Diff of the two buildlogs: -- --- b1/build.log 2021-08-24 00:19:25.386036813 +0000 +++ b2/build.log 2021-08-24 00:39:07.073879975 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 23 12:00:52 -12 2021 -I: pbuilder-time-stamp: 1629763252 +I: Current time: Tue Aug 24 14:20:10 +14 2021 +I: pbuilder-time-stamp: 1629764410 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.72Q_3gmw/trustedkeys.kbx': General error -gpgv: Signature made Wed Nov 18 02:03:14 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.5cVaFJTG/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/4936/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/7639/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +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/7639/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/7639/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='a5882269815843e3aff3ed48019875b9' - 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='4936' - PS1='# ' - PS2='> ' + INVOCATION_ID=ffeb25222fff47de91c7ad5355cf593f + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=7639 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.9BWV4sNWlz/pbuilderrc_OZt4 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9BWV4sNWlz/b1 --logfile b1/build.log garli_2.1-4.dsc' - SUDO_GID='114' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.9BWV4sNWlz/pbuilderrc_5trU --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9BWV4sNWlz/b2 --logfile b2/build.log garli_2.1-4.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux jtx1b 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 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 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 20 21:28 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/4936/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 24 14:20 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 2021 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/7639/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -286,7 +320,7 @@ Get: 85 http://deb.debian.org/debian bullseye/main armhf openmpi-bin armhf 4.1.0-10 [206 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf libopenmpi-dev armhf 4.1.0-10 [1143 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf ncl-tools armhf 2.1.21+git20190531.feceb81-3 [140 kB] -Fetched 37.3 MB in 4s (10.3 MB/s) +Fetched 37.3 MB in 10s (3624 kB/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 ... 19398 files and directories currently installed.) @@ -653,7 +687,8 @@ 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 @@ -715,8 +750,8 @@ 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 @@ -794,7 +829,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j3 + make -j4 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' @@ -804,6 +839,32 @@ 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 bipartition.o bipartition.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 condlike.o condlike.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 configoptions.o configoptions.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); + | ^~ +configoptions.cpp:337:20: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /usr/include/c++/10/cstdio:42, + from /usr/include/c++/10/ext/string_conversions.h:43, + from /usr/include/c++/10/bits/basic_string.h:6545, + from /usr/include/c++/10/string:55, + from /usr/include/c++/10/bits/locale_classes.h:40, + from /usr/include/c++/10/bits/ios_base.h:41, + from /usr/include/c++/10/ios:42, + from /usr/include/c++/10/ostream:38, + from /usr/include/c++/10/iostream:39, + from configoptions.cpp:20: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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 configreader.o configreader.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 datamatr.o datamatr.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 funcs.o funcs.cpp adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); @@ -865,32 +926,13 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 configreader.o configreader.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); - | ^~ -configoptions.cpp:337:20: note: directive argument in the range [0, 2147483647] - 337 | sprintf(modName, "model%d", modelNum); - | ^~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /usr/include/c++/10/cstdio:42, - from /usr/include/c++/10/ext/string_conversions.h:43, - from /usr/include/c++/10/bits/basic_string.h:6545, - from /usr/include/c++/10/string:55, - from /usr/include/c++/10/bits/locale_classes.h:40, - from /usr/include/c++/10/bits/ios_base.h:41, - from /usr/include/c++/10/ios:42, - from /usr/include/c++/10/ostream:38, - from /usr/include/c++/10/iostream:39, - from configoptions.cpp:20: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 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 datamatr.o datamatr.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 funcs.o funcs.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 garlimain.o garlimain.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__); + | ^~~~~~~~ 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); @@ -902,15 +944,9 @@ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 garlimain.o garlimain.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 garlireader.o garlireader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 individual.o individual.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 linalg.o linalg.cpp garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:323:28: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] 323 | else sprintf(temp, ".run%d", rank); @@ -974,7 +1010,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 linalg.o linalg.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 model.o model.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 @@ -1013,6 +1048,8 @@ 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 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 In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1044,22 +1081,8 @@ 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 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 -In file included from /usr/include/c++/10/vector:72, - from model.h:28, - from model.cpp:25: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from model.h:28, - from model.cpp:25: -/usr/include/c++/10/bits/stl_vector.h: In constructor 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:22: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); @@ -1078,7 +1101,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +In file included from /usr/include/c++/10/vector:72, + from model.h:28, + from model.cpp:25: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from model.h:28, + from model.cpp:25: +/usr/include/c++/10/bits/stl_vector.h: In constructor 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ @@ -1088,6 +1121,21 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from population.cpp:23: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: @@ -1103,12 +1151,6 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from population.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void Model::ReadGarliFormattedModelString(std::string&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1119,10 +1161,6 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1158,82 +1196,7 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from model.h:28, - from model.cpp:25: -/usr/include/c++/10/bits/vector.tcc: In constructor 'ModelPartition::ModelPartition()': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from model.h:28, - from model.cpp:25: -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from model.h:28, - from model.cpp:25: -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from population.cpp:23: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/10/vector:67, - from population.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::OptimizeSiteRates()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from population.cpp:23: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -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 -In file included from /usr/include/c++/10/vector:67, - from population.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from population.cpp:23: -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from population.cpp:23: -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from population.cpp:23: -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from population.cpp:23: -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 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); @@ -1302,6 +1265,78 @@ 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, + from population.cpp:23: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:67, + from population.cpp:23: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::OptimizeSiteRates()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from population.cpp:23: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:72, + from model.h:28, + from model.cpp:25: +/usr/include/c++/10/bits/vector.tcc: In constructor 'ModelPartition::ModelPartition()': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from model.h:28, + from model.cpp:25: +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from model.h:28, + from model.cpp:25: +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from population.cpp:23: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from population.cpp:23: +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from population.cpp:23: +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from population.cpp:23: +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from population.cpp:23: +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 +In file included from /usr/include/c++/10/vector:72, from tree.cpp:21: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -1387,8 +1422,8 @@ 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 @@ -1464,7 +1499,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/garli-2.1' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/garli-2.1' make all-recursive make[2]: Entering directory '/build/garli-2.1' @@ -1474,6 +1509,31 @@ 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 bipartition.o bipartition.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 condlike.o condlike.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 configoptions.o configoptions.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); + | ^~ +configoptions.cpp:337:20: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /usr/include/c++/10/cstdio:42, + from /usr/include/c++/10/ext/string_conversions.h:43, + from /usr/include/c++/10/bits/basic_string.h:6545, + from /usr/include/c++/10/string:55, + from /usr/include/c++/10/bits/locale_classes.h:40, + from /usr/include/c++/10/bits/ios_base.h:41, + from /usr/include/c++/10/ios:42, + from /usr/include/c++/10/ostream:38, + from /usr/include/c++/10/iostream:39, + from configoptions.cpp:20: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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 configreader.o configreader.