986461815, best lnL -485.263 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1904, seed 764369954, best lnL -484.584 +gen current_lnL precision last_tree_imp +1904 -484.5840 0.010 1054 +2000 -484.5836 0.010 1054 +2100 -484.5821 0.010 1054 +2200 -484.5818 0.010 1054 +2300 -484.5816 0.010 1054 +2400 -484.5813 0.010 1054 +2500 -484.5812 0.010 1054 +2600 -484.5812 0.010 1054 +Reached termination condition! +last topological improvement at gen 1054 +Improvement over last 500 gen = 0.00091 +Current score = -484.5812 +Performing final optimizations... +pass 1 : -484.5811 (branch= 0.0000 subset rates= 0.0001) +pass 2 : -484.5512 (branch= 0.0299 subset rates= 0.0000) +pass 3 : -484.5512 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -484.5479 (branch= 0.0033 subset rates= 0.0000) +pass 5 : -484.5464 (branch= 0.0016 subset rates= 0.0000) +pass 6 : -484.5449 (branch= 0.0014 subset rates= 0.0000) +pass 7 : -484.5446 (branch= 0.0003 subset rates= 0.0000) +pass 8 : -484.5441 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -484.5440 (branch= 0.0001 subset rates= 0.0000) +pass 10: -484.5436 (branch= 0.0001 subset rates= 0.0003) +pass 11: -484.5435 (branch= 0.0001 subset rates= 0.0000) +pass 12: -484.5435 (branch= 0.0000 subset rates= 0.0000) +pass 13: -484.5434 (branch= 0.0000 subset rates= 0.0000) +pass 14: -484.5434 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -484.5434 +Time used so far = 0 hours, 0 minutes and 6 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.66 2.00 2.94 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 7 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=1576203752 + +Initial ln Likelihood: -678.8220 +optimizing: starting branch lengths, subset rates... +pass 1:+ 160.281 (branch= 150.61 scale= 0.11 subset rates= 9.56) +pass 2:+ 7.789 (branch= 4.20 scale= 0.01 subset rates= 3.58) +pass 3:+ 7.313 (branch= 5.59 scale= 0.03 subset rates= 1.70) +pass 4:+ 4.548 (branch= 4.28 scale= 0.00 subset rates= 0.27) +pass 5:+ 0.362 (branch= 0.36 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.372 (branch= 0.37 scale= 0.00 subset rates= 0.00) +pass 7:+ 1.243 (branch= 1.22 scale= 0.02 subset rates= 0.00) +pass 8:+ 0.334 (branch= 0.31 scale= 0.00 subset rates= 0.02) +pass 9:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -496.5797 gen current_lnL precision last_tree_imp -962 -485.2632 0.010 480 +0 -496.5797 0.010 0 +100 -492.2457 0.010 96 +200 -486.0384 0.010 168 +300 -485.4244 0.010 267 +400 -485.3902 0.010 267 +500 -485.3043 0.010 480 +600 -485.2846 0.010 480 +700 -485.2751 0.010 480 +800 -485.2723 0.010 480 +900 -485.2643 0.010 480 1000 -485.2623 0.010 480 1100 -485.2588 0.010 480 1200 -485.2581 0.010 480 @@ -17270,7 +17051,7 @@ pass 13: -485.2134 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -485.2134 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17329,71 +17110,26 @@ 800 -485.7259 0.010 783 900 -485.7099 0.010 847 1000 -485.6596 0.010 927 -1100 -485.6532 0.010 927 -1200 -485.6524 0.010 927 -1300 -485.6510 0.010 927 -1400 -485.6487 0.010 927 -1500 -485.6454 0.010 927 -1600 -485.6449 0.010 927 -1700 -485.6443 0.010 927 -1800 -485.6438 0.010 927 -1900 -485.6420 0.010 927 -2000 -485.6383 0.010 927 -2100 -485.6362 0.010 927 -2200 -485.6353 0.010 927 -2300 -485.6348 0.010 927 -2400 -485.6330 0.010 927 -2500 -485.6329 0.010 927 -2600 -485.6313 0.010 927 -2700 -485.6307 0.010 927 -2800 -485.6307 0.010 927 -2900 -485.6304 0.010 927 -3000 -485.6301 0.010 927 -3100 -485.6286 0.010 927 -3200 -485.6280 0.010 927 -3300 -485.6272 0.010 927 -3400 -485.6262 0.010 927 -3500 -485.6262 0.010 927 -3600 -485.6260 0.010 927 -3700 -485.6257 0.010 927 -3800 -485.6251 0.010 927 -3900 -485.6250 0.010 927 -4000 -485.6239 0.010 927 -4100 -485.6235 0.010 927 -4200 -485.6233 0.010 927 -4300 -485.6214 0.010 927 -4400 -485.6210 0.010 927 -4500 -485.6207 0.010 927 -4600 -485.6193 0.010 927 -4700 -485.6190 0.010 927 -4800 -485.6186 0.010 927 -4900 -485.6186 0.010 927 -5000 -485.6181 0.010 927 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -5100 -485.6178 0.010 927 -5200 -485.6176 0.010 927 -5300 -485.6175 0.010 927 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -485.6175 +Current score = -485.6532 Performing final optimizations... -pass 1 : -485.6052 (branch= 0.0056 subset rates= 0.0067) -pass 2 : -485.5971 (branch= 0.0071 subset rates= 0.0010) -pass 3 : -485.5912 (branch= 0.0059 subset rates= 0.0000) -pass 4 : -485.5866 (branch= 0.0046 subset rates= 0.0000) -pass 5 : -485.5845 (branch= 0.0021 subset rates= 0.0000) -pass 6 : -485.5817 (branch= 0.0028 subset rates= 0.0000) -pass 7 : -485.5805 (branch= 0.0012 subset rates= 0.0000) -pass 8 : -485.5797 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -485.5795 (branch= 0.0003 subset rates= 0.0000) -pass 10: -485.5794 (branch= 0.0001 subset rates= 0.0000) -pass 11: -485.5793 (branch= 0.0001 subset rates= 0.0000) -pass 12: -485.5793 (branch= 0.0000 subset rates= 0.0000) -pass 13: -485.5793 (branch= 0.0000 subset rates= 0.0000) -pass 14: -485.5792 (branch= 0.0000 subset rates= 0.0000) -pass 15: -485.5792 (branch= 0.0000 subset rates= 0.0001) +pass 1 : -485.6372 (branch= 0.0121 subset rates= 0.0038) +pass 2 : -485.6133 (branch= 0.0219 subset rates= 0.0020) +pass 3 : -485.6033 (branch= 0.0100 subset rates= 0.0000) +pass 4 : -485.5951 (branch= 0.0082 subset rates= 0.0000) +pass 5 : -485.5889 (branch= 0.0062 subset rates= 0.0000) +pass 6 : -485.5868 (branch= 0.0021 subset rates= 0.0000) +pass 7 : -485.5824 (branch= 0.0021 subset rates= 0.0023) +pass 8 : -485.5817 (branch= 0.0008 subset rates= 0.0000) +pass 9 : -485.5813 (branch= 0.0004 subset rates= 0.0000) +pass 10: -485.5811 (branch= 0.0001 subset rates= 0.0000) +pass 11: -485.5799 (branch= 0.0001 subset rates= 0.0012) +pass 12: -485.5796 (branch= 0.0002 subset rates= 0.0000) +pass 13: -485.5796 (branch= 0.0001 subset rates= 0.0000) +pass 14: -485.5796 (branch= 0.0000 subset rates= 0.0000) +pass 15: -485.5795 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -485.5792 +Final score = -485.5795 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17422,7 +17158,7 @@ no rate heterogeneity Subset rate multipliers: - 0.65 2.01 3.19 + 0.65 2.00 3.17 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -17442,7 +17178,7 @@ Replicate 1 : -484.5428 (best) Replicate 2 : -484.5434 Replicate 3 : -485.2134 -Replicate 4 : -485.5792 (TERMINATED PREMATURELY) +Replicate 4 : -485.5795 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17460,7 +17196,7 @@ rep 1: 3.519 0.661 2.000 2.947 rep 2: 3.520 0.660 2.003 2.944 rep 3: 3.569 0.669 1.975 2.905 -rep 4: 3.675 0.647 2.006 3.186 +rep 4: 3.674 0.649 1.998 3.173 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre @@ -17685,7 +17421,7 @@ pass 16: -473.9509 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9509 -Time used so far = 0 hours, 0 minutes and 3 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17770,26 +17506,6 @@ 600 -474.5541 0.010 476 700 -474.5467 0.010 476 800 -474.5377 0.010 476 -900 -474.5302 0.010 476 -1000 -474.5273 0.010 476 -1100 -474.5253 0.010 476 -1200 -474.5239 0.010 476 -1300 -474.5142 0.010 476 -1400 -474.5122 0.010 476 -1500 -474.5086 0.010 476 -1600 -474.5067 0.010 476 -1700 -474.5062 0.010 476 -1800 -474.5050 0.010 476 -1900 -474.5037 0.010 476 -2000 -474.5011 0.010 476 -2100 -474.5010 0.010 476 -2200 -474.4999 0.010 476 -2300 -474.4991 0.010 476 -2400 -474.4948 0.010 476 -2500 -474.4942 0.010 476 -2600 -474.4908 0.010 476 -2700 -474.4902 0.010 476 -2800 -474.4893 0.010 476 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17915,9 +17631,29 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 2854, seed 1933990198, best lnL -474.489 +Search rep 2 (of 5) generation 816, seed 1425541281, best lnL -474.535 gen current_lnL precision