Diff of the two buildlogs: -- --- b1/build.log 2021-08-22 21:41:34.528824169 +0000 +++ b2/build.log 2021-08-22 21:52:26.752291371 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Sep 24 15:55:09 -12 2022 -I: pbuilder-time-stamp: 1664078109 +I: Current time: Mon Aug 23 11:41:39 +14 2021 +I: pbuilder-time-stamp: 1629668499 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.LZsiMDCH/trustedkeys.kbx': General error -gpgv: Signature made Wed Nov 18 02:03:14 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.vzeDFHRP/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/17286/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/20439/tmp/hooks/D01_modify_environment starting +debug: Running on codethink14-arm64. +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/20439/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/20439/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='17286' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=20439 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.7V4iHVsDG8/pbuilderrc_RWR7 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7V4iHVsDG8/b1 --logfile b1/build.log garli_2.1-4.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.7V4iHVsDG8/pbuilderrc_plYi --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7V4iHVsDG8/b2 --logfile b2/build.log garli_2.1-4.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink11-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 2021 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 2021 more - -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount - -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 23 03:47 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 2021 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/17286/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 178400 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 93744 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 09:09 more + -rwsr-xr-x 1 root root 51360 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 14496 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 134808 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 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 23 11:41 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 09:09 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 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/20439/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -287,7 +321,7 @@ Get: 86 http://deb.debian.org/debian bullseye/main arm64 openmpi-bin arm64 4.1.0-10 [237 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 libopenmpi-dev arm64 4.1.0-10 [1192 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 ncl-tools arm64 2.1.21+git20190531.feceb81-3 [184 kB] -Fetched 41.2 MB in 1s (33.6 MB/s) +Fetched 41.2 MB in 1s (48.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) @@ -658,7 +692,8 @@ 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: Temporary failure in name resolution +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 @@ -720,8 +755,8 @@ 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 @@ -969,10 +1004,6 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -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 model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -1008,6 +1039,10 @@ 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 set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp +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 In file included from tree.h:35, from individual.h:21, @@ -1199,8 +1234,8 @@ 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 @@ -1321,6 +1356,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 602 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': +datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); @@ -1355,10 +1401,6 @@ adaptation.cpp:292:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': -datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:293:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1386,18 +1428,15 @@ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': -configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 602 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 +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 model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -1433,10 +1472,6 @@ model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 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 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 -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 In file included from tree.h:35, @@ -4241,7 +4276,7 @@ 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 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4538,7 +4573,7 @@ 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 25 seconds +Time used = 0 hours, 0 minutes and 27 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4690,7 +4725,7 @@ 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 17 seconds +Time used = 0 hours, 0 minutes and 20 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4894,7 +4929,7 @@ pass 76: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2333 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5102,7 +5137,7 @@ 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 ... ####################################################### @@ -5264,7 +5299,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5419,7 +5454,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5583,7 +5618,7 @@ pass 12: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -6686,7 +6721,7 @@ pass 17: -477.6848 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6848 