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 datamatr.o datamatr.cpp adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); @@ -1535,43 +1595,7 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~ -configoptions.cpp:337:20: note: directive argument in the range [0, 2147483647] - 337 | sprintf(modName, "model%d", modelNum); - | ^~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /usr/include/c++/10/cstdio:42, - from /usr/include/c++/10/ext/string_conversions.h:43, - from /usr/include/c++/10/bits/basic_string.h:6545, - from /usr/include/c++/10/string:55, - from /usr/include/c++/10/bits/locale_classes.h:40, - from /usr/include/c++/10/bits/ios_base.h:41, - from /usr/include/c++/10/ios:42, - from /usr/include/c++/10/ostream:38, - from /usr/include/c++/10/iostream:39, - from configoptions.cpp:20: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 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 configreader.o configreader.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 datamatr.o datamatr.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 funcs.o funcs.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); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 garlimain.o garlimain.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); @@ -1579,8 +1603,20 @@ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 garlireader.o garlireader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 individual.o individual.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 linalg.o linalg.cpp In file included from /usr/include/c++/10/vector:72, from population.h:24, from funcs.h:25, @@ -1597,7 +1633,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 linalg.o linalg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 model.o model.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 @@ -1636,6 +1671,8 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1667,8 +1704,8 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -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 +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 In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: @@ -1711,6 +1748,12 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from population.cpp:23: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: @@ -1726,6 +1769,11 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void Model::ReadGarliFormattedModelString(std::string&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1736,16 +1784,6 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from population.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1781,6 +1819,73 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6815:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6815 | fread((char*) &lnL, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6816:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6816 | fread((char*) &numTipsAdded, sizeof(numTipsAdded), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6817:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6817 | fread((char*) &numNodesAdded, sizeof(numNodesAdded), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6818:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6818 | fread((char*) &numBranchesAdded, sizeof(numBranchesAdded), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6819:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6819 | fread((char*) &numNodesTotal, sizeof(numNodesTotal), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6823:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6823 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6826:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6826 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6829:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6829 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6833:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6833 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6837:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6837 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6841:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6841 | fread((char*) &allNodes[0]->dlen, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6845:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6845 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6849:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6849 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6855:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6855 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6858:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6862:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6862 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6865:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6865 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6868:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6868 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6872:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6872 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6878:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6878 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: @@ -1806,6 +1911,7 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': @@ -1826,8 +1932,7 @@ 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -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 mpitrick.o mpitrick.cpp In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': @@ -1854,76 +1959,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -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 -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6815:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6815 | fread((char*) &lnL, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6816:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6816 | fread((char*) &numTipsAdded, sizeof(numTipsAdded), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6817:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6817 | fread((char*) &numNodesAdded, sizeof(numNodesAdded), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6818:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6818 | fread((char*) &numBranchesAdded, sizeof(numBranchesAdded), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6819:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6819 | fread((char*) &numNodesTotal, sizeof(numNodesTotal), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6823:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6823 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6826:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6826 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6829:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6829 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6833:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6833 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6837:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6837 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6841:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6841 | fread((char*) &allNodes[0]->dlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6845:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6845 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6849:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6849 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6855:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6855 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6858:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6862:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6862 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6865:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6865 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6868:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6868 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6872:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6872 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6878:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6878 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from tree.cpp:21: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': @@ -1952,7 +1987,7 @@ # 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 -j3 check VERBOSE=1 + make -j4 check VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' @@ -4472,7 +4507,7 @@ pass 13: -6242.8580 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6242.8580 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4622,7 +4657,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4919,7 +4954,7 @@ 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 36 seconds +Time used = 0 hours, 0 minutes and 52 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5071,7 +5106,7 @@ 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 25 seconds +Time used = 0 hours, 0 minutes and 37 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5275,7 +5310,7 @@ pass 80: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2337 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5483,7 +5518,7 @@ pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5800,7 +5835,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5969,7 +6004,7 @@ pass 17: -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 8 seconds +Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -6223,7 +6258,7 @@ pass 37: -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 9 seconds +Time used = 0 hours, 0 minutes and 16 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6437,7 +6472,7 @@ pass 14: -474.1864 (branch= 0.0000) Looking for minimum length branches... Final score = -474.1864 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8192,7 +8227,7 @@ pass 490: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3588 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8456,7 +8491,7 @@ 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 6 seconds +Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8757,7 +8792,7 @@ pass 496: -208.3578 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3578 -Time used = 0 hours, 0 minutes and 9 seconds +Time used = 0 hours, 0 minutes and 15 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -9050,7 +9085,7 @@ pass 492: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3584 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -11758,8 +11793,6 @@ 200 -100.8816 0.500 183 300 -100.5813 0.500 183 400 -100.3300 0.500 183 -500 -100.0135 0.500 183 -600 -99.2983 0.500 549 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11856,9 +11889,11 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 634, seed 276364763, best lnL -99.264 +Bootstrap rep 1 (of 1) generation 453, seed 671311345, best lnL -100.106 gen current_lnL precision last_tree_imp -634 -99.2638 0.500 549 +453 -100.1064 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 @@ -12031,8 +12066,6 @@ 0 -116.1434 0.500 0 100 -112.9555 0.500 84 200 -112.4964 0.500 84 -300 -112.3224 0.500 84 -400 -112.1061 0.500 84 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12119,9 +12152,11 @@ STARTING RUN Restarting from checkpoint... - generation 418, seed 1667153938, best lnL -112.048 + generation 283, seed 1273007385, best lnL -112.372 gen current_lnL precision last_tree_imp -418 -112.0477 0.500 84 +283 -112.3724 0.500 84 +300 -112.3224 0.500 84 +400 -112.1061 0.500 84 500 -111.8129 0.500 84 600 -111.7788 0.500 84 Optimization precision reduced @@ -12297,22 +12332,6 @@ 100 -113.6842 0.500 91 200 -112.5462 0.500 160 300 -112.1250 0.500 160 -400 -111.8851 0.500 160 -500 -111.7755 0.500 160 -600 -111.6975 0.500 563 -700 -111.6876 0.500 563 -800 -111.6844 0.500 563 -900 -111.6835 0.500 563 -1000 -111.6829 0.500 563 -1100 -111.6827 0.500 563 -Optimization precision reduced - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -1200 -111.6824 0.010 563 -1300 -111.6822 0.010 563 -1400 -111.6821 0.010 563 -1500 -111.6819 0.010 563 -1600 -111.6818 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12398,11 +12417,19 @@ STARTING RUN Restarting from checkpoint... - generation 1618, seed 598468670, best lnL -111.682 + generation 300, seed 2142722754, best lnL -112.125 gen current_lnL precision last_tree_imp -1618 -111.6818 0.010 563 +300 -112.1250 0.500 160 +400 -111.8851 0.500 160 +500 -111.7755 0.500 160 +600 -111.6975 0.500 563 +700 -111.6876 0.500 563 +800 -111.6844 0.500 563 +900 -111.6835 0.500 563 +1000 -111.6829 0.500 563 +NOTE: ****Specified generation limit (1000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -12419,23 +12446,30 @@ No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.