last_tree_imp -2854 -474.4887 0.010 476 +816 -474.5346 0.010 476 +900 -474.5302 0.010 476 +1000 -474.5273 0.010 476 +1100 -474.5253 0.010 476 +1200 -474.5239 0.010 476 +1300 -474.5142 0.010 476 +1400 -474.5122 0.010 476 +1500 -474.5086 0.010 476 +1600 -474.5067 0.010 476 +1700 -474.5062 0.010 476 +1800 -474.5050 0.010 476 +1900 -474.5037 0.010 476 +2000 -474.5011 0.010 476 +2100 -474.5010 0.010 476 +2200 -474.4999 0.010 476 +2300 -474.4991 0.010 476 +2400 -474.4948 0.010 476 +2500 -474.4942 0.010 476 +2600 -474.4908 0.010 476 +2700 -474.4902 0.010 476 +2800 -474.4893 0.010 476 2900 -474.4883 0.010 476 3000 -474.4860 0.010 476 3100 -474.4849 0.010 476 @@ -17949,164 +17685,26 @@ 5500 -474.4662 0.010 476 5600 -474.4650 0.010 476 5700 -474.4647 0.010 476 -5800 -474.4641 0.010 476 -5900 -474.4641 0.010 476 -6000 -474.4638 0.010 476 -6100 -474.4629 0.010 476 -6200 -474.4628 0.010 476 -6300 -474.4616 0.010 476 -6400 -474.4616 0.010 476 -6500 -474.4611 0.010 476 -6600 -474.4609 0.010 476 -6700 -474.4609 0.010 476 -6800 -474.4602 0.010 476 -6900 -474.4601 0.010 476 -7000 -474.4594 0.010 476 -7100 -474.4594 0.010 476 -7200 -474.4591 0.010 476 -7300 -474.4591 0.010 476 -7400 -474.4588 0.010 476 -7500 -474.4588 0.010 476 -Reached termination condition! -last topological improvement at gen 476 -Improvement over last 500 gen = 0.00063 -Current score = -474.4588 -Performing final optimizations... -pass 1 : -474.4530 (branch= 0.0055 subset rates= 0.0002) -pass 2 : -474.4436 (branch= 0.0094 subset rates= 0.0000) -pass 3 : -474.4353 (branch= 0.0083 subset rates= 0.0000) -pass 4 : -474.4345 (branch= 0.0008 subset rates= 0.0000) -pass 5 : -474.4331 (branch= 0.0014 subset rates= 0.0000) -pass 6 : -474.4306 (branch= 0.0025 subset rates= 0.0000) -pass 7 : -474.4296 (branch= 0.0010 subset rates= 0.0000) -pass 8 : -474.4289 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -474.4286 (branch= 0.0004 subset rates= 0.0000) -pass 10: -474.4284 (branch= 0.0001 subset rates= 0.0000) -pass 11: -474.4284 (branch= 0.0001 subset rates= 0.0000) -pass 12: -474.4283 (branch= 0.0000 subset rates= 0.0000) -pass 13: -474.4283 (branch= 0.0000 subset rates= 0.0000) -pass 14: -474.4283 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -474.4283 -Time used so far = 0 hours, 0 minutes and 9 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 2.03 2.92 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. - ->>>Completed Search rep 2 (of 5)<<< - ->>>Search rep 3 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate 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=84478279 - -Initial ln Likelihood: -606.8218 -optimizing: starting branch lengths, subset rates... -pass 1:+ 113.411 (branch= 102.20 scale= 0.34 subset rates= 10.88) -pass 2:+ 13.972 (branch= 9.25 scale= 0.00 subset rates= 4.73) -pass 3:+ 3.195 (branch= 1.61 scale= 0.02 subset rates= 1.57) -pass 4:+ 1.099 (branch= 0.54 scale= 0.00 subset rates= 0.56) -pass 5:+ 0.204 (branch= 0.17 scale= 0.00 subset rates= 0.04) -pass 6:+ 0.039 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.025 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass 9:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8654 -gen current_lnL precision last_tree_imp -0 -474.8654 0.010 0 -100 -474.8535 0.010 0 -200 -474.7425 0.010 154 -300 -474.7012 0.010 252 -400 -474.0514 0.010 352 -500 -474.0391 0.010 352 -600 -474.0292 0.010 352 -700 -474.0202 0.010 352 -800 -474.0146 0.010 352 -900 -474.0055 0.010 352 -1000 -474.0042 0.010 352 -1100 -474.0013 0.010 352 -1200 -473.9993 0.010 352 -1300 -473.9974 0.010 352 -1400 -473.9963 0.010 352 -1500 -473.9925 0.010 352 -1600 -473.9919 0.010 352 -1700 -473.9918 0.010 352 -1800 -473.9910 0.010 352 -1900 -473.9906 0.010 352 -2000 -473.9898 0.010 352 -2100 -473.9884 0.010 352 -2200 -473.9874 0.010 352 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -473.9867 +Current score = -474.4644 Performing final optimizations... -pass 1 : -473.9837 (branch= 0.0000 subset rates= 0.0030) -pass 2 : -473.9590 (branch= 0.0247 subset rates= 0.0000) -pass 3 : -473.9551 (branch= 0.0024 subset rates= 0.0015) -pass 4 : -473.9534 (branch= 0.0012 subset rates= 0.0005) -pass 5 : -473.9513 (branch= 0.0021 subset rates= 0.0000) -pass 6 : -473.9495 (branch= 0.0017 subset rates= 0.0000) -pass 7 : -473.9492 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -473.9489 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -473.9488 (branch= 0.0001 subset rates= 0.0000) -pass 10: -473.9487 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9486 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9486 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9486 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4586 (branch= 0.0058 subset rates= 0.0000) +pass 2 : -474.4458 (branch= 0.0129 subset rates= 0.0000) +pass 3 : -474.4373 (branch= 0.0084 subset rates= 0.0000) +pass 4 : -474.4351 (branch= 0.0021 subset rates= 0.0002) +pass 5 : -474.4347 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -474.4325 (branch= 0.0022 subset rates= 0.0000) +pass 7 : -474.4303 (branch= 0.0022 subset rates= 0.0000) +pass 8 : -474.4296 (branch= 0.0006 subset rates= 0.0001) +pass 9 : -474.4291 (branch= 0.0005 subset rates= 0.0000) +pass 10: -474.4289 (branch= 0.0002 subset rates= 0.0000) +pass 11: -474.4288 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4287 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.4287 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4286 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4286 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9486 +Final score = -474.4286 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18135,11 +17733,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.81 + 0.59 2.03 2.91 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -18147,14 +17745,13 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -473.9509 -Replicate 2 : -474.4283 -Replicate 3 : -473.9486 (best) (TERMINATED PREMATURELY) +Replicate 1 : -473.9509 (best) +Replicate 2 : -474.4286 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18170,10 +17767,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.349 0.588 2.069 2.792 -rep 2: 4.598 0.588 2.030 2.916 -rep 3: 4.351 0.585 2.075 2.807 +rep 2: 4.596 0.589 2.029 2.906 -Saving final tree from best search rep (#3) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -18189,13 +17785,13 @@ create-stamp debian/debhelper-build-stamp 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' make[3]: Entering directory '/build/garli-2.1/src' -make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/garli-2.1/debian/tmp/usr/bin' +make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Garli '/build/garli-2.1/debian/tmp/usr/bin' make install-exec-hook make[4]: Entering directory '/build/garli-2.1/src' @@ -18238,10 +17834,10 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli' in '../garli_2.1-4_amd64.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-4_amd64.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-4_amd64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-4_amd64.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-4_amd64.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-4_amd64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../garli_2.1-4_amd64.changes @@ -18250,12 +17846,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2362957/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2362957/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/3681189 and its subdirectories -I: Current time: Thu Jan 20 13:24:24 -12 2022 -I: pbuilder-time-stamp: 1642728264 +I: removing directory /srv/workspace/pbuilder/2362957 and its subdirectories +I: Current time: Thu Feb 23 21:56:33 +14 2023 +I: pbuilder-time-stamp: 1677138993