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8366,7 +8401,7 @@ pass 499: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3584 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -11368,6 +11403,7 @@ 500 -100.0135 0.500 183 600 -99.2983 0.500 549 700 -99.1955 0.500 549 +800 -99.0437 0.500 783 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11464,10 +11500,9 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 762, seed 1776040782, best lnL -99.129 +Bootstrap rep 1 (of 1) generation 852, seed 211111587, best lnL -99.015 gen current_lnL precision last_tree_imp -762 -99.1288 0.500 549 -800 -99.0437 0.500 783 +852 -99.0153 0.500 783 900 -99.0045 0.500 783 1000 -98.8740 0.500 949 NOTE: ****Specified generation limit (1000) reached... @@ -11727,9 +11762,9 @@ STARTING RUN Restarting from checkpoint... - generation 527, seed 118097787, best lnL -111.802 + generation 505, seed 747348448, best lnL -111.804 gen current_lnL precision last_tree_imp -527 -111.8016 0.500 84 +505 -111.8042 0.500 84 600 -111.7788 0.500 84 Optimization precision reduced Optimizing parameters... improved 0.386 lnL @@ -11921,6 +11956,7 @@ 1500 -111.6819 0.010 563 1600 -111.6818 0.010 563 1700 -111.6818 0.010 563 +1800 -111.6818 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12006,9 +12042,9 @@ STARTING RUN Restarting from checkpoint... - generation 1747, seed 1385510638, best lnL -111.682 + generation 1800, seed 753617861, best lnL -111.682 gen current_lnL precision last_tree_imp -1747 -111.6818 0.010 563 +1800 -111.6818 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -12039,7 +12075,7 @@ Treelengths: TL -rep 1: 2.605 +rep 1: 2.606 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log @@ -12452,7 +12488,6 @@ 10 -202.1994 0.500 4 20 -201.8889 0.500 17 30 -201.7046 0.500 24 -40 -197.9483 0.500 33 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12540,9 +12575,10 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 45, seed 1279743899, best lnL -197.948 +Bootstrap rep 1 (of 1) generation 32, seed 586802293, best lnL -199.691 gen current_lnL precision last_tree_imp -45 -197.9483 0.500 33 +32 -199.6911 0.500 31 +40 -197.9483 0.500 33 50 -197.9463 0.500 33 60 -197.2208 0.500 60 70 -197.1918 0.500 60 @@ -12870,9 +12906,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1684, seed 1653438617, best lnL -3352.269 +Search rep 1 (of 2) generation 1678, seed 1030543368, best lnL -3352.269 gen current_lnL precision last_tree_imp -1684 -3352.2687 0.010 0 +1678 -3352.2687 0.010 0 1700 -3352.2687 0.010 0 1800 -3352.1820 0.010 0 1900 -3351.8309 0.010 0 @@ -12886,40 +12922,39 @@ 2700 -3351.1151 0.010 0 2800 -3351.1102 0.010 0 2900 -3351.0655 0.010 0 -3000 -3351.0636 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.0546 +Current score = -3351.0655 Performing final optimizations... -pass 1 : -3350.9661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0255 eq freqs= 0.0178 rel rates= 0.0453 subset rates= 0.0000) -pass 2 : -3350.8735 (branch= 0.0055 alpha= 0.0120 pinv= 0.0172 eq freqs= 0.0038 rel rates= 0.0541 subset rates= 0.0000) -pass 3 : -3350.7952 (branch= 0.0075 alpha= 0.0163 pinv= 0.0155 eq freqs= 0.0000 rel rates= 0.0375 subset rates= 0.0014) -pass 4 : -3350.7264 (branch= 0.0090 alpha= 0.0132 pinv= 0.0146 eq freqs= 0.0000 rel rates= 0.0303 subset rates= 0.0017) -pass 5 : -3350.6666 (branch= 0.0047 alpha= 0.0123 pinv= 0.0134 eq freqs= 0.0009 rel rates= 0.0285 subset rates= 0.0000) -pass 6 : -3350.6127 (branch= 0.0019 alpha= 0.0125 pinv= 0.0122 eq freqs= 0.0000 rel rates= 0.0252 subset rates= 0.0020) -pass 7 : -3350.5671 (branch= 0.0028 alpha= 0.0112 pinv= 0.0112 eq freqs= 0.0001 rel rates= 0.0203 subset rates= 0.0000) -pass 8 : -3350.5259 (branch= 0.0005 alpha= 0.0102 pinv= 0.0102 eq freqs= 0.0000 rel rates= 0.0188 subset rates= 0.0015) -pass 9 : -3350.4899 (branch= 0.0017 alpha= 0.0095 pinv= 0.0093 eq freqs= 0.0001 rel rates= 0.0154 subset rates= 0.0000) -pass 10: -3350.4588 (branch= 0.0002 alpha= 0.0085 pinv= 0.0084 eq freqs= 0.0000 rel rates= 0.0141 subset rates= 0.0000) -pass 11: -3350.4294 (branch= 0.0001 alpha= 0.0082 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0124 subset rates= 0.0011) -pass 12: -3350.4047 (branch= 0.0009 alpha= 0.0071 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0099 subset rates= 0.0000) -pass 13: -3350.3833 (branch= 0.0001 alpha= 0.0062 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0090 subset rates= 0.0000) -pass 14: -3350.3641 (branch= 0.0000 alpha= 0.0059 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0079 subset rates= 0.0000) -pass 15: -3350.3469 (branch= 0.0000 alpha= 0.0053 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0070 subset rates= 0.0000) -pass 16: -3350.3319 (branch= 0.0000 alpha= 0.0048 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0060 subset rates= 0.0000) -pass 17: -3350.3188 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0052 subset rates= 0.0000) -pass 18: -3350.3074 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0044 subset rates= 0.0000) -pass 19: -3350.2974 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0038 subset rates= 0.0000) -pass 20: -3350.2887 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0033 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2454 (branch= 0.0000 alpha= 0.0143 pinv= 0.0129 eq freqs= 0.0000 rel rates= 0.0160 subset rates= 0.0000) +pass 1 : -3350.9769 (branch= 0.0000 alpha= 0.0000 pinv= 0.0216 eq freqs= 0.0183 rel rates= 0.0449 subset rates= 0.0038) +pass 2 : -3350.8758 (branch= 0.0179 alpha= 0.0108 pinv= 0.0174 eq freqs= 0.0032 rel rates= 0.0502 subset rates= 0.0015) +pass 3 : -3350.8002 (branch= 0.0075 alpha= 0.0151 