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 : -111.6818 +Replicate 1 : -111.6829 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.606 +rep 1: 2.616 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/c.M3x2.conf @@ -12559,7 +12593,6 @@ gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 10 -207.1401 0.500 10 -20 -205.6892 0.500 18 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12646,9 +12679,10 @@ STARTING RUN Restarting from checkpoint... - generation 25, seed 2069048048, best lnL -205.650 + generation 10, seed 1509658266, best lnL -207.140 gen current_lnL precision last_tree_imp -25 -205.6499 0.500 18 +10 -207.1401 0.500 10 +20 -205.6892 0.500 18 30 -205.6499 0.500 18 40 -205.6371 0.500 18 50 -205.6175 0.500 18 @@ -12841,8 +12875,6 @@ lnL after optimization: -203.6354 gen current_lnL precision last_tree_imp 0 -203.6354 0.500 0 -10 -200.0495 0.500 7 -20 -198.2138 0.500 20 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12930,8 +12962,10 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 20, seed 268317158, best lnL -198.214 +Bootstrap rep 1 (of 1) generation 1, seed 1398556760, best lnL -203.624 gen current_lnL precision last_tree_imp +1 -203.6241 0.500 0 +10 -200.0495 0.500 7 20 -198.2138 0.500 20 30 -198.1347 0.500 20 40 -197.7953 0.500 33 @@ -13153,7 +13187,6 @@ Optimization precision reduced Optimizing parameters... improved 0.834 lnL Optimizing branchlengths... improved 0.086 lnL -1100 -3352.7118 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13257,54 +13290,51 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1184, seed 506006923, best lnL -3352.650 +Search rep 1 (of 2) generation 1012, seed 1956843275, best lnL -3352.756 gen current_lnL precision last_tree_imp -1184 -3352.6500 0.010 0 +1012 -3352.7564 0.010 0 +1100 -3352.7118 0.010 0 1200 -3352.6304 0.010 0 1300 -3352.5083 0.010 0 1400 -3352.3976 0.010 0 1500 -3352.3929 0.010 0 1600 -3352.2848 0.010 0 1700 -3352.2769 0.010 0 -1800 -3352.1985 0.010 0 -1900 -3351.8445 0.010 0 -2000 -3351.7633 0.010 0 -2100 -3351.6181 0.010 0 -2200 -3351.3705 0.010 0 -2300 -3351.3467 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.3446 +Current score = -3352.1986 Performing final optimizations... -pass 1 : -3351.2188 (branch= 0.0084 alpha= 0.0000 pinv= 0.0155 eq freqs= 0.0268 rel rates= 0.0735 subset rates= 0.0017) -pass 2 : -3351.0857 (branch= 0.0120 alpha= 0.0129 pinv= 0.0189 eq freqs= 0.0035 rel rates= 0.0848 subset rates= 0.0010) -pass 3 : -3350.9802 (branch= 0.0085 alpha= 0.0144 pinv= 0.0173 eq freqs= 0.0000 rel rates= 0.0643 subset rates= 0.0010) -pass 4 : -3350.8810 (branch= 0.0107 alpha= 0.0148 pinv= 0.0162 eq freqs= 0.0018 rel rates= 0.0545 subset rates= 0.0013) -pass 5 : -3350.7990 (branch= 0.0051 alpha= 0.0149 pinv= 0.0148 eq freqs= 0.0000 rel rates= 0.0461 subset rates= 0.0011) -pass 6 : -3350.7298 (branch= 0.0033 alpha= 0.0133 pinv= 0.0137 eq freqs= 0.0005 rel rates= 0.0384 subset rates= 0.0000) -pass 7 : -3350.6670 (branch= 0.0016 alpha= 0.0123 pinv= 0.0126 eq freqs= 0.0001 rel rates= 0.0347 subset rates= 0.0017) -pass 8 : -3350.6134 (branch= 0.0019 alpha= 0.0117 pinv= 0.0115 eq freqs= 0.0001 rel rates= 0.0284 subset rates= 0.0000) -pass 9 : -3350.5665 (branch= 0.0004 alpha= 0.0107 pinv= 0.0105 eq freqs= 0.0000 rel rates= 0.0254 subset rates= 0.0000) -pass 10: -3350.5225 (branch= 0.0002 alpha= 0.0104 pinv= 0.0102 eq freqs= 0.0000 rel rates= 0.0218 subset rates= 0.0013) -pass 11: -3350.4856 (branch= 0.0012 alpha= 0.0091 pinv= 0.0092 eq freqs= 0.0001 rel rates= 0.0175 subset rates= 0.0000) -pass 12: -3350.4541 (branch= 0.0002 alpha= 0.0079 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0156 subset rates= 0.0000) -pass 13: -3350.4258 (branch= 0.0001 alpha= 0.0076 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0137 subset rates= 0.0000) -pass 14: -3350.4008 (branch= 0.0000 alpha= 0.0069 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0118 subset rates= 0.0000) -pass 15: -3350.3790 (branch= 0.0000 alpha= 0.0062 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0100 subset rates= 0.0000) -pass 16: -3350.3599 (branch= 0.0000 alpha= 0.0056 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0086 subset rates= 0.0000) -pass 17: -3350.3431 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0074 subset rates= 0.0000) -pass 18: -3350.3285 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0063 subset rates= 0.0000) -pass 19: -3350.3158 (branch= 0.0000 alpha= 0.0039 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0054 subset rates= 0.0000) -pass 20: -3350.3047 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0047 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2494 (branch= 0.0000 alpha= 0.0172 pinv= 0.0155 eq freqs= 0.0001 rel rates= 0.0225 subset rates= 0.0000) +pass 1 : -3351.9351 (branch= 0.0070 alpha= 0.0160 pinv= 0.0201 eq freqs= 0.0159 rel rates= 0.1964 subset rates= 0.0081) +pass 2 : -3351.6690 (branch= 0.0137 alpha= 0.0121 pinv= 0.0184 eq freqs= 0.0031 rel rates= 0.2177 subset rates= 0.0012) +pass 3 : -3351.4433 (branch= 0.0133 alpha= 0.0169 pinv= 0.0160 eq freqs= 0.0091 rel rates= 0.1678 subset rates= 0.0026) +pass 4 : -3351.2653 (branch= 0.0097 alpha= 0.0133 pinv= 0.0152 eq freqs= 0.0019 rel rates= 0.1353 subset rates= 0.0025) +pass 5 : -3351.1188 (branch= 0.0082 alpha= 0.0119 pinv= 0.0146 eq freqs= 0.0004 rel rates= 0.1093 subset rates= 0.0022) +pass 6 : -3350.9936 (branch= 0.0045 alpha= 0.0115 pinv= 0.0134 eq freqs= 0.0006 rel rates= 0.0933 subset rates= 0.0018) +pass 7 : -3350.8872 (branch= 0.0038 alpha= 0.0109 pinv= 0.0124 eq freqs= 0.0002 rel rates= 0.0779 subset rates= 0.0012) +pass 8 : -3350.7955 (branch= 0.0035 alpha= 0.0105 pinv= 0.0114 eq freqs= 0.0001 rel rates= 0.0661 subset rates= 0.0000) +pass 9 : -3350.7166 (branch= 0.0007 alpha= 0.0100 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0564 subset rates= 0.0013) +pass 10: -3350.6489 (branch= 0.0017 alpha= 0.0094 pinv= 0.0101 eq freqs= 0.0002 rel rates= 0.0464 subset rates= 0.0000) +pass 11: -3350.5905 (branch= 0.0004 alpha= 0.0086 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0399 subset rates= 0.0009) +pass 12: -3350.5413 (branch= 0.0009 alpha= 0.0080 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0324 subset rates= 0.0000) +pass 13: -3350.4998 (branch= 0.0002 alpha= 0.0072 pinv= 0.0070 eq freqs= 0.0001 rel rates= 0.0271 subset rates= 0.0000) +pass 14: -3350.4636 (branch= 0.0001 alpha= 0.0068 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0230 subset rates= 0.0000) +pass 15: -3350.4322 (branch= 0.0000 alpha= 0.0062 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0196 subset rates= 0.0000) +pass 16: -3350.4052 (branch= 0.0000 alpha= 0.0055 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0165 subset rates= 0.0000) +pass 17: -3350.3818 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0141 subset rates= 0.0000) +pass 18: -3350.3616 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0119 subset rates= 0.0000) +pass 19: -3350.3441 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0102 subset rates= 0.0000) +pass 20: -3350.3290 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0087 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2551 (branch= 0.0000 alpha= 0.0171 pinv= 0.0156 eq freqs= 0.0001 rel rates= 0.0410 subset rates= 0.0000) + optimization up to ... +pass 40: -3350.2382 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0095 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2367 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0053 subset rates= 0.0000) +pass 50: -3350.2344 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0024 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2340 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0013 subset rates= 0.0000) +pass 60: -3350.2336 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) +pass 70: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 69: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 73: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2334 Time used so far = 0 hours, 0 minutes and 13 seconds @@ -13313,21 +13343,21 @@ Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.116, AG = 10.413, AT = 2.690, CG = 0.001, CT = 21.902, GT = 1.000 + AC = 3.111, AG = 10.402, AT = 2.688, CG = 0.001, CT = 21.879, 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 - 0.5782 + 0.5788 with an invariant (invariable) site category, proportion estimated - 0.3659 + 0.3661 Substitution rate categories under this model: rate proportion - 0.0000 0.3659 - 0.0486 0.1585 - 0.2999 0.1585 - 0.8698 0.1585 - 2.7816 0.1585 + 0.0000 0.3661 + 0.0488 0.1585 + 0.3003 0.1585 + 0.8701 0.1585 + 2.7809 0.1585 Model 2 Number of states = 2 (binary data) @@ -13358,7 +13388,7 @@ Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.116 10.41 2.69 0.001 21.9 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.111 10.4 2.688 0.001 21.88 1 0.333 0.222 0.157 0.288 0.579 0.366 Partition model subset 2: Model contains no estimated parameters @@ -13513,8 +13543,6 @@ 0 -3332.4700 0.500 0 100 -3324.9856 0.500 1 200 -3324.7543 0.500 1 -300 -3324.3007 0.500 1 -400 -3323.9848 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13615,66 +13643,61 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 453, seed 922520793, best lnL -3323.716 +Search rep 1 (of 2) generation 298, seed 2120134428, best lnL -3324.301 gen current_lnL precision last_tree_imp -453 -3323.7158 0.500 1 +298 -3324.3007 0.500 1 +300 -3324.3007 0.500 1 +400 -3323.9848 0.500 1 500 -3323.6818 0.500 1 -600 -3323.3460 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 -3321.0295 0.255 1 -900 -3321.0142 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.9773 +Current score = -3323.3791 Performing final optimizations... -pass 1 : -3320.2915 (branch= 0.0904 alpha= 0.0000 pinv= 0.0166 eq freqs= 0.0001 rel rates= 0.5599 ins/del rates= 0.0188) -pass 2 : -3319.8397 (branch= 0.0587 alpha= 0.0068 pinv= 0.0160 eq freqs= 0.0000 rel rates= 0.3543 ins/del rates= 0.0159) -pass 3 : -3319.4954 (branch= 0.0434 alpha= 0.0093 pinv= 0.0154 eq freqs= 0.0000 rel rates= 0.2576 ins/del rates= 0.0185) -pass 4 : -3319.2238 (branch= 0.0275 alpha= 0.0096 pinv= 0.0153 eq freqs= 0.0020 rel rates= 0.2070 ins/del rates= 0.0102) -pass 5 : -3318.9992 (branch= 0.0194 alpha= 0.0100 pinv= 0.0146 eq freqs= 0.0011 rel rates= 0.1719 ins/del rates= 0.0076) -pass 6 : -3318.8110 (branch= 0.0122 alpha= 0.0103 pinv= 0.0138 eq freqs= 0.0013 rel rates= 0.1457 ins/del rates= 0.0050) -pass 7 : -3318.6535 (branch= 0.0089 alpha= 0.0098 pinv= 0.0130 eq freqs= 0.0002 rel rates= 0.1218 ins/del rates= 0.0038) -pass 8 : -3318.5258 (branch= 0.0054 alpha= 0.0106 pinv= 0.0121 eq freqs= 0.0004 rel rates= 0.0969 ins/del rates= 0.0023) -pass 9 : -3318.4171 (branch= 0.0039 alpha= 0.0095 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0822 ins/del rates= 0.0016) -pass 10: -3318.3244 (branch= 0.0026 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0684 ins/del rates= 0.0011) -pass 11: -3318.2486 (branch= 0.0017 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0549 ins/del rates= 0.0007) -pass 12: -3318.1843 (branch= 0.0011 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0457 ins/del rates= 0.0005) -pass 13: -3318.1295 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0381 ins/del rates= 0.0003) -pass 14: -3318.0826 (branch= 0.0005 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0319 ins/del rates= 0.0002) -pass 15: -3318.0431 (branch= 0.0003 alpha= 0.0067 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0259 ins/del rates= 0.0001) -pass 16: -3318.0090 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0220 ins/del rates= 0.0001) -pass 17: -3317.9795 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0187 ins/del rates= 0.0000) -pass 18: -3317.9539 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0159 ins/del rates= 0.0000) -pass 19: -3317.9317 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0136 ins/del rates= 0.0000) -pass 20: -3317.9124 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0116 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8166 (branch= 0.0001 alpha= 0.0213 pinv= 0.0196 eq freqs= 0.0001 rel rates= 0.0548 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7937 (branch= 0.0001 alpha= 0.0053 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0126 ins/del rates= 0.0000) +pass 1 : -3321.1625 (branch= 0.0809 alpha= 0.0053 pinv= 0.0162 eq freqs= 0.0760 rel rates= 0.6741 ins/del rates= 1.3641) +pass 2 : -3320.4671 (branch= 0.1141 alpha= 0.0000 pinv= 0.0300 eq freqs= 0.0144 rel rates= 0.5069 ins/del rates= 0.0299) +pass 3 : -3319.9579 (branch= 0.0614 alpha= 0.0048 pinv= 0.0162 eq freqs= 0.0150 rel rates= 0.3871 ins/del rates= 0.0246) +pass 4 : -3319.5645 (branch= 0.0361 alpha= 0.0091 pinv= 0.0153 eq freqs= 0.0039 rel rates= 0.3142 ins/del rates= 0.0147) +pass 5 : -3319.2468 (branch= 0.0239 alpha= 0.0102 pinv= 0.0145 eq freqs= 0.0021 rel rates= 0.2576 ins/del rates= 0.0094) +pass 6 : -3318.9921 (branch= 0.0149 alpha= 0.0098 pinv= 0.0140 eq freqs= 0.0008 rel rates= 0.2091 ins/del rates= 0.0061) +pass 7 : -3318.7934 (branch= 0.0094 alpha= 0.0104 pinv= 0.0131 eq freqs= 0.0008 rel rates= 0.1612 ins/del rates= 0.0039) +pass 8 : -3318.6302 (branch= 0.0060 alpha= 0.0102 pinv= 0.0122 eq freqs= 0.0006 rel rates= 0.1315 ins/del rates= 0.0026) +pass 9 : -3318.4984 (branch= 0.0040 alpha= 0.0099 pinv= 0.0113 eq freqs= 0.0004 rel rates= 0.1045 ins/del rates= 0.0017) +pass 10: -3318.3897 (branch= 0.0026 alpha= 0.0095 pinv= 0.0111 eq freqs= 0.0003 rel rates= 0.0841 ins/del rates= 0.0011) +pass 11: -3318.3003 (branch= 0.0017 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0681 ins/del rates= 0.0008) +pass 12: -3318.2263 (branch= 0.0011 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0002 rel rates= 0.0550 ins/del rates= 0.0005) +pass 13: -3318.1643 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0450 ins/del rates= 0.0003) +pass 14: -3318.1116 (branch= 0.0005 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0374 ins/del rates= 0.0002) +pass 15: -3318.0670 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0307 ins/del rates= 0.0001) +pass 16: -3318.0292 (branch= 0.0002 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0254 ins/del rates= 0.0001) +pass 17: -3317.9966 (branch= 0.0001 alpha= 0.0056 pinv= 0.0053 eq freqs= 0.0001 rel rates= 0.0215 ins/del rates= 0.0000) +pass 18: -3317.9685 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0182 ins/del rates= 0.0000) +pass 19: -3317.9442 (branch= 0.0001 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0155 ins/del rates= 0.0000) +pass 20: -3317.9231 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0132 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8190 (branch= 0.0001 alpha= 0.0217 pinv= 0.0200 eq freqs= 0.0001 rel rates= 0.0622 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7943 (branch= 0.0001 alpha= 0.0054 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0142 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 ins/del rates= 0.0000) +pass 50: -3317.7887 (branch= 0.0000 alpha= 0.0012 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0034 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) +pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0009 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 76: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 74: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 13 seconds +Time used so far = 0 hours, 0 minutes and 15 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.066, AG = 10.265, AT = 2.657, CG = 0.001, CT = 21.541, GT = 1.000 + AC = 3.066, AG = 10.265, AT = 2.655, CG = 0.001, CT = 21.537, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5749 + 0.5751 with an invariant (invariable) site category, proportion estimated 0.3614 Substitution rate categories under this model: @@ -13683,7 +13706,7 @@ 0.0480 0.1596 0.2981 0.1596 0.8680 0.1596 - 2.7860 0.1596 + 2.7858 0.1596 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -13715,7 +13738,7 @@ Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.066 10.26 2.657 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.066 10.26 2.655 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -13859,17 +13882,6 @@ 3600 -210.7287 0.010 1104 3800 -210.7084 0.010 1104 4000 -210.6947 0.010 1104 -4200 -210.6741 0.010 1104 -4400 -210.6493 0.010 1104 -4600 -210.6257 0.010 1104 -4800 -210.5949 0.010 1104 -5000 -210.5740 0.010 1104 -5200 -210.5694 0.010 1104 -5400 -210.5451 0.010 1104 -5600 -210.5083 0.010 1104 -5800 -210.4709 0.010 1104 -6000 -210.4363 0.010 1104 -6200 -210.4333 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13949,67 +13961,35 @@ STARTING RUN Restarting from checkpoint... - generation 6205, seed 805740742, best lnL -210.433 + generation 4082, seed 1920124649, best lnL -210.694 gen current_lnL precision last_tree_imp -6205 -210.4333 0.010 1104 -6300 -210.3894 0.010 1104 -6400 -210.3828 0.010 1104 -6500 -210.3682 0.010 1104 -6600 -210.3672 0.010 1104 -6700 -210.3649 0.010 1104 -6800 -210.3388 0.010 1104 -6900 -210.2789 0.010 1104 -7000 -210.2678 0.010 1104 -7100 -210.2669 0.010 1104 -7200 -210.2658 0.010 1104 -7300 -210.2112 0.010 1104 -7400 -210.2005 0.010 1104 -7500 -210.1759 0.010 1104 -7600 -210.1719 0.010 1104 -7700 -210.1248 0.010 1104 -7800 -210.1109 0.010 1104 -7900 -210.1075 0.010 1104 -8000 -210.1051 0.010 1104 -8100 -210.0631 0.010 1104 -8200 -210.0542 0.010 1104 -8300 -210.0443 0.010 1104 -8400 -210.0362 0.010 1104 -8500 -210.0345 0.010 1104 -8600 -210.0072 0.010 1104 -8700 -209.9622 0.010 1104 -8800 -209.9561 0.010 1104 -8900 -209.9495 0.010 1104 -9000 -209.9142 0.010 1104 -9100 -209.9062 0.010 1104 -9200 -209.9044 0.010 1104 -9300 -209.8883 0.010 1104 -9400 -209.8881 0.010 1104 -9500 -209.8846 0.010 1104 +4082 -210.6944 0.010 1104 +4100 -210.6826 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.02958 +Improvement over last 500 gen = 0.04606 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 4.463, AG = 7.646, AT = 0.194, CG = 8.002, CT = 13.103, GT = 1.000 + AC = 2.570, AG = 4.757, AT = 0.222, CG = 4.460, CT = 6.969, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2355 0.3330 0.2090 0.2224 + (ACGT) 0.2329 0.3364 0.2106 0.2201 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 2.0184 + 1.1902 with an invariant (invariable) site category, proportion estimated - 0.2338 + 0.1148 Substitution rate categories under this model: rate proportion - 0.0000 0.2338 - 0.3565 0.2554 - 0.8504 0.2554 - 1.7931 0.2554 + 0.0000 0.1148 + 0.2293 0.2951 + 0.7543 0.2951 + 2.0164 0.2951 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... @@ -14017,15 +13997,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.8846 +Replicate 1 : -210.6826 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: 4.463 7.646 0.1943 8.002 13.1 1 0.236 0.333 0.209 0.222 2.018 0.234 +rep 1: 2.57 4.757 0.2216 4.46 6.969 1 0.233 0.336 0.211 0.220 1.190 0.115 Treelengths: TL -rep 1: 2.364 +rep 1: 2.232 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log @@ -14164,23 +14144,6 @@ 3200 -190.8648 0.010 1979 3400 -190.8494 0.010 1979 3600 -190.8372 0.010 1979 -3800 -190.7695 0.010 1979 -4000 -190.7609 0.010 1979 -4200 -190.7108 0.010 1979 -4400 -190.6941 0.010 1979 -4600 -190.6596 0.010 1979 -4800 -190.6553 0.010 1979 -5000 -190.6512 0.010 1979 -5200 -190.6443 0.010 1979 -5400 -190.6435 0.010 1979 -5600 -190.6010 0.010 1979 -5800 -190.5523 0.010 1979 -6000 -190.5495 0.010 1979 -6200 -190.5464 0.010 1979 -6400 -190.5268 0.010 1979 -6600 -190.5081 0.010 1979 -6800 -190.5071 0.010 1979 -7000 -190.5058 0.010 1979 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14261,33 +14224,43 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 7057, seed 301406992, best lnL -190.500 +Bootstrap rep 1 (of 1) generation 3793, seed 235346773, best lnL -190.769 gen current_lnL precision last_tree_imp -7057 -190.5002 0.010 1979 -7100 -190.4949 0.010 1979 +3793 -190.7695 0.010 1979 +3800 -190.7695 0.010 1979 +3900 -190.7629 0.010 1979 +4000 -190.7609 0.010 1979 +4100 -190.7297 0.010 1979 +4200 -190.7108 0.010 1979 +4300 -190.6997 0.010 1979 +4400 -190.6941 0.010 1979 +4500 -190.6698 0.010 1979 +4600 -190.6596 0.010 1979 +4700 -190.6594 0.010 1979 +4800 -190.6553 0.010 1979 Reached termination condition! last topological improvement at gen 1979 -Improvement over last 500 gen = 0.01314 +Improvement over last 500 gen = 0.04442 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.654, AG = 1.342, AT = 0.009, CG = 2.993, CT = 14.463, GT = 1.000 + AC = 0.525, AG = 1.103, AT = 0.009, CG = 2.352, CT = 10.994, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3161 0.3192 0.2594 0.1053 + (ACGT) 0.3118 0.3242 0.2589 0.1052 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 6.7629 + 6.3163 with an invariant (invariable) site category, proportion estimated - 0.1389 + 0.1380 Substitution rate categories under this model: rate proportion - 0.0000 0.1389 - 0.5621 0.2153 - 0.8368 0.2153 - 1.0795 0.2153 - 1.5216 0.2153 + 0.0000 0.1380 + 0.5490 0.2155 + 0.8299 0.2155 + 1.0805 0.2155 + 1.5405 0.2155 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. @@ -14297,15 +14270,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -190.4949 +Replicate 1 : -190.6553 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 0.6542 1.342 0.008904 2.993 14.46 1 0.316 0.319 0.259 0.105 6.763 0.139 +rep 1: 0.5248 1.103 0.00911 2.352 10.99 1 0.312 0.324 0.259 0.105 6.316 0.138 Treelengths: TL -rep 1: 2.315 +rep 1: 2.271 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -14435,75 +14408,15 @@ 4600 -212.8794 0.010 3769 4800 -212.8766 0.010 3769 5000 -212.8761 0.010 3769 -5200 -212.8556 0.010 3769 -5400 -212.8533 0.010 3769 -5600 -212.8185 0.010 3769 -5800 -212.7686 0.010 3769 -6000 -212.7263 0.010 3769 -6200 -212.7248 0.010 3769 -6400 -212.7244 0.010 3769 -6600 -212.7154 0.010 3769 -6800 -212.7057 0.010 3769 -7000 -212.7025 0.010 3769 -7200 -212.7020 0.010 3769 -7400 -212.6750 0.010 3769 -7600 -212.6701 0.010 3769 -7800 -212.6661 0.010 3769 -8000 -212.6646 0.010 3769 -8200 -212.6594 0.010 3769 -8400 -212.6591 0.010 3769 -8600 -212.6390 0.010 3769 -8800 -212.5865 0.010 3769 -9000 -212.5495 0.010 3769 -9200 -212.5341 0.010 3769 -9400 -212.5173 0.010 3769 -9600 -212.4987 0.010 3769 -9800 -212.4933 0.010 3769 -10000 -212.4848 0.010 3769 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 8.255, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.080, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2186 0.2862 0.1832 0.3120 - Rate Heterogeneity Model: - no rate heterogeneity - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. - -Saving site likelihoods to file ch.n.