pinv= 0.0156 eq freqs= 0.0000 rel rates= 0.0373 subset rates= 0.0000) +pass 4 : -3350.7303 (branch= 0.0059 alpha= 0.0144 pinv= 0.0145 eq freqs= 0.0000 rel rates= 0.0317 subset rates= 0.0034) +pass 5 : -3350.6693 (branch= 0.0048 alpha= 0.0124 pinv= 0.0135 eq freqs= 0.0009 rel rates= 0.0281 subset rates= 0.0014) +pass 6 : -3350.6155 (branch= 0.0050 alpha= 0.0119 pinv= 0.0124 eq freqs= 0.0000 rel rates= 0.0234 subset rates= 0.0011) +pass 7 : -3350.5703 (branch= 0.0026 alpha= 0.0105 pinv= 0.0114 eq freqs= 0.0000 rel rates= 0.0207 subset rates= 0.0000) +pass 8 : -3350.5286 (branch= 0.0005 alpha= 0.0104 pinv= 0.0103 eq freqs= 0.0001 rel rates= 0.0190 subset rates= 0.0015) +pass 9 : -3350.4927 (branch= 0.0014 alpha= 0.0096 pinv= 0.0093 eq freqs= 0.0001 rel rates= 0.0156 subset rates= 0.0000) +pass 10: -3350.4611 (branch= 0.0002 alpha= 0.0087 pinv= 0.0084 eq freqs= 0.0000 rel rates= 0.0143 subset rates= 0.0000) +pass 11: -3350.4314 (branch= 0.0001 alpha= 0.0083 pinv= 0.0076 eq freqs= 0.0000 rel rates= 0.0125 subset rates= 0.0012) +pass 12: -3350.4065 (branch= 0.0008 alpha= 0.0072 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0100 subset rates= 0.0000) +pass 13: -3350.3848 (branch= 0.0001 alpha= 0.0063 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0091 subset rates= 0.0000) +pass 14: -3350.3654 (branch= 0.0000 alpha= 0.0059 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0080 subset rates= 0.0000) +pass 15: -3350.3482 (branch= 0.0000 alpha= 0.0054 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0070 subset rates= 0.0000) +pass 16: -3350.3330 (branch= 0.0000 alpha= 0.0048 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0060 subset rates= 0.0000) +pass 17: -3350.3198 (branch= 0.0000 alpha= 0.0043 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0052 subset rates= 0.0000) +pass 18: -3350.3082 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0044 subset rates= 0.0000) +pass 19: -3350.2981 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0039 subset rates= 0.0000) +pass 20: -3350.2893 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0033 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2456 (branch= 0.0000 alpha= 0.0145 pinv= 0.0131 eq freqs= 0.0000 rel rates= 0.0160 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2357 (branch= 0.0000 alpha= 0.0031 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0038 subset rates= 0.0000) +pass 40: -3350.2358 (branch= 0.0000 alpha= 0.0031 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0038 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2336 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) +pass 50: -3350.2337 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 60: -3350.2333 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 68: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 69: -3350.2332 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2332 Time used so far = 0 hours, 0 minutes and 13 seconds @@ -12928,7 +12963,7 @@ Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.115, AG = 10.416, AT = 2.691, CG = 0.001, CT = 21.916, GT = 1.000 + AC = 3.114, AG = 10.413, AT = 2.690, CG = 0.001, CT = 21.910, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3329 0.2222 0.1567 0.2882 Rate Heterogeneity Model: @@ -12939,10 +12974,10 @@ Substitution rate categories under this model: rate proportion 0.0000 0.3658 - 0.0486 0.1586 - 0.2997 0.1586 - 0.8696 0.1586 - 2.7821 0.1586 + 0.0486 0.1585 + 0.2997 0.1585 + 0.8696 0.1585 + 2.7821 0.1585 Model 2 Number of states = 2 (binary data) @@ -12973,7 +13008,7 @@ 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: 3.115 10.42 2.691 0.001 21.92 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.114 10.41 2.69 0.001 21.91 1 0.333 0.222 0.157 0.288 0.578 0.366 Partition model subset 2: Model contains no estimated parameters @@ -13230,9 +13265,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 462, seed 2139486126, best lnL -3323.707 +Search rep 1 (of 2) generation 435, seed 151550502, best lnL -3323.902 gen current_lnL precision last_tree_imp -462 -3323.7073 0.500 1 +435 -3323.9019 0.500 1 500 -3323.6818 0.500 1 600 -3323.3459 0.500 1 Optimization precision reduced @@ -13240,65 +13275,64 @@ Optimizing branchlengths... improved 0.023 lnL 700 -3321.3650 0.255 1 800 -3321.0294 0.255 1 -900 -3321.0142 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3321.0117 +Current score = -3321.0142 Performing final optimizations... -pass 1 : -3320.3838 (branch= 0.0457 alpha= 0.0000 pinv= 0.0123 eq freqs= 0.0126 rel rates= 0.5388 ins/del rates= 0.0185) -pass 2 : -3319.9129 (branch= 0.0595 alpha= 0.0039 pinv= 0.0165 eq freqs= 0.0039 rel rates= 0.3699 ins/del rates= 0.0172) -pass 3 : -3319.5398 (branch= 0.0430 alpha= 0.0079 pinv= 0.0161 eq freqs= 0.0068 rel rates= 0.2781 ins/del rates= 0.0213) -pass 4 : -3319.2583 (branch= 0.0263 alpha= 0.0117 pinv= 0.0153 eq freqs= 0.0020 rel rates= 0.2159 ins/del rates= 0.0102) -pass 5 : -3319.0284 (branch= 0.0161 alpha= 0.0098 pinv= 0.0148 eq freqs= 0.0010 rel rates= 0.1817 ins/del rates= 0.0066) -pass 6 : -3318.8321 (branch= 0.0126 alpha= 0.0100 pinv= 0.0139 eq freqs= 0.0007 rel rates= 0.1539 ins/del rates= 0.0052) -pass 7 : -3318.6692 (branch= 0.0083 alpha= 0.0101 pinv= 0.0131 eq freqs= 0.0004 rel rates= 0.1274 ins/del rates= 0.0035) -pass 8 : -3318.5368 (branch= 0.0054 alpha= 0.0104 pinv= 0.0122 eq freqs= 0.0004 rel rates= 0.1017 ins/del rates= 0.0023) -pass 9 : -3318.4254 (branch= 0.0036 alpha= 0.0100 pinv= 0.0113 eq freqs= 0.0003 rel rates= 0.0847 ins/del rates= 0.0015) -pass 10: -3318.3311 (branch= 0.0023 alpha= 0.0097 pinv= 0.0110 eq freqs= 0.0002 rel rates= 0.0699 ins/del rates= 