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -212.4847 - -Parameter estimates: - r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 8.255 15.55 0.6481 15.52 10.08 1 0.219 0.286 0.183 0.312 - -Treelengths: - TL -rep 1: 1.718 - -Saving final tree from best search rep (#1) to ch.n.best.tre -Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -14574,22 +14487,37 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 1459438551, best lnL -212.485 + generation 5106, seed 539354435, best lnL -212.865 gen current_lnL precision last_tree_imp -10001 -212.4847 0.010 3769 +5106 -212.8649 0.010 3769 +5200 -212.8556 0.010 3769 +5300 -212.8534 0.010 3769 +5400 -212.8533 0.010 3769 +5500 -212.8216 0.010 3769 +5600 -212.8185 0.010 3769 +5700 -212.8105 0.010 3769 +5800 -212.7686 0.010 3769 +5900 -212.7273 0.010 3769 +6000 -212.7263 0.010 3769 +6100 -212.7249 0.010 3769 +6200 -212.7248 0.010 3769 +6300 -212.7245 0.010 3769 +Reached termination condition! +last topological improvement at gen 3769 +Improvement over last 500 gen = 0.04407 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 8.255, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.080, GT = 1.000 + AC = 4.838, AG = 9.614, AT = 0.397, CG = 9.746, CT = 6.242, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2186 0.2862 0.1832 0.3120 + (ACGT) 0.2212 0.2915 0.1818 0.3056 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. Saving site likelihoods to file ch.n.sitelikes.log ... @@ -14597,15 +14525,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.4847 +Replicate 1 : -212.7245 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 8.255 15.55 0.6481 15.52 10.08 1 0.219 0.286 0.183 0.312 +rep 1: 4.838 9.614 0.397 9.746 6.242 1 0.221 0.291 0.182 0.306 Treelengths: TL -rep 1: 1.718 +rep 1: 1.732 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log @@ -14743,30 +14671,6 @@ 2600 -210.8172 0.010 1502 2800 -210.7847 0.010 1502 3000 -210.7510 0.010 2883 -3200 -210.7243 0.010 2883 -3400 -210.7005 0.010 2883 -3600 -210.6993 0.010 2883 -3800 -210.6778 0.010 2883 -4000 -210.6775 0.010 2883 -4200 -210.6761 0.010 2883 -4400 -210.6526 0.010 2883 -4600 -210.6396 0.010 2883 -4800 -210.6026 0.010 4692 -5000 -210.5940 0.010 4692 -5200 -210.5720 0.010 4692 -5400 -210.5439 0.010 5207 -5600 -210.5367 0.010 5207 -5800 -210.4677 0.010 5207 -6000 -210.4081 0.010 5812 -6200 -210.4005 0.010 5812 -6400 -210.3714 0.010 5812 -6600 -210.3661 0.010 5812 -6800 -210.3533 0.010 5812 -7000 -210.3450 0.010 5812 -7200 -210.3444 0.010 5812 -7400 -210.3290 0.010 5812 -7600 -210.3233 0.010 5812 -7800 -210.2350 0.010 7789 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14854,9 +14758,57 @@ STARTING RUN Restarting from checkpoint... - generation 7994, seed 1910171639, best lnL -210.189 + generation 3123, seed 1015968022, best lnL -210.741 gen current_lnL precision last_tree_imp -7994 -210.1893 0.010 7789 +3123 -210.7406 0.010 2883 +3200 -210.7243 0.010 2883 +3300 -210.7025 0.010 2883 +3400 -210.7005 0.010 2883 +3500 -210.7005 0.010 2883 +3600 -210.6993 0.010 2883 +3700 -210.6819 0.010 2883 +3800 -210.6778 0.010 2883 +3900 -210.6775 0.010 2883 +4000 -210.6775 0.010 2883 +4100 -210.6766 0.010 2883 +4200 -210.6761 0.010 2883 +4300 -210.6650 0.010 2883 +4400 -210.6526 0.010 2883 +4500 -210.6526 0.010 2883 +4600 -210.6396 0.010 2883 +4700 -210.6054 0.010 4692 +4800 -210.6026 0.010 4692 +4900 -210.5999 0.010 4692 +5000 -210.5940 0.010 4692 +5100 -210.5801 0.010 4692 +5200 -210.5720 0.010 4692 +5300 -210.5447 0.010 5207 +5400 -210.5439 0.010 5207 +5500 -210.5367 0.010 5207 +5600 -210.5367 0.010 5207 +5700 -210.4850 0.010 5207 +5800 -210.4677 0.010 5207 +5900 -210.4312 0.010 5812 +6000 -210.4081 0.010 5812 +6100 -210.4039 0.010 5812 +6200 -210.4005 0.010 5812 +6300 -210.3745 0.010 5812 +6400 -210.3714 0.010 5812 +6500 -210.3701 0.010 5812 +6600 -210.3661 0.010 5812 +6700 -210.3557 0.010 5812 +6800 -210.3533 0.010 5812 +6900 -210.3475 0.010 5812 +7000 -210.3450 0.010 5812 +7100 -210.3444 0.010 5812 +7200 -210.3444 0.010 5812 +7300 -210.3290 0.010 5812 +7400 -210.3290 0.010 5812 +7500 -210.3290 0.010 5812 +7600 -210.3233 0.010 5812 +7700 -210.2878 0.010 5812 +7800 -210.2350 0.010 7789 +7900 -210.2072 0.010 7789 8000 -210.1893 0.010 7789 8100 -210.1876 0.010 7789 8200 -210.1873 0.010 7789 @@ -15119,16 +15071,6 @@ gen current_lnL precision last_tree_imp 0 -13187.7578 0.500 0 100 -13185.0341 0.500 1 -200 -13183.9652 0.500 1 -300 -13183.5099 0.500 1 -400 -13182.4431 0.500 1 -500 -13182.2598 0.500 1 -600 -13181.9021 0.500 1 -Optimization precision reduced - Optimizing parameters... improved 0.055 lnL - Optimizing branchlengths... improved 0.000 lnL -700 -13181.7193 0.402 1 -800 -13181.6899 0.402 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15251,15 +15193,10 @@ Subset 3: Random seed for bootstrap reweighting: 1903425807 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 867, seed 1800452886, best lnL -13181.607 +Bootstrap rep 1 (of 1) generation 166, seed 375495465, best lnL -13184.536 gen current_lnL precision last_tree_imp -867 -13181.6070 0.402 1 -900 -13181.6040 0.402 1 -1000 -13181.4970 0.402 1 -1100 -13181.4426 0.402 1 -Optimization precision reduced - Optimizing parameters... improved 0.019 lnL - Optimizing branchlengths... improved 0.000 lnL +166 -13184.5360 0.500 1 +200 -13183.9652 0.500 1 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15267,58 +15204,58 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 2.015, AG = 3.173, AT = 1.167, CG = 1.167, CT = 2.631, GT = 1.000 + AC = 1.611, AG = 2.740, AT = 0.977, CG = 0.977, CT = 2.038, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3054 0.1867 0.2740 0.2339 + (ACGT) 0.3090 0.1926 0.2635 0.2349 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3876 + 0.3622 Substitution rate categories under this model: rate proportion - 0.0150 0.2500 - 0.1724 0.2500 - 0.7175 0.2500 - 3.0952 0.2500 + 0.0117 0.2500 + 0.1530 0.2500 + 0.6868 0.2500 + 3.1485 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 = 3.906, AG = 4.801, AT = 0.742, CG = 4.801, CT = 3.906, GT = 1.000 + AC = 3.941, AG = 4.705, AT = 0.756, CG = 4.705, CT = 3.941, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2514 0.1562 0.1902 0.4022 + (ACGT) 0.2477 0.1591 0.1965 0.3967 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.4487 + 0.4030 Substitution rate categories under this model: rate proportion - 0.0243 0.2500 - 0.2171 0.2500 - 0.7790 0.2500 - 2.9796 0.2500 + 0.0171 0.2500 + 0.1840 0.2500 + 0.7345 0.2500 + 3.0644 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 = 7.157, AT = 5.571, CG = 1.050, CT = 7.157, GT = 1.000 + AC = 1.000, AG = 7.207, AT = 5.557, CG = 1.037, CT = 7.207, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1612 0.3397 0.2962 0.2030 + (ACGT) 0.1648 0.3350 0.2990 0.2012 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.5458 + 4.1515 with an invariant (invariable) site category, proportion estimated - 0.0111 + 0.0098 Substitution rate categories under this model: rate proportion - 0.0000 0.0111 - 0.4820 0.2472 - 0.7922 0.2472 - 1.0840 0.2472 - 1.6418 0.2472 + 0.0000 0.0098 + 0.4625 0.2475 + 0.7803 0.2475 + 1.0843 0.2475 + 1.6729 0.2475 Subset rate multipliers: - 0.53 0.28 2.20 + 0.50 0.28 2.22 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -15332,25 +15269,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13181.4112 (TERMINATED PREMATURELY) +Replicate 1 : -13183.7286 (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: 2.015 3.173 1.167 1.167 2.631 1 0.305 0.187 0.274 0.234 0.388 +rep 1: 1.611 2.74 0.9772 0.9772 2.038 1 0.309 0.193 0.264 0.235 0.362 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: 3.906 4.801 0.7415 4.801 3.906 1 0.251 0.156 0.190 0.402 0.449 +rep 1: 3.941 4.705 0.7563 4.705 3.941 1 0.248 0.159 0.197 0.397 0.403 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 7.157 5.571 1.05 7.157 1 0.161 0.340 0.296 0.203 4.546 0.011 +rep 1: 1 7.207 5.557 1.037 7.207 1 0.165 0.335 0.299 0.201 4.151 0.010 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.673 0.526 0.278 2.196 +rep 1: 1.691 0.501 0.276 2.224 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -15535,127 +15472,6 @@ 1700 -467.7288 0.010 76 1800 -467.7270 0.010 76 1900 -467.7270 0.010 76 -2000 -467.7247 0.010 76 -2100 -467.7240 0.010 76 -2200 -467.7237 0.010 76 -2300 -467.7235 0.010 76 -2400 -467.7217 0.010 76 -2500 -467.7212 0.010 76 -2600 -467.7209 0.010 76 -2700 -467.7204 0.010 76 -2800 -467.7202 0.010 76 -2900 -467.7200 0.010 76 -3000 -467.7200 0.010 76 -3100 -467.7184 0.010 76 -3200 -467.7183 0.010 76 -3300 -467.7165 0.010 76 -3400 -467.7165 0.010 76 -3500 -467.7162 0.010 76 -3600 -467.7160 0.010 76 -3700 -467.7160 0.010 76 -3800 -467.7159 0.010 76 -Reached termination condition! -last topological improvement at gen 76 -Improvement over last 500 gen = 0.00059 -Current score = -467.7159 -Performing final optimizations... -pass 1 : -467.7120 (branch= 0.0000 subset rates= 0.0039) -pass 2 : -467.6911 (branch= 0.0209 subset rates= 0.0000) -pass 3 : -467.6869 (branch= 0.0042 subset rates= 0.0000) -pass 4 : -467.6843 (branch= 0.0026 subset rates= 0.0000) -pass 5 : -467.6817 (branch= 0.0026 subset rates= 0.0000) -pass 6 : -467.6803 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -467.6795 (branch= 0.0007 subset rates= 0.0001) -pass 8 : -467.6788 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -467.6786 (branch= 0.0002 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: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 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 1.48 2.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=1831048457 - -Initial ln Likelihood: -637.1584 -optimizing: starting branch lengths, subset rates... -pass 1:+ 151.120 (branch= 144.13 scale= 2.32 subset rates= 4.67) -pass 2:+ 14.959 (branch= 13.95 scale= 0.00 subset rates= 1.01) -pass 3:+ 2.985 (branch= 2.78 scale= 0.01 subset rates= 0.19) -pass 4:+ 0.213 (branch= 0.21 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.025 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8409 -gen current_lnL precision last_tree_imp -0 -467.8409 0.010 0 -100 -467.8006 0.010 88 -200 -467.7829 0.010 88 -300 -467.7645 0.010 88 -400 -467.7572 0.010 88 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15781,56 +15597,50 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 483, seed 1667434309, best lnL -467.753 +Search rep 1 (of 5) generation 1928, seed 56721740, best lnL -467.725 gen current_lnL precision last_tree_imp -483 -467.7525 0.010 88 -500 -467.7508 0.010 88 -600 -467.7420 0.010 88 -700 -467.7377 0.010 88 -800 -467.7326 0.010 88 -900 -467.7300 0.010 88 -1000 -467.7251 0.010 88 -1100 -467.7186 0.010 88 -1200 -467.7174 0.010 88 -1300 -467.7143 0.010 88 -1400 -467.7139 0.010 88 -1500 -467.7130 0.010 88 -1600 -467.7128 0.010 88 -1700 -467.7101 0.010 88 -1800 -467.7076 0.010 88 -1900 -467.7072 0.010 88 -2000 -467.7065 0.010 88 -2100 -467.7061 0.010 88 -2200 -467.7057 0.010 88 -2300 -467.7052 0.010 88 -2400 -467.7043 0.010 88 -2500 -467.7039 0.010 88 -2600 -467.7039 0.010 88 -2700 -467.7038 0.010 88 -2800 -467.7036 0.010 88 -2900 -467.7035 0.010 88 +1928 -467.7251 0.010 76 +2000 -467.7247 0.010 76 +2100 -467.7240 0.010 76 +2200 -467.7237 0.010 76 +2300 -467.7235 0.010 76 +2400 -467.7217 0.010 76 +2500 -467.7212 0.010 76 +2600 -467.7209 0.010 76 +2700 -467.7204 0.010 76 +2800 -467.7202 0.010 76 +2900 -467.7200 0.010 76 +3000 -467.7200 0.010 76 +3100 -467.7184 0.010 76 +3200 -467.7183 0.010 76 +3300 -467.7165 0.010 76 +3400 -467.7165 0.010 76 +3500 -467.7162 0.010 76 +3600 -467.7160 0.010 76 +3700 -467.7160 0.010 76 +3800 -467.7159 0.010 76 Reached termination condition! -last topological improvement at gen 88 -Improvement over last 500 gen = 0.00077 -Current score = -467.7035 +last topological improvement at gen 76 +Improvement over last 500 gen = 0.00059 +Current score = -467.7159 Performing final optimizations... -pass 1 : -467.7035 (branch= 0.0000 subset rates= 0.0001) -pass 2 : -467.6923 (branch= 0.0112 subset rates= 0.0000) -pass 3 : -467.6861 (branch= 0.0060 subset rates= 0.0001) -pass 4 : -467.6835 (branch= 0.0027 subset rates= 0.0000) -pass 5 : -467.6821 (branch= 0.0013 subset rates= 0.0000) -pass 6 : -467.6810 (branch= 0.0011 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 : -467.6792 (branch= 0.0003 subset rates= 0.0000) -pass 10: -467.6789 (branch= 0.0002 subset rates= 0.0001) -pass 11: -467.6788 (branch= 0.0002 subset rates= 0.0000) -pass 12: -467.6787 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6787 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6787 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7120 (branch= 0.0000 subset rates= 0.0039) +pass 2 : -467.6911 (branch= 0.0209 subset rates= 0.0000) +pass 3 : -467.6869 (branch= 0.0042 subset rates= 0.0000) +pass 4 : -467.6843 (branch= 0.0026 subset rates= 0.0000) +pass 5 : -467.6817 (branch= 0.0026 subset rates= 0.0000) +pass 6 : -467.6803 (branch= 0.0014 subset rates= 0.0000) +pass 7 : -467.6795 (branch= 0.0007 subset rates= 0.0001) +pass 8 : -467.6788 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -467.6786 (branch= 0.0002 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: -467.6783 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6787 -Time used so far = 0 hours, 0 minutes and 9 seconds +Final score = -467.6782 +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -15858,13 +15668,13 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.47 2.18 + 0.79 1.48 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 2 (of 5)<<< +>>>Completed Search rep 1 (of 5)<<< ->>>Search rep 3 (of 5)<<< +>>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -15893,60 +15703,45 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=387765568 +Starting with seed=1831048457 -Initial ln Likelihood: -629.3844 +Initial ln Likelihood: -637.1584 optimizing: starting branch lengths, subset rates... -pass 1:+ 145.913 (branch= 138.38 scale= 3.36 subset rates= 4.18) -pass 2:+ 12.537 (branch= 11.64 scale= 0.00 subset rates= 0.90) -pass 3:+ 2.852 (branch= 2.62 scale= 0.06 subset rates= 0.18) -pass 4:+ 0.211 (branch= 0.21 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.034 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8378 +pass 1:+ 151.120 (branch= 144.13 scale= 2.32 subset rates= 4.67) +pass 2:+ 14.959 (branch= 13.95 scale= 0.00 subset rates= 1.01) +pass 3:+ 2.985 (branch= 2.78 scale= 0.01 subset rates= 0.19) +pass 4:+ 0.213 (branch= 0.21 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.025 (branch= 0.03 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -467.8409 gen current_lnL precision last_tree_imp -0 -467.8378 0.010 0 -100 -467.8202 0.010 0 -200 -467.7910 0.010 0 -300 -467.7852 0.010 0 -400 -467.7649 0.010 0 -500 -467.7557 0.010 0 -600 -467.7482 0.010 0 -700 -467.7383 0.010 0 -800 -467.7308 0.010 0 -900 -467.7283 0.010 0 -1000 -467.7269 0.010 0 -1100 -467.7258 0.010 0 -1200 -467.7235 0.010 0 -1300 -467.7213 0.010 0 -1400 -467.7173 0.010 0 -1500 -467.7162 0.010 0 -1600 -467.7145 0.010 0 -1700 -467.7136 0.010 0 -1800 -467.7115 0.010 0 -1900 -467.7100 0.010 0 -2000 -467.7098 0.010 0 -2100 -467.7097 0.010 0 +0 -467.8409 0.010 0 +100 -467.8006 0.010 88 +200 -467.7829 0.010 88 +300 -467.7645 0.010 88 +400 -467.7572 0.010 88 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7095 +Current score = -467.7525 Performing final optimizations... -pass 1 : -467.7084 (branch= 0.0000 subset rates= 0.0011) -pass 2 : -467.6965 (branch= 0.0118 subset rates= 0.0001) -pass 3 : -467.6923 (branch= 0.0038 subset rates= 0.0005) -pass 4 : -467.6881 (branch= 0.0040 subset rates= 0.0001) -pass 5 : -467.6848 (branch= 0.0034 subset rates= 0.0000) -pass 6 : -467.6818 (branch= 0.0030 subset rates= 0.0000) -pass 7 : -467.6801 (branch= 0.0017 subset rates= 0.0000) -pass 8 : -467.6794 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -467.6789 (branch= 0.0004 subset rates= 0.0001) +pass 1 : -467.7525 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.7145 (branch= 0.0380 subset rates= 0.0000) +pass 3 : -467.6987 (branch= 0.0158 subset rates= 0.0000) +pass 4 : -467.6903 (branch= 0.0076 subset rates= 0.0008) +pass 5 : -467.6867 (branch= 0.0035 subset rates= 0.0000) +pass 6 : -467.6818 (branch= 0.0049 subset rates= 0.0000) +pass 7 : -467.6801 (branch= 0.0018 subset rates= 0.0000) +pass 8 : -467.6792 (branch= 0.0007 subset rates= 0.0001) +pass 9 : -467.6788 (branch= 0.0005 subset rates= 0.0000) pass 10: -467.6786 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6785 (branch= 0.0002 subset rates= 0.0000) -pass 12: -467.6784 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6785 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6784 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6784 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0001) +pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 16: -467.6784 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6782 +Final score = -467.6784 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15975,11 +15770,11 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.19 + 0.79 1.47 2.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -15987,14 +15782,13 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -467.6782 -Replicate 2 : -467.6787 (same topology as 1) -Replicate 3 : -467.6782 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -467.6782 (best) +Replicate 2 : -467.6784 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16010,10 +15804,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.844 0.786 1.480 2.180 -rep 2: 3.839 0.788 1.472 2.178 -rep 3: 3.844 0.786 1.477 2.188 +rep 2: 3.841 0.787 1.473 2.186 -Saving final tree from best search rep (#3) to ch.p.mk.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf @@ -16199,124 +15992,6 @@ 2100 -477.4739 0.010 373 2200 -477.4732 0.010 373 2300 -477.4729 0.010 373 -2400 -477.4726 0.010 373 -2500 -477.4723 0.010 373 -2600 -477.4711 0.010 373 -2700 -477.4707 0.010 373 -2800 -477.4706 0.010 373 -2900 -477.4705 0.010 373 -3000 -477.4702 0.010 373 -3100 -477.4701 0.010 373 -Reached termination condition! -last topological improvement at gen 373 -Improvement over last 500 gen = 0.00099 -Current score = -477.4701 -Performing final optimizations... -pass 1 : -477.4701 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -477.4430 (branch= 0.0269 subset rates= 0.0002) -pass 3 : -477.4394 (branch= 0.0036 subset rates= 0.0000) -pass 4 : -477.4366 (branch= 0.0027 subset rates= 0.0000) -pass 5 : -477.4354 (branch= 0.0013 subset rates= 0.0000) -pass 6 : -477.4347 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -477.4334 (branch= 0.0013 subset rates= 0.0000) -pass 8 : -477.4324 (branch= 0.0010 subset rates= 0.0000) -pass 9 : -477.4321 (branch= 0.0004 subset rates= 0.0000) -pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0001) -pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.4316 -Time used so far = 0 hours, 0 minutes and 4 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.63 1.92 2.74 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=200420059 - -Initial ln Likelihood: -656.4902 -optimizing: starting branch lengths, subset rates... -pass 1:+ 148.906 (branch= 137.62 scale= 1.92 subset rates= 9.37) -pass 2:+ 19.722 (branch= 15.83 scale= 0.00 subset rates= 3.89) -pass 3:+ 3.562 (branch= 2.11 scale= 0.00 subset rates= 1.45) -pass 4:+ 2.460 (branch= 2.02 scale= 0.00 subset rates= 0.44) -pass 5:+ 3.227 (branch= 3.23 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.745 (branch= 0.71 scale= 0.01 subset rates= 0.02) -pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8527 -gen current_lnL precision last_tree_imp -0 -477.8527 0.010 0 -100 -477.7879 0.010 74 -200 -477.7665 0.010 74 -300 -477.7486 0.010 74 -400 -477.7424 0.010 74 -500 -477.7295 0.010 74 -600 -477.7267 0.010 74 -700 -477.7205 0.010 74 -800 -477.7194 0.010 74 -900 -477.7186 0.010 74 -1000 -477.7135 0.010 74 -1100 -477.7094 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16442,62 +16117,39 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1110, seed 1892573554, best lnL -477.709 +Search rep 1 (of 5) generation 2394, seed 1645090745, best lnL -477.473 gen current_lnL precision last_tree_imp -1110 -477.7094 0.010 74 -1200 -477.7090 0.010 74 -1300 -477.7060 0.010 74 -1400 -477.7036 0.010 74 -1500 -477.7019 0.010 74 -1600 -477.7004 0.010 74 -1700 -477.6994 0.010 74 -1800 -477.6984 0.010 74 -1900 -477.6977 0.010 74 -2000 -477.6953 0.010 74 -2100 -477.3774 0.010 2081 -2200 -477.3631 0.010 2170 -2300 -477.3559 0.010 2170 -2400 -477.3497 0.010 2170 -2500 -477.3452 0.010 2170 -2600 -477.3293 0.010 2170 -2700 -477.3261 0.010 2170 -2800 -477.3186 0.010 2170 -2900 -477.3149 0.010 2170 -3000 -477.3144 0.010 2170 -3100 -477.3140 0.010 2170 -3200 -477.3125 0.010 2170 -3300 -477.3125 0.010 2170 -3400 -477.3123 0.010 2170 -3500 -477.3110 0.010 2170 -3600 -477.3109 0.010 2170 -3700 -477.3101 0.010 2170 -3800 -477.3085 0.010 2170 -3900 -477.3085 0.010 2170 -4000 -477.3085 0.010 2170 -4100 -477.3082 0.010 2170 -4200 -477.3082 0.010 2170 -4300 -477.3079 0.010 2170 +2394 -477.4726 0.010 373 +2400 -477.4726 0.010 373 +2500 -477.4723 0.010 373 +2600 -477.4711 0.010 373 +2700 -477.4707 0.010 373 +2800 -477.4706 0.010 373 +2900 -477.4705 0.010 373 +3000 -477.4702 0.010 373 +3100 -477.4701 0.010 373 Reached termination condition! -last topological improvement at gen 2170 -Improvement over last 500 gen = 0.00067 -Current score = -477.3079 +last topological improvement at gen 373 +Improvement over last 500 gen = 0.00099 +Current score = -477.4701 Performing final optimizations... -pass 1 : -477.2447 (branch= 0.0000 subset rates= 0.0632) -pass 2 : -477.2336 (branch= 0.0111 subset rates= 0.0000) -pass 3 : -477.2150 (branch= 0.0106 subset rates= 0.0080) -pass 4 : -477.2129 (branch= 0.0020 subset rates= 0.0000) -pass 5 : -477.2082 (branch= 0.0047 subset rates= 0.0000) -pass 6 : -477.2060 (branch= 0.0019 subset rates= 0.0003) -pass 7 : -477.2056 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -477.2049 (branch= 0.0006 subset rates= 0.0001) -pass 9 : -477.2047 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2046 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2045 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.2045 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.4701 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.4430 (branch= 0.0269 subset rates= 0.0002) +pass 3 : -477.4394 (branch= 0.0036 subset rates= 0.0000) +pass 4 : -477.4366 (branch= 0.0027 subset rates= 0.0000) +pass 5 : -477.4354 (branch= 