0.0010) -pass 11: -3318.2536 (branch= 0.0015 alpha= 0.0091 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0566 ins/del rates= 0.0007) -pass 12: -3318.1885 (branch= 0.0010 alpha= 0.0085 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0464 ins/del rates= 0.0004) -pass 13: -3318.1331 (branch= 0.0007 alpha= 0.0079 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0386 ins/del rates= 0.0003) -pass 14: -3318.0857 (branch= 0.0005 alpha= 0.0073 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0322 ins/del rates= 0.0002) -pass 15: -3318.0456 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0263 ins/del rates= 0.0001) -pass 16: -3318.0112 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0221 ins/del rates= 0.0001) -pass 17: -3317.9814 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0189 ins/del rates= 0.0000) -pass 18: -3317.9555 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0160 ins/del rates= 0.0000) -pass 19: -3317.9331 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0137 ins/del rates= 0.0000) -pass 20: -3317.9137 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0116 ins/del rates= 0.0000) +pass 1 : -3320.3913 (branch= 0.0389 alpha= 0.0000 pinv= 0.0127 eq freqs= 0.0124 rel rates= 0.5420 ins/del rates= 0.0170) +pass 2 : -3319.9212 (branch= 0.0586 alpha= 0.0040 pinv= 0.0163 eq freqs= 0.0044 rel rates= 0.3700 ins/del rates= 0.0168) +pass 3 : -3319.5422 (branch= 0.0505 alpha= 0.0084 pinv= 0.0157 eq freqs= 0.0072 rel rates= 0.2796 ins/del rates= 0.0175) +pass 4 : -3319.2530 (branch= 0.0301 alpha= 0.0115 pinv= 0.0151 eq freqs= 0.0016 rel rates= 0.2198 ins/del rates= 0.0110) +pass 5 : -3319.0185 (branch= 0.0202 alpha= 0.0089 pinv= 0.0147 eq freqs= 0.0009 rel rates= 0.1817 ins/del rates= 0.0082) +pass 6 : -3318.8237 (branch= 0.0137 alpha= 0.0103 pinv= 0.0138 eq freqs= 0.0005 rel rates= 0.1508 ins/del rates= 0.0055) +pass 7 : -3318.6638 (branch= 0.0088 alpha= 0.0099 pinv= 0.0132 eq freqs= 0.0005 rel rates= 0.1239 ins/del rates= 0.0037) +pass 8 : -3318.5328 (branch= 0.0054 alpha= 0.0107 pinv= 0.0122 eq freqs= 0.0006 rel rates= 0.0998 ins/del rates= 0.0023) +pass 9 : -3318.4216 (branch= 0.0038 alpha= 0.0099 pinv= 0.0113 eq freqs= 0.0003 rel rates= 0.0844 ins/del rates= 0.0016) +pass 10: -3318.3283 (branch= 0.0025 alpha= 0.0096 pinv= 0.0111 eq freqs= 0.0002 rel rates= 0.0688 ins/del rates= 0.0011) +pass 11: -3318.2514 (branch= 0.0016 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0559 ins/del rates= 0.0007) +pass 12: -3318.1868 (branch= 0.0011 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0458 ins/del rates= 0.0005) +pass 13: -3318.1317 (branch= 0.0007 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0382 ins/del rates= 0.0003) +pass 14: -3318.0847 (branch= 0.0005 alpha= 0.0073 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0318 ins/del rates= 0.0002) +pass 15: -3318.0448 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0261 ins/del rates= 0.0001) +pass 16: -3318.0106 (branch= 0.0002 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0219 ins/del rates= 0.0001) +pass 17: -3317.9809 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0187 ins/del rates= 0.0000) +pass 18: -3317.9551 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0159 ins/del rates= 0.0000) +pass 19: -3317.9328 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0136 ins/del rates= 0.0000) +pass 20: -3317.9134 (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: -3317.8169 (branch= 0.0001 alpha= 0.0216 pinv= 0.0199 eq freqs= 0.0001 rel rates= 0.0552 ins/del rates= 0.0000) +pass 30: -3317.8168 (branch= 0.0001 alpha= 0.0216 pinv= 0.0199 eq freqs= 0.0001 rel rates= 0.0549 ins/del rates= 0.0000) optimization up to ... pass 40: -3317.7938 (branch= 0.0001 alpha= 0.0054 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0126 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: -3317.7885 (branch= 0.0000 alpha= 0.0012 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 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) optimization up to ... pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 73: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 75: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 13 seconds +Final score = -3317.7870 +Time used so far = 0 hours, 0 minutes and 14 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.067, AG = 10.268, AT = 2.656, CG = 0.001, CT = 21.547, GT = 1.000 + AC = 3.066, AG = 10.264, AT = 2.656, CG = 0.001, CT = 21.541, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5745 + 0.5751 with an invariant (invariable) site category, proportion estimated - 0.3611 + 0.3615 Substitution rate categories under this model: rate proportion - 0.0000 0.3611 - 0.0479 0.1597 - 0.2978 0.1597 - 0.8677 0.1597 - 2.7866 0.1597 + 0.0000 0.3615 + 0.0480 0.1596 + 0.2982 0.1596 + 0.8681 0.1596 + 2.7857 0.1596 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -13324,13 +13358,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.067 10.27 2.656 0.001 21.55 1 0.333 0.222 0.157 0.288 0.574 0.361 +rep 1: 3.066 10.26 2.656 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -13340,7 +13374,7 @@ Treelengths: TL -rep 1: 1.419 +rep 1: 1.418 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### @@ -13485,6 +13519,8 @@ 5800 -210.4823 0.010 1104 6000 -210.4633 0.010 1104 6200 -210.4596 0.010 1104 +6400 -210.4468 0.010 1104 +6600 -210.4214 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13564,32 +13600,50 @@ STARTING RUN Restarting from checkpoint... - generation 6248, seed 497135681, best lnL -210.450 + generation 6711, seed 1117136890, best lnL -210.418 gen current_lnL precision last_tree_imp -6248 -210.4498 0.010 1104 -6300 -210.4492 0.010 1104 +6711 -210.4181 0.010 1104 +6800 -210.3965 0.010 1104 +6900 -210.3560 0.010 1104 +7000 -210.3384 0.010 1104 +7100 -210.3220 0.010 1104 +7200 -210.3218 0.010 1104 +7300 -210.2908 0.010 1104 +7400 -210.2807 0.010 1104 +7500 -210.2794 0.010 1104 +7600 -210.2625 0.010 1104 +7700 -210.2314 0.010 1104 +7800 -210.1872 0.010 1104 +7900 -210.1766 0.010 1104 +8000 -210.1732 0.010 1104 +8100 -210.1381 0.010 1104 +8200 -210.1275 0.010 1104 +8300 -210.1114 0.010 1104 +8400 -210.1089 0.010 1104 +8500 -210.1073 0.010 1104 +8600 -210.0887 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.03308 +Improvement over last 500 gen = 0.04949 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.108, AG = 5.588, AT = 0.197, CG = 5.424, CT = 8.980, GT = 1.000 + AC = 3.918, AG = 6.880, AT = 0.186, CG = 6.926, CT = 11.161, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2383 0.3335 0.2107 0.2175 + (ACGT) 0.2363 0.3327 0.2105 0.2206 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.3086 + 1.8479 with an invariant (invariable) site category, proportion estimated - 0.1556 + 0.1921 Substitution rate categories under this model: rate proportion - 0.0000 0.1556 - 0.2518 0.2815 - 0.7748 0.2815 - 1.9734 0.2815 + 0.0000 0.1921 + 0.3353 0.2693 + 0.8372 0.2693 + 1.8275 0.2693 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -13600,15 +13654,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.4492 +Replicate 1 : -210.0887 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.108 5.588 0.1974 5.424 8.98 1 0.238 0.333 0.211 0.218 1.309 0.156 +rep 1: 3.918 6.88 0.186 6.926 11.16 1 0.236 0.333 0.210 0.221 1.848 0.192 Treelengths: TL -rep 1: 2.297 +rep 1: 2.342 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 @@ -13757,13 +13811,6 @@ 5200 -190.6786 0.010 1979 5400 -190.6781 0.010 1979 5600 -190.6306 0.010 1979 -5800 -190.5767 0.010 1979 -6000 -190.5743 0.010 1979 -6200 -190.5703 0.010 1979 -6400 -190.5511 0.010 1979 -6600 -190.5307 0.010 1979 -6800 -190.5294 0.010 1979 -7000 -190.5278 0.010 1979 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13844,51 +13891,56 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 7179, seed 1463878479, best lnL -190.515 +Bootstrap rep 1 (of 1) generation 5606, seed 1118205640, best lnL -190.630 gen current_lnL precision last_tree_imp -7179 -190.5149 0.010 1979 -7200 -190.5148 0.010 1979 +5606 -190.6303 0.010 1979 +5700 -190.6095 0.010 1979 +5800 -190.5767 0.010 1979 +5900 -190.5744 0.010 1979 +6000 -190.5743 0.010 1979 +6100 -190.5720 0.010 1979 +6200 -190.5703 0.010 1979 Reached termination condition! last topological improvement at gen 1979 -Improvement over last 500 gen = 0.01488 +Improvement over last 500 gen = 0.03912 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.628, AG = 1.304, AT = 0.009, CG = 2.879, CT = 13.853, GT = 1.000 + AC = 0.596, AG = 1.225, AT = 0.010, CG = 2.680, CT = 12.575, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3148 0.3227 0.2577 0.1047 + (ACGT) 0.3139 0.3231 0.2581 0.1049 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 6.6810 + 6.8021 with an invariant (invariable) site category, proportion estimated 0.1385 Substitution rate categories under this model: rate proportion 0.0000 0.1385 - 0.5598 0.2154 - 0.8356 0.2154 - 1.0797 0.2154 - 1.5249 0.2154 + 0.5632 0.2154 + 0.8374 0.2154 + 1.0794 0.2154 + 1.5200 0.2154 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -190.5148 +Replicate 1 : -190.5703 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: 0.6281 1.304 0.00935 2.879 13.85 1 0.315 0.323 0.258 0.105 6.681 0.138 +rep 1: 0.5961 1.225 0.009625 2.68 12.57 1 0.314 0.323 0.258 0.105 6.802 0.138 Treelengths: TL -rep 1: 2.323 +rep 1: 2.302 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -14439,9 +14491,9 @@ STARTING RUN Restarting from checkpoint... - generation 8205, seed 610301520, best lnL -210.115 + generation 8226, seed 963634534, best lnL -210.113 gen current_lnL precision last_tree_imp -8205 -210.1149 0.010 2883 +8226 -210.1128 0.010 2883 8300 -210.1036 0.010 2883 8400 -210.1006 0.010 2883 Reached termination condition! @@ -14820,16 +14872,15 @@ Subset 3: Random seed for bootstrap reweighting: 1903425807 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 999, seed 318252662, best lnL -13181.497 +Bootstrap rep 1 (of 1) generation 950, seed 1740726170, best lnL -13181.581 gen current_lnL precision last_tree_imp -999 -13181.4969 0.402 1 +950 -13181.5807 0.402 1 1000 -13181.4969 0.402 1 1100 -13181.4426 0.402 1 Optimization precision reduced Optimizing parameters... improved 0.019 lnL Optimizing branchlengths... improved 0.000 lnL 1200 -13181.4112 0.304 1 -1300 -13181.3755 0.304 1 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -14837,7 +14888,7 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 2.042, AG = 3.173, AT = 1.174, CG = 1.174, CT = 2.631, GT = 1.000 + AC = 2.042, AG = 3.173, AT = 1.167, CG = 1.167, CT = 2.631, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3054 0.1867 0.2740 0.2339 Rate Heterogeneity Model: @@ -14856,7 +14907,7 @@ 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 Equilibrium State Frequencies: estimated - (ACGT) 0.2508 0.1558 0.1899 0.4036 + (ACGT) 0.2514 0.1562 0.1902 0.4022 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4487 @@ -14876,16 +14927,16 @@ (ACGT) 0.1612 0.3397 0.2962 0.2030 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.6133 + 4.5459 with an invariant (invariable) site category, proportion estimated - 0.0116 + 0.0111 Substitution rate categories under this model: rate proportion - 0.0000 0.0116 - 0.4852 0.2471 - 0.7941 0.2471 - 1.0839 0.2471 - 1.6369 0.2471 + 0.0000 0.0111 + 0.4820 0.2472 + 0.7922 0.2472 + 1.0840 0.2472 + 1.6418 0.2472 Subset rate multipliers: 0.53 0.28 2.20 @@ -14902,21 +14953,21 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13181.3755 (TERMINATED PREMATURELY) +Replicate 1 : -13181.4065 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.042 3.173 1.174 1.174 2.631 1 0.305 0.187 0.274 0.234 0.388 +rep 1: 2.042 3.173 1.167 1.167 2.631 1 0.305 0.187 0.274 0.234 0.388 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 3.906 4.801 0.7415 4.801 3.906 1 0.251 0.156 0.190 0.404 0.449 +rep 1: 3.906 4.801 0.7415 4.801 3.906 1 0.251 0.156 0.190 0.402 0.449 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 7.157 5.572 1.05 7.157 1 0.161 0.340 0.296 0.203 4.613 0.012 +rep 1: 1 7.157 5.572 1.05 7.157 1 0.161 0.340 0.296 0.203 4.546 0.011 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) @@ -15229,10 +15280,6 @@ 1700 -467.7297 0.010 230 1800 -467.7285 0.010 230 1900 -467.7233 0.010 230 -2000 -467.7212 0.010 230 -2100 -467.7195 0.010 230 -2200 -467.7184 0.010 230 -2300 -467.7179 0.010 230 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15358,9 +15405,13 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 2346, seed 4433699, best lnL -467.716 +Search rep 2 (of 5) generation 1919, seed 1671426242, best lnL -467.723 gen current_lnL precision last_tree_imp -2346 -467.7161 0.010 230 +1919 -467.7233 0.010 230 +2000 -467.7212 0.010 230 +2100 -467.7195 0.010 230 +2200 -467.7184 0.010 230 +2300 -467.7179 0.010 230 2400 -467.7160 0.010 230 2500 -467.7153 0.010 230 2600 -467.7151 0.010 230 @@ -15508,33 +15559,26 @@ 1500 -467.7271 0.010 68 1600 -467.7266 0.010 68 1700 -467.7253 0.010 68 -1800 -467.7242 0.010 68 -1900 -467.7234 0.010 68 -2000 -467.7224 0.010 68 -2100 -467.7200 0.010 68 -2200 -467.7195 0.010 68 -2300 -467.7193 0.010 68 -2400 -467.7190 0.010 68 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7190 +Current score = -467.7253 Performing final optimizations... -pass 1 : -467.7188 (branch= 0.0000 subset rates= 0.0001) -pass 2 : -467.7097 (branch= 0.0091 subset rates= 0.0000) -pass 3 : -467.7040 (branch= 0.0057 subset rates= 0.0000) -pass 4 : -467.7019 (branch= 0.0021 subset rates= 0.0000) -pass 5 : -467.6966 (branch= 0.0053 subset rates= 0.0000) -pass 6 : -467.6956 (branch= 0.0010 subset rates= 0.0000) -pass 7 : -467.6948 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -467.6940 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -467.6936 (branch= 0.0003 subset rates= 0.0000) -pass 10: -467.6934 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6934 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6933 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6933 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6933 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6933 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7253 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.7105 (branch= 0.0147 subset rates= 0.0000) +pass 3 : -467.7040 (branch= 0.0062 subset rates= 0.0003) +pass 4 : -467.6945 (branch= 0.0096 subset rates= 0.0000) +pass 5 : -467.6889 (branch= 0.0052 subset rates= 0.0004) +pass 6 : -467.6842 (branch= 0.0047 subset rates= 0.0000) +pass 7 : -467.6816 (branch= 0.0026 subset rates= 0.0000) +pass 8 : -467.6798 (branch= 0.0013 subset rates= 0.0005) +pass 9 : -467.6791 (branch= 0.0007 subset rates= 0.0000) +pass 10: -467.6787 (branch= 0.0004 subset rates= 0.0000) +pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6785 (branch= 0.0001 subset rates= 0.0000) +pass 13: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6784 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6933 +Final score = -467.6784 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15563,7 +15607,7 @@ no rate heterogeneity Subset rate multipliers: - 0.78 1.49 2.19 + 0.78 1.48 2.20 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -15582,7 +15626,7 @@ Results: Replicate 1 : -467.6782 Replicate 2 : -467.6782 (best) (same topology as 1) -Replicate 3 : -467.6933 (TERMINATED PREMATURELY) +Replicate 3 : -467.6784 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -15599,7 +15643,7 @@ TL R(1) R(2) R(3) rep 1: 3.843 0.787 1.478 2.181 rep 2: 3.843 0.787 1.477 2.186 -rep 3: 3.883 0.783 1.487 2.192 +rep 3: 3.846 0.785 1.481 2.196 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -15908,10 +15952,6 @@ 800 -477.6168 0.010 738 900 -477.5598 0.010 822 1000 -477.5348 0.010 822 -1100 -477.3605 0.010 1061 -1200 -477.3447 0.010 1061 -1300 -477.3387 0.010 1061 -1400 -477.2956 0.010 1061 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16037,9 +16077,13 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1481, seed 537164595, best lnL -477.293 +Search rep 2 (of 5) generation 1070, seed 713117163, best lnL -477.366 gen current_lnL precision last_tree_imp -1481 -477.2935 0.010 1061 +1070 -477.3655 0.010 1061 +1100 -477.3605 0.010 1061 +1200 -477.3447 0.010 1061 +1300 -477.3387 0.010 1061 +1400 -477.2956 0.010 1061 1500 -477.2903 0.010 1061 1600 -477.2785 0.010 1061 1700 -477.2670 0.010 1061 @@ -16090,7 +16134,7 @@ pass 14: -477.2122 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2122 -Time used so far = 0 hours, 0 minutes and 9 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16178,38 +16222,26 @@ 900 -477.6954 0.010 381 1000 -477.6942 0.010 381 1100 -477.6933 0.010 381 -1200 -477.6912 0.010 381 -1300 -477.6854 0.010 381 -1400 -477.6823 0.010 381 -1500 -477.6794 0.010 381 -1600 -477.6785 0.010 381 -1700 -477.6757 0.010 381 -1800 -477.6739 0.010 381 -1900 -477.6724 0.010 381 -2000 -477.6708 0.010 381 -2100 -477.6700 0.010 381 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.6692 +Current score = -477.6933 Performing final optimizations... -pass 1 : -477.6626 (branch= 0.0001 subset rates= 0.0065) -pass 2 : -477.6474 (branch= 0.0152 subset rates= 0.0000) -pass 3 : -477.6364 (branch= 0.0110 subset rates= 0.0000) -pass 4 : -477.6311 (branch= 0.0053 subset rates= 0.0000) -pass 5 : -477.6247 (branch= 0.0045 subset rates= 0.0019) -pass 6 : -477.6233 (branch= 0.0015 subset rates= 0.0000) -pass 7 : -477.6202 (branch= 0.0015 subset rates= 0.0016) -pass 8 : -477.6190 (branch= 0.0012 subset rates= 0.0000) -pass 9 : -477.6184 (branch= 0.0006 subset rates= 0.0000) -pass 10: -477.6176 (branch= 0.0002 subset rates= 0.0006) -pass 11: -477.6172 (branch= 0.0004 subset rates= 0.0000) -pass 12: -477.6170 (branch= 0.0002 subset rates= 0.0000) -pass 13: -477.6169 (branch= 0.0001 subset rates= 0.0000) -pass 14: -477.6169 (branch= 0.0001 subset rates= 0.0000) +pass 1 : -477.6848 (branch= 0.0065 subset rates= 0.0020) +pass 2 : -477.6509 (branch= 0.0303 subset rates= 0.0037) +pass 3 : -477.6367 (branch= 0.0123 subset rates= 0.0018) +pass 4 : -477.6312 (branch= 0.0047 subset rates= 0.0009) +pass 5 : -477.6259 (branch= 0.0044 subset rates= 0.0009) +pass 6 : -477.6211 (branch= 0.0047 subset rates= 0.0000) +pass 7 : -477.6197 (branch= 0.0014 subset rates= 0.0000) +pass 8 : -477.6189 (branch= 0.0008 subset rates= 0.0000) +pass 9 : -477.6181 (branch= 0.0005 subset rates= 0.0003) +pass 10: -477.6175 (branch= 0.0003 subset rates= 0.0002) +pass 11: -477.6171 (branch= 0.0004 subset rates= 0.0000) +pass 12: -477.6169 (branch= 0.0002 subset rates= 0.0000) +pass 13: -477.6168 (branch= 0.0001 subset rates= 0.0000) +pass 14: -477.6168 (branch= 0.0001 subset rates= 0.0000) pass 15: -477.6168 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.6168 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.6167 (branch= 0.0000 subset rates= 0.0000) pass 17: -477.6167 (branch= 0.0000 subset rates= 0.0000) -pass 18: -477.6167 (branch= 0.0000 subset rates= 0.0000) -pass 19: -477.6167 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6167 Time used so far = 0 hours, 0 minutes and 12 seconds @@ -16276,7 +16308,7 @@ TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.918 2.738 rep 2: 4.674 0.641 1.914 2.615 -rep 3: 4.894 0.633 1.911 2.737 +rep 3: 4.894 0.633 1.911 2.738 Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre ####################################################### @@ -16505,7 +16537,7 @@ 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 4 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16557,12 +16589,6 @@ 0 -496.5990 0.010 0 100 -496.1537 0.010 56 200 -496.1374 0.010 56 -300 -495.6766 0.010 257 -400 -485.8540 0.010 375 -500 -485.8342 0.010 375 -600 -485.2995 0.010 538 -700 -485.2880 0.010 538 -800 -485.2770 0.010 538 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16691,9 +16717,15 @@ Subset 3: Random seed for bootstrap reweighting: 585640194 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 817, seed 1043549692, best lnL -485.276 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 281, seed 1670414175, best lnL -495.685 gen current_lnL precision last_tree_imp -817 -485.2760 0.010 538 +281 -495.6854 0.010 257 +300 -495.6766 0.010 257 +400 -485.8540 0.010 375 +500 -485.8342 0.010 375 +600 -485.2995 0.010 538 +700 -485.2880 0.010 538 +800 -485.2770 0.010 538 900 -485.2739 0.010 538 1000 -485.2663 0.010 538 1100 -485.2623 0.010 538 @@ -16740,7 +16772,7 @@ pass 13: -485.2141 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -485.2141 -Time used so far = 0 hours, 0 minutes and 9 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16801,37 +16833,27 @@ 1000 -485.0655 0.010 772 1100 -485.0613 0.010 772 1200 -485.0484 0.010 772 -1300 -485.0454 0.010 772 -1400 -485.0347 0.010 772 -1500 -485.0293 0.010 772 -1600 -485.0251 0.010 772 -1700 -485.0227 0.010 772 -1800 -485.0212 0.010 772 -1900 -485.0190 0.010 772 -2000 -485.0159 0.010 772 -2100 -485.0147 0.010 772 -2200 -485.0134 0.010 772 -2300 -485.0121 0.010 772 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -485.0115 +Current score = -485.0480 Performing final optimizations... -pass 1 : -484.9847 (branch= 0.0091 subset rates= 0.0177) -pass 2 : -484.9609 (branch= 0.0216 subset rates= 0.0023) -pass 3 : -484.9568 (branch= 0.0040 subset rates= 0.0000) -pass 4 : -484.9478 (branch= 0.0090 subset rates= 0.0000) -pass 5 : -484.9437 (branch= 0.0041 subset rates= 0.0000) -pass 6 : -484.9411 (branch= 0.0024 subset rates= 0.0002) -pass 7 : -484.9394 (branch= 0.0016 subset rates= 0.0000) -pass 8 : -484.9382 (branch= 0.0012 subset rates= 0.0000) -pass 9 : -484.9376 (branch= 0.0004 subset rates= 0.0001) -pass 10: -484.9373 (branch= 0.0003 subset rates= 0.0000) -pass 11: -484.9372 (branch= 0.0001 subset rates= 0.0000) -pass 12: -484.9372 (branch= 0.0000 subset rates= 0.0000) -pass 13: -484.9372 (branch= 0.0000 subset rates= 0.0000) -pass 14: -484.9372 (branch= 0.0000 subset rates= 0.0000) -pass 15: -484.9372 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -485.0266 (branch= 0.0073 subset rates= 0.0141) +pass 2 : -484.9867 (branch= 0.0399 subset rates= 0.0000) +pass 3 : -484.9673 (branch= 0.0194 subset rates= 0.0000) +pass 4 : -484.9520 (branch= 0.0107 subset rates= 0.0045) +pass 5 : -484.9454 (branch= 0.0045 subset rates= 0.0021) +pass 6 : -484.9422 (branch= 0.0032 subset rates= 0.0000) +pass 7 : -484.9414 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -484.9393 (branch= 0.0009 subset rates= 0.0011) +pass 9 : -484.9385 (branch= 0.0008 subset rates= 0.0000) +pass 10: -484.9382 (branch= 0.0003 subset rates= 0.0000) +pass 11: -484.9382 (branch= 0.0001 subset rates= 0.0000) +pass 12: -484.9381 (branch= 0.0000 subset rates= 0.0001) +pass 13: -484.9379 (branch= 0.0002 subset rates= 0.0000) +pass 14: -484.9378 (branch= 0.0001 subset rates= 0.0000) +pass 15: -484.9378 (branch= 0.0000 subset rates= 0.0000) +pass 16: -484.9378 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -484.9372 +Final score = -484.9378 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16860,7 +16882,7 @@ no rate heterogeneity Subset rate multipliers: - 0.64 2.02 3.23 + 0.64 2.03 3.24 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 6 branches were collapsed. @@ -16879,7 +16901,7 @@ Results: Replicate 1 : -484.5428 (best) Replicate 2 : -485.2141 -Replicate 3 : -484.9372 (TERMINATED PREMATURELY) +Replicate 3 : -484.9378 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16896,7 +16918,7 @@ TL R(1) R(2) R(3) rep 1: 3.520 0.660 2.001 2.956 rep 2: 3.572 0.667 1.985 2.899 -rep 3: 3.627 0.640 2.024 3.226 +rep 3: 3.626 0.639 2.027 3.237 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre @@ -17196,10 +17218,6 @@ gen current_lnL precision last_tree_imp 0 -474.8238 0.010 0 100 -474.7999 0.010 0 -200 -474.7019 0.010 199 -300 -474.6990 0.010 199 -400 -474.6894 0.010 199 -500 -474.5616 0.010 476 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17325,9 +17343,13 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 596, seed 1355563832, best lnL -474.555 +Search rep 2 (of 5) generation 175, seed 1179205549, best lnL -474.773 gen current_lnL precision last_tree_imp -596 -474.5552 0.010 476 +175 -474.7726 0.010 0 +200 -474.7019 0.010 199 +300 -474.6990 0.010 199 +400 -474.6894 0.010 199 +500 -474.5616 0.010 476 600 -474.5540 0.010 476 700 -474.5466 0.010 476 800 -474.5377 0.010 476 @@ -17367,33 +17389,29 @@ 4200 -474.4761 0.010 476 4300 -474.4755 0.010 476 4400 -474.4743 0.010 476 -4500 -474.4736 0.010 476 -4600 -474.4713 0.010 476 -4700 -474.4702 0.010 476 -4800 -474.4689 0.010 476 -4900 -474.4689 0.010 476 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4684 +Current score = -474.4736 Performing final optimizations... -pass 1 : -474.4624 (branch= 0.0060 subset rates= 0.0000) -pass 2 : -474.4497 (branch= 0.0127 subset rates= 0.0000) -pass 3 : -474.4386 (branch= 0.0108 subset rates= 0.0003) -pass 4 : -474.4371 (branch= 0.0016 subset rates= 0.0000) -pass 5 : -474.4345 (branch= 0.0026 subset rates= 0.0000) -pass 6 : -474.4321 (branch= 0.0023 subset rates= 0.0000) -pass 7 : -474.4302 (branch= 0.0019 subset rates= 0.0000) -pass 8 : -474.4297 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -474.4293 (branch= 0.0003 subset rates= 0.0000) -pass 10: -474.4290 (branch= 0.0002 subset rates= 0.0001) -pass 11: -474.4288 (branch= 0.0002 subset rates= 0.0000) -pass 12: -474.4288 (branch= 0.0001 subset rates= 0.0000) -pass 13: -474.4284 (branch= 0.0000 subset rates= 0.0004) -pass 14: -474.4283 (branch= 0.0001 subset rates= 0.0000) -pass 15: -474.4283 (branch= 0.0000 subset rates= 0.0000) -pass 16: -474.4282 (branch= 0.0000 subset rates= 0.0000) -pass 17: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4677 (branch= 0.0059 subset rates= 0.0000) +pass 2 : -474.4551 (branch= 0.0120 subset rates= 0.0006) +pass 3 : -474.4419 (branch= 0.0132 subset rates= 0.0000) +pass 4 : -474.4347 (branch= 0.0072 subset rates= 0.0000) +pass 5 : -474.4335 (branch= 0.0013 subset rates= 0.0000) +pass 6 : -474.4318 (branch= 0.0016 subset rates= 0.0001) +pass 7 : -474.4301 (branch= 0.0017 subset rates= 0.0000) +pass 8 : -474.4295 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -474.4290 (branch= 0.0005 subset rates= 0.0000) +pass 10: -474.4288 (branch= 0.0002 subset rates= 0.0000) +pass 11: -474.4287 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4286 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.4286 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4285 (branch= 0.0000 subset rates= 0.0001) +pass 15: -474.4282 (branch= 0.0001 subset rates= 0.0002) +pass 16: -474.4282 (branch= 0.0001 subset rates= 0.0000) +pass 17: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 18: -474.4281 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -474.4282 +Final score = -474.4281 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17422,7 +17440,7 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.91 + 0.59 2.04 2.92 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. @@ -17440,7 +17458,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9509 (best) -Replicate 2 : -474.4282 (TERMINATED PREMATURELY) +Replicate 2 : -474.4281 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17456,7 +17474,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.348 0.589 2.061 2.803 -rep 2: 4.599 0.588 2.035 2.910 +rep 2: 4.602 0.587 2.036 2.921 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -17525,8 +17543,8 @@ dh_builddeb dpkg-deb: building package 'garli' in '../garli_2.1-4_arm64.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-4_arm64.deb'. -dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-4_arm64.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-4_arm64.deb'. +dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-4_arm64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../garli_2.1-4_arm64.changes @@ -17535,12 +17553,14 @@ 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/20439/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/20439/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/17286 and its subdirectories -I: Current time: Sat Sep 24 16:04:31 -12 2022 -I: pbuilder-time-stamp: 1664078671 +I: removing directory /srv/workspace/pbuilder/20439 and its subdirectories +I: Current time: Mon Aug 23 11:52:25 +14 2021 +I: pbuilder-time-stamp: 1629669145