0.0013 subset rates= 0.0000) +pass 6 : -477.4347 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -477.4334 (branch= 0.0013 subset rates= 0.0000) +pass 8 : -477.4324 (branch= 0.0010 subset rates= 0.0000) +pass 9 : -477.4321 (branch= 0.0004 subset rates= 0.0000) +pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0001) +pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.2045 -Time used so far = 0 hours, 0 minutes and 10 seconds +Final score = -477.4316 +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16525,13 +16177,13 @@ no rate heterogeneity Subset rate multipliers: - 0.64 1.93 2.63 + 0.63 1.92 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. ->>>Completed Search rep 2 (of 5)<<< +>>>Completed Search rep 1 (of 5)<<< ->>>Search rep 3 (of 5)<<< +>>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -16560,54 +16212,59 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=1602142636 +Starting with seed=200420059 -Initial ln Likelihood: -662.4976 +Initial ln Likelihood: -656.4902 optimizing: starting branch lengths, subset rates... -pass 1:+ 159.344 (branch= 147.93 scale= 1.33 subset rates= 10.09) -pass 2:+ 18.362 (branch= 14.32 scale= 0.01 subset rates= 4.02) -pass 3:+ 5.723 (branch= 4.51 scale= 0.00 subset rates= 1.22) -pass 4:+ 1.012 (branch= 0.74 scale= 0.00 subset rates= 0.28) -pass 5:+ 0.186 (branch= 0.17 scale= 0.00 subset rates= 0.02) -pass 6:+ 0.016 (branch= 0.00 scale= 0.02 subset rates= 0.00) -pass 7:+ 0.035 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 1:+ 148.906 (branch= 137.62 scale= 1.92 subset rates= 9.37) +pass 2:+ 19.722 (branch= 15.83 scale= 0.00 subset rates= 3.89) +pass 3:+ 3.562 (branch= 2.11 scale= 0.00 subset rates= 1.45) +pass 4:+ 2.460 (branch= 2.02 scale= 0.00 subset rates= 0.44) +pass 5:+ 3.227 (branch= 3.23 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.745 (branch= 0.71 scale= 0.01 subset rates= 0.02) +pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8200 +lnL after optimization: -477.8527 gen current_lnL precision last_tree_imp -0 -477.8200 0.010 0 -100 -477.7127 0.010 12 -200 -477.6994 0.010 12 -300 -477.6923 0.010 12 -400 -477.5173 0.010 372 -500 -477.5116 0.010 372 -600 -477.5057 0.010 372 -700 -477.4981 0.010 372 -800 -477.4917 0.010 372 -900 -477.4851 0.010 372 -1000 -477.4827 0.010 372 -1100 -477.4798 0.010 372 -1200 -477.4747 0.010 372 +0 -477.8527 0.010 0 +100 -477.7879 0.010 74 +200 -477.7665 0.010 74 +300 -477.7486 0.010 74 +400 -477.7424 0.010 74 +500 -477.7295 0.010 74 +600 -477.7267 0.010 74 +700 -477.7205 0.010 74 +800 -477.7194 0.010 74 +900 -477.7186 0.010 74 +1000 -477.7135 0.010 74 +1100 -477.7094 0.010 74 +1200 -477.7090 0.010 74 +1300 -477.7060 0.010 74 +1400 -477.7036 0.010 74 +1500 -477.7019 0.010 74 +1600 -477.7004 0.010 74 +1700 -477.6994 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.4747 +Current score = -477.6984 Performing final optimizations... -pass 1 : -477.4747 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -477.4598 (branch= 0.0148 subset rates= 0.0001) -pass 3 : -477.4461 (branch= 0.0137 subset rates= 0.0000) -pass 4 : -477.4414 (branch= 0.0042 subset rates= 0.0005) -pass 5 : -477.4386 (branch= 0.0028 subset rates= 0.0000) -pass 6 : -477.4354 (branch= 0.0032 subset rates= 0.0000) -pass 7 : -477.4341 (branch= 0.0013 subset rates= 0.0000) -pass 8 : -477.4329 (branch= 0.0013 subset rates= 0.0000) -pass 9 : -477.4324 (branch= 0.0004 subset rates= 0.0000) -pass 10: -477.4322 (branch= 0.0003 subset rates= 0.0000) -pass 11: -477.4320 (branch= 0.0002 subset rates= 0.0000) -pass 12: -477.4319 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4319 (branch= 0.0001 subset rates= 0.0000) -pass 14: -477.4318 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4318 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4318 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.6884 (branch= 0.0064 subset rates= 0.0036) +pass 2 : -477.6539 (branch= 0.0257 subset rates= 0.0088) +pass 3 : -477.6360 (branch= 0.0180 subset rates= 0.0000) +pass 4 : -477.6278 (branch= 0.0075 subset rates= 0.0006) +pass 5 : -477.6230 (branch= 0.0049 subset rates= 0.0000) +pass 6 : -477.6199 (branch= 0.0031 subset rates= 0.0000) +pass 7 : -477.6188 (branch= 0.0011 subset rates= 0.0000) +pass 8 : -477.6179 (branch= 0.0009 subset rates= 0.0000) +pass 9 : -477.6176 (branch= 0.0003 subset rates= 0.0000) +pass 10: -477.6171 (branch= 0.0002 subset rates= 0.0003) +pass 11: -477.6169 (branch= 0.0002 subset rates= 0.0000) +pass 12: -477.6168 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.6168 (branch= 0.0001 subset rates= 0.0000) +pass 14: -477.6167 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.6167 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.6167 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4318 +Final score = -477.6167 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16638,9 +16295,9 @@ Subset rate multipliers: 0.63 1.91 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -16648,14 +16305,13 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -477.4316 -Replicate 2 : -477.2045 (best) -Replicate 3 : -477.4318 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -477.4316 (best) +Replicate 2 : -477.6167 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16671,10 +16327,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.917 2.740 -rep 2: 4.695 0.635 1.931 2.634 -rep 3: 4.925 0.633 1.909 2.740 +rep 2: 4.894 0.633 1.909 2.743 -Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf @@ -16866,94 +16521,6 @@ 2300 -484.5861 0.010 661 2400 -484.5846 0.010 661 2500 -484.5845 0.010 661 -2600 -484.5838 0.010 661 -2700 -484.5830 0.010 661 -2800 -484.5823 0.010 661 -2900 -484.5822 0.010 661 -3000 -484.5818 0.010 661 -3100 -484.5812 0.010 661 -3200 -484.5805 0.010 661 -3300 -484.5794 0.010 661 -3400 -484.5791 0.010 661 -3500 -484.5745 0.010 661 -3600 -484.5745 0.010 661 -3700 -484.5745 0.010 661 -3800 -484.5745 0.010 661 -3900 -484.5741 0.010 661 -4000 -484.5740 0.010 661 -Reached termination condition! -last topological improvement at gen 661 -Improvement over last 500 gen = 0.00055 -Current score = -484.5740 -Performing final optimizations... -pass 1 : -484.5688 (branch= 0.0049 subset rates= 0.0003) -pass 2 : -484.5554 (branch= 0.0134 subset rates= 0.0000) -pass 3 : -484.5488 (branch= 0.0067 subset rates= 0.0000) -pass 4 : -484.5460 (branch= 0.0027 subset rates= 0.0000) -pass 5 : -484.5448 (branch= 0.0012 subset rates= 0.0000) -pass 6 : -484.5440 (branch= 0.0008 subset rates= 0.0000) -pass 7 : -484.5436 (branch= 0.0005 subset rates= 0.0000) -pass 8 : -484.5430 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -484.5430 (branch= 0.0001 subset rates= 0.0000) -pass 10: -484.5429 (branch= 0.0001 subset rates= 0.0000) -pass 11: -484.5429 (branch= 0.0000 subset rates= 0.0000) -pass 12: -484.5428 (branch= 0.0000 subset rates= 0.0000) -pass 13: -484.5428 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -484.5428 -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 2.95 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. - ->>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< - ->>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -Starting with seed=1418804583 - -Initial ln Likelihood: -694.9819 -optimizing: starting branch lengths, subset rates... -pass 1:+ 174.392 (branch= 164.34 scale= 0.02 subset rates= 10.04) -pass 2:+ 9.231 (branch= 5.66 scale= 0.05 subset rates= 3.52) -pass 3:+ 4.898 (branch= 3.30 scale= 0.00 subset rates= 1.59) -pass 4:+ 9.221 (branch= 8.95 scale= 0.00 subset rates= 0.27) -pass 5:+ 0.626 (branch= 0.62 scale= 0.00 subset rates= 0.01) -pass 6:+ 0.018 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -496.5963 -gen current_lnL precision last_tree_imp -0 -496.5963 0.010 0 -100 -496.1522 0.010 56 -200 -493.1251 0.010 188 -300 -489.5913 0.010 276 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17082,73 +16649,118 @@ Subset 3: Random seed for bootstrap reweighting: 585640194 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 313, seed 1644352132, best lnL -486.385 +Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 2578, seed 488980718, best lnL -484.584 +gen current_lnL precision last_tree_imp +2578 -484.5844 0.010 661 +2600 -484.5838 0.010 661 +2700 -484.5830 0.010 661 +2800 -484.5823 0.010 661 +2900 -484.5822 0.010 661 +3000 -484.5818 0.010 661 +3100 -484.5812 0.010 661 +3200 -484.5805 0.010 661 +3300 -484.5794 0.010 661 +3400 -484.5791 0.010 661 +3500 -484.5745 0.010 661 +3600 -484.5745 0.010 661 +3700 -484.5745 0.010 661 +3800 -484.5745 0.010 661 +3900 -484.5741 0.010 661 +4000 -484.5740 0.010 661 +Reached termination condition! +last topological improvement at gen 661 +Improvement over last 500 gen = 0.00055 +Current score = -484.5740 +Performing final optimizations... +pass 1 : -484.5688 (branch= 0.0049 subset rates= 0.0003) +pass 2 : -484.5554 (branch= 0.0134 subset rates= 0.0000) +pass 3 : -484.5488 (branch= 0.0067 subset rates= 0.0000) +pass 4 : -484.5460 (branch= 0.0027 subset rates= 0.0000) +pass 5 : -484.5448 (branch= 0.0012 subset rates= 0.0000) +pass 6 : -484.5440 (branch= 0.0008 subset rates= 0.0000) +pass 7 : -484.5436 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -484.5430 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -484.5430 (branch= 0.0001 subset rates= 0.0000) +pass 10: -484.5429 (branch= 0.0001 subset rates= 0.0000) +pass 11: -484.5429 (branch= 0.0000 subset rates= 0.0000) +pass 12: -484.5428 (branch= 0.0000 subset rates= 0.0000) +pass 13: -484.5428 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -484.5428 +Time used so far = 0 hours, 0 minutes and 9 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 2.95 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 7 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=1418804583 + +Initial ln Likelihood: -694.9819 +optimizing: starting branch lengths, subset rates... +pass 1:+ 174.392 (branch= 164.34 scale= 0.02 subset rates= 10.04) +pass 2:+ 9.231 (branch= 5.66 scale= 0.05 subset rates= 3.52) +pass 3:+ 4.898 (branch= 3.30 scale= 0.00 subset rates= 1.59) +pass 4:+ 9.221 (branch= 8.95 scale= 0.00 subset rates= 0.27) +pass 5:+ 0.626 (branch= 0.62 scale= 0.00 subset rates= 0.01) +pass 6:+ 0.018 (branch= 0.02 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -496.5963 gen current_lnL precision last_tree_imp -313 -486.3847 0.010 301 +0 -496.5963 0.010 0 +100 -496.1522 0.010 56 +200 -493.1251 0.010 188 +300 -489.5913 0.010 276 400 -485.3399 0.010 377 500 -484.8544 0.010 500 600 -484.8310 0.010 577 -700 -484.6771 0.010 682 -800 -484.6429 0.010 728 -900 -484.6380 0.010 728 -1000 -484.6310 0.010 728 -1100 -484.6267 0.010 728 -1200 -484.6197 0.010 728 -1300 -484.6177 0.010 728 -1400 -484.6124 0.010 728 -1500 -484.6118 0.010 728 -1600 -484.6080 0.010 728 -1700 -484.6059 0.010 728 -1800 -484.6058 0.010 728 -1900 -484.6038 0.010 728 -2000 -484.6033 0.010 728 -2100 -484.6025 0.010 728 -2200 -484.6021 0.010 728 -2300 -484.6015 0.010 728 -2400 -484.6007 0.010 728 -2500 -484.6002 0.010 728 -2600 -484.5988 0.010 728 -2700 -484.5983 0.010 728 -2800 -484.5979 0.010 728 -2900 -484.5969 0.010 728 -3000 -484.5963 0.010 728 -3100 -484.5962 0.010 728 -3200 -484.5952 0.010 728 -3300 -484.5950 0.010 728 -3400 -484.5950 0.010 728 -3500 -484.5930 0.010 728 -3600 -484.5930 0.010 728 -3700 -484.5922 0.010 728 -3800 -484.5918 0.010 728 -3900 -484.5905 0.010 728 -4000 -484.5899 0.010 728 -4100 -484.5893 0.010 728 -4200 -484.5881 0.010 728 -4300 -484.5864 0.010 728 -4400 -484.5862 0.010 728 -4500 -484.5860 0.010 728 -4600 -484.5850 0.010 728 -4700 -484.5850 0.010 728 -4800 -484.5844 0.010 728 -4900 -484.5838 0.010 728 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -484.5837 +Current score = -484.8121 Performing final optimizations... -pass 1 : -484.5732 (branch= 0.0102 subset rates= 0.0002) -pass 2 : -484.5529 (branch= 0.0202 subset rates= 0.0002) -pass 3 : -484.5495 (branch= 0.0015 subset rates= 0.0020) -pass 4 : -484.5470 (branch= 0.0025 subset rates= 0.0000) -pass 5 : -484.5455 (branch= 0.0014 subset rates= 0.0000) -pass 6 : -484.5444 (branch= 0.0012 subset rates= 0.0000) -pass 7 : -484.5438 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -484.5437 (branch= 0.0001 subset rates= 0.0000) -pass 9 : -484.5435 (branch= 0.0002 subset rates= 0.0001) -pass 10: -484.5433 (branch= 0.0001 subset rates= 0.0000) -pass 11: -484.5433 (branch= 0.0000 subset rates= 0.0000) -pass 12: -484.5433 (branch= 0.0000 subset rates= 0.0000) -pass 13: -484.5433 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -484.7786 (branch= 0.0335 subset rates= 0.0000) +pass 2 : -484.7307 (branch= 0.0457 subset rates= 0.0022) +pass 3 : -484.7048 (branch= 0.0259 subset rates= 0.0000) +pass 4 : -484.6982 (branch= 0.0066 subset rates= 0.0000) +pass 5 : -484.6951 (branch= 0.0031 subset rates= 0.0000) +pass 6 : -484.6944 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -484.6939 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -484.6934 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -484.6933 (branch= 0.0001 subset rates= 0.0000) +pass 10: -484.6932 (branch= 0.0001 subset rates= 0.0000) +pass 11: -484.6932 (branch= 0.0001 subset rates= 0.0000) +pass 12: -484.6931 (branch= 0.0000 subset rates= 0.0000) +pass 13: -484.6931 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -484.5433 +Final score = -484.6931 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17177,7 +16789,7 @@ no rate heterogeneity Subset rate multipliers: - 0.66 2.00 2.95 + 0.66 2.00 2.91 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. @@ -17195,7 +16807,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -484.5428 (best) -Replicate 2 : -484.5433 (TERMINATED PREMATURELY) +Replicate 2 : -484.6931 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17211,7 +16823,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.520 0.660 2.002 2.951 -rep 2: 3.519 0.661 1.999 2.951 +rep 2: 3.512 0.663 2.000 2.909 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre @@ -17395,122 +17007,6 @@ 1500 -473.9930 0.010 653 1600 -473.9888 0.010 653 1700 -473.9875 0.010 653 -1800 -473.9857 0.010 653 -1900 -473.9846 0.010 653 -2000 -473.9839 0.010 653 -2100 -473.9834 0.010 653 -2200 -473.9820 0.010 653 -2300 -473.9814 0.010 653 -2400 -473.9804 0.010 653 -2500 -473.9804 0.010 653 -2600 -473.9801 0.010 653 -2700 -473.9793 0.010 653 -2800 -473.9779 0.010 653 -2900 -473.9777 0.010 653 -3000 -473.9777 0.010 653 -3100 -473.9773 0.010 653 -3200 -473.9772 0.010 653 -3300 -473.9770 0.010 653 -Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00088 -Current score = -473.9770 -Performing final optimizations... -pass 1 : -473.9770 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -473.9587 (branch= 0.0183 subset rates= 0.0000) -pass 3 : -473.9587 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9562 (branch= 0.0011 subset rates= 0.0014) -pass 5 : -473.9537 (branch= 0.0013 subset rates= 0.0013) -pass 6 : -473.9523 (branch= 0.0010 subset rates= 0.0003) -pass 7 : -473.9516 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -473.9511 (branch= 0.0004 subset rates= 0.0001) -pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9507 -Time used so far = 0 hours, 0 minutes and 5 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.59 2.07 2.80 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=2125680066 - -Initial ln Likelihood: -649.8224 -optimizing: starting branch lengths, subset rates... -pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) -pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) -pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) -pass 4:+ 2.345 (branch= 1.67 scale= 0.00 subset rates= 0.67) -pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) -pass 6:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8071 -gen current_lnL precision last_tree_imp -0 -474.8071 0.010 0 -100 -474.7912 0.010 0 -200 -474.7021 0.010 123 -300 -474.5642 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17636,70 +17132,143 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 384, seed 582863206, best lnL -474.519 +Search rep 1 (of 5) generation 1711, seed 1025479712, best lnL -473.987 +gen current_lnL precision last_tree_imp +1711 -473.9875 0.010 653 +1800 -473.9857 0.010 653 +1900 -473.9846 0.010 653 +2000 -473.9839 0.010 653 +2100 -473.9834 0.010 653 +2200 -473.9820 0.010 653 +2300 -473.9814 0.010 653 +2400 -473.9804 0.010 653 +2500 -473.9804 0.010 653 +2600 -473.9801 0.010 653 +2700 -473.9793 0.010 653 +2800 -473.9779 0.010 653 +2900 -473.9777 0.010 653 +3000 -473.9777 0.010 653 +3100 -473.9773 0.010 653 +3200 -473.9772 0.010 653 +3300 -473.9770 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00088 +Current score = -473.9770 +Performing final optimizations... +pass 1 : -473.9770 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -473.9587 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -473.9587 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9562 (branch= 0.0011 subset rates= 0.0014) +pass 5 : -473.9537 (branch= 0.0013 subset rates= 0.0013) +pass 6 : -473.9523 (branch= 0.0010 subset rates= 0.0003) +pass 7 : -473.9516 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -473.9511 (branch= 0.0004 subset rates= 0.0001) +pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9507 +Time used so far = 0 hours, 0 minutes and 11 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.59 2.07 2.80 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=2125680066 + +Initial ln Likelihood: -649.8224 +optimizing: starting branch lengths, subset rates... +pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) +pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) +pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) +pass 4:+ 2.345 (branch= 1.67 scale= 0.00 subset rates= 0.67) +pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) +pass 6:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8071 gen current_lnL precision last_tree_imp -384 -474.5190 0.010 272 -400 -474.5190 0.010 272 -500 -474.5075 0.010 272 -600 -474.5034 0.010 272 -700 -474.4997 0.010 272 -800 -474.4937 0.010 272 -900 -474.4913 0.010 272 -1000 -474.4880 0.010 272 -1100 -474.4855 0.010 272 -1200 -474.4847 0.010 272 -1300 -474.4838 0.010 272 -1400 -474.4822 0.010 272 -1500 -474.4804 0.010 272 -1600 -474.4798 0.010 272 -1700 -474.4795 0.010 272 -1800 -474.4790 0.010 272 -1900 -474.4786 0.010 272 -2000 -474.4786 0.010 272 -2100 -474.4782 0.010 272 -2200 -474.4775 0.010 272 -2300 -474.4768 0.010 272 -2400 -474.4764 0.010 272 -2500 -474.4764 0.010 272 -2600 -474.4747 0.010 272 -2700 -474.4736 0.010 272 -2800 -474.4720 0.010 272 -2900 -474.4720 0.010 272 -3000 -474.4652 0.010 272 -3100 -474.4597 0.010 272 -3200 -474.4561 0.010 272 -3300 -474.4551 0.010 272 -3400 -474.4539 0.010 272 -3500 -474.4525 0.010 272 -3600 -474.4521 0.010 272 -3700 -474.4507 0.010 272 -3800 -474.4505 0.010 272 -3900 -474.4503 0.010 272 -4000 -474.4502 0.010 272 -4100 -474.4501 0.010 272 -4200 -474.4492 0.010 272 -4300 -474.4491 0.010 272 -4400 -474.4486 0.010 272 +0 -474.8071 0.010 0 +100 -474.7912 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4484 +Current score = -474.7891 Performing final optimizations... -pass 1 : -474.4484 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -474.4367 (branch= 0.0117 subset rates= 0.0000) -pass 3 : -474.4325 (branch= 0.0041 subset rates= 0.0000) -pass 4 : -474.4311 (branch= 0.0014 subset rates= 0.0000) -pass 5 : -474.4307 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -474.4298 (branch= 0.0009 subset rates= 0.0000) -pass 7 : -474.4292 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -474.4287 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -474.4285 (branch= 0.0003 subset rates= 0.0000) -pass 10: -474.4283 (branch= 0.0001 subset rates= 0.0000) -pass 11: -474.4283 (branch= 0.0001 subset rates= 0.0000) -pass 12: -474.4282 (branch= 0.0000 subset rates= 0.0000) -pass 13: -474.4282 (branch= 0.0000 subset rates= 0.0000) -pass 14: -474.4282 (branch= 0.0000 subset rates= 0.0000) -pass 15: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.7369 (branch= 0.0522 subset rates= 0.0000) +pass 2 : -474.6751 (branch= 0.0616 subset rates= 0.0003) +pass 3 : -474.6624 (branch= 0.0104 subset rates= 0.0023) +pass 4 : -474.6552 (branch= 0.0071 subset rates= 0.0000) +pass 5 : -474.6534 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -474.6495 (branch= 0.0026 subset rates= 0.0013) +pass 7 : -474.6473 (branch= 0.0018 subset rates= 0.0004) +pass 8 : -474.6465 (branch= 0.0009 subset rates= 0.0000) +pass 9 : -474.6460 (branch= 0.0004 subset rates= 0.0000) +pass 10: -474.6458 (branch= 0.0003 subset rates= 0.0000) +pass 11: -474.6456 (branch= 0.0002 subset rates= 0.0000) +pass 12: -474.6456 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.6456 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.6455 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.6455 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -474.4282 +Final score = -474.6455 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17728,9 +17297,9 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.93 + 0.59 2.02 2.99 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 9 branches were collapsed. >>>Terminated Search rep 2 (of 5)<<< @@ -17746,7 +17315,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9507 (best) -Replicate 2 : -474.4282 (TERMINATED PREMATURELY) +Replicate 2 : -474.6455 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17762,7 +17331,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.349 0.588 2.066 2.804 -rep 2: 4.601 0.588 2.030 2.926 +rep 2: 4.584 0.586 2.017 2.990 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -17780,13 +17349,13 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j3 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j4 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' @@ -17825,15 +17394,15 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/garli-mpi/usr/lib/garli/bin/Garli-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/garli/usr/lib/garli/bin/Garli-2.1 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/garli-mpi/usr/lib/garli/bin/Garli-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-4_all.deb'. -dpkg-deb: building package 'garli' in '../garli_2.1-4_armhf.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-4_armhf.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-4_armhf.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-4_armhf.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-4_armhf.deb'. dpkg-genbuildinfo --build=binary @@ -17843,12 +17412,14 @@ 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/7639/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/7639/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/4936 and its subdirectories -I: Current time: Mon Aug 23 12:19:15 -12 2021 -I: pbuilder-time-stamp: 1629764355 +I: removing directory /srv/workspace/pbuilder/7639 and its subdirectories +I: Current time: Tue Aug 24 14:39:01 +14 2021 +I: pbuilder-time-stamp: 1629765541