Diff of the two buildlogs: -- --- b1/build.log 2024-05-05 23:28:39.424577497 +0000 +++ b2/build.log 2024-05-05 23:35:20.287512429 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 5 11:23:02 -12 2024 -I: pbuilder-time-stamp: 1714951382 +I: Current time: Sun Jun 8 19:51:42 +14 2025 +I: pbuilder-time-stamp: 1749361902 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,51 +25,83 @@ dpkg-source: info: unpacking garli_2.1-7.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/28240/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3069313/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 8 05:51 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3069313/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3069313/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c44c461357964d58b8175c061adb8f61' - 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='28240' - PS1='# ' - PS2='> ' + INVOCATION_ID=d553d620e038470397e561ea32c6c1d9 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3069313 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qPx5oJ85/pbuilderrc_4mlA --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qPx5oJ85/b1 --logfile b1/build.log garli_2.1-7.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qPx5oJ85/pbuilderrc_1Z3T --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qPx5oJ85/b2 --logfile b2/build.log garli_2.1-7.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-20-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 11:23 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/28240/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3069313/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -217,7 +249,7 @@ Get: 102 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-5 [226 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 4.1.6-5 [972 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-5+b1 [206 kB] -Fetched 105 MB in 1s (76.5 MB/s) +Fetched 105 MB in 1s (111 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19694 files and directories currently installed.) @@ -656,7 +688,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../garli_2.1-7_source.changes +I: user script /srv/workspace/pbuilder/3069313/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3069313/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../garli_2.1-7_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-7 dpkg-buildpackage: info: source distribution unstable @@ -760,8 +796,8 @@ 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 @@ -943,17 +979,16 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from garlimain.cpp:40: + from funcs.h:25, + from individual.cpp:28: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from population.h:23: + from /usr/include/c++/13/iomanip:42, + from individual.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -991,17 +1026,11 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp -In file included from garlimain.cpp:46: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1011,7 +1040,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from adaptation.cpp:18: + from configreader.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1027,41 +1056,20 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_function.h:1438: -/usr/include/c++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from individual.cpp:28: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from population.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1071,16 +1079,27 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_function.h:1438: +/usr/include/c++/13/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -1103,11 +1122,16 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ In file included from tree.h:35, from individual.h:21, - from population.h:31, - from funcs.h:25, - from configreader.cpp:30: + from model.cpp:26: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1117,7 +1141,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from configreader.cpp:21: + from model.cpp:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1148,6 +1172,10 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -1155,13 +1183,11 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1171,7 +1197,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from model.cpp:17: + from adaptation.cpp:18: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1213,6 +1239,15 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1381,37 +1453,6 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': -model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -1419,16 +1460,6 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from optimization.cpp:21: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/13/cstdio:42, - from /usr/include/c++/13/ext/string_conversions.h:45, - from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/13/cstdio:42, - from /usr/include/c++/13/ext/string_conversions.h:45, - from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54, - from population.cpp:25: +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -2252,6 +2266,28 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/13/cstdio:42, + from /usr/include/c++/13/ext/string_conversions.h:45, + from /usr/include/c++/13/bits/basic_string.h:4109, + from /usr/include/c++/13/string:54, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from configoptions.cpp:20: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); @@ -2319,6 +2355,7 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -2328,7 +2365,7 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from funcs.cpp:30: + from configreader.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2338,7 +2375,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from population.h:23: + from configreader.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2376,11 +2413,16 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2390,7 +2432,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from adaptation.cpp:18: + from population.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2428,29 +2470,19 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from adaptation.cpp:18: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2538,28 +2576,19 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from model.cpp:17: + from /usr/include/c++/13/iomanip:42, + from individual.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2597,8 +2626,50 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2740,7 +2769,6 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -2748,15 +2776,22 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:14: 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:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from optimization.cpp:21: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~ -population.cpp:3066:47: note: directive argument in the range [1, 2147483647] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, @@ -3204,6 +3224,22 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~ +population.cpp:3066:47: note: directive argument in the range [1, 2147483647] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, @@ -5781,7 +5817,7 @@ 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 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5931,7 +5967,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6228,7 +6264,7 @@ 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 6 seconds +Time used = 0 hours, 0 minutes and 7 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6380,7 +6416,7 @@ 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 6 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6586,7 +6622,7 @@ pass 81: -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 = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6794,7 +6830,7 @@ pass 78: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7111,7 +7147,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7532,7 +7568,7 @@ pass 35: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -13306.2061 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9227,7 +9263,7 @@ pass 17: -474.6455 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.6455 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9768,7 +9804,7 @@ pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10356,7 +10392,7 @@ pass 502: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3585 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -13089,7 +13125,6 @@ 2400 -88.6058 0.010 879 2500 -88.5913 0.010 879 2600 -88.5622 0.010 879 -2700 -88.5467 0.010 879 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13186,9 +13221,9 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 2715, seed 1716948518, best lnL -88.547 +Bootstrap rep 1 (of 1) generation 2696, seed 2052145877, best lnL -88.547 gen current_lnL precision last_tree_imp -2715 -88.5467 0.010 879 +2696 -88.5467 0.010 879 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13372,7 +13407,6 @@ 1700 -110.2780 0.010 707 1800 -110.2330 0.010 707 1900 -110.2137 0.010 707 -2000 -110.1885 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13459,9 +13493,9 @@ STARTING RUN Restarting from checkpoint... - generation 2025, seed 305202749, best lnL -110.188 + generation 1956, seed 154962926, best lnL -110.196 gen current_lnL precision last_tree_imp -2025 -110.1884 0.010 707 +1956 -110.1960 0.010 707 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13477,17 +13511,17 @@ 4 discrete gamma distributed rate categories, alpha param estimated 2.9337 with an invariant (invariable) site category, proportion estimated - 0.1638 + 0.1544 Substitution rate categories under this model: rate proportion - 0.0000 0.1638 - 0.3841 0.2090 - 0.7278 0.2090 - 1.0822 0.2090 - 1.8060 0.2090 + 0.0000 0.1544 + 0.3841 0.2114 + 0.7278 0.2114 + 1.0822 0.2114 + 1.8060 0.2114 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.a.G4.sitelikes.log ... @@ -13495,11 +13529,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -110.1884 +Replicate 1 : -110.1960 Parameter estimates: alpha pinv -rep 1: 2.934 0.164 +rep 1: 2.934 0.154 Treelengths: TL @@ -13951,7 +13985,6 @@ 220 -204.6664 0.500 209 230 -204.3372 0.500 228 240 -204.3152 0.500 228 -250 -203.9441 0.500 245 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14038,9 +14071,9 @@ STARTING RUN Restarting from checkpoint... - generation 250, seed 235164890, best lnL -203.944 + generation 247, seed 1619791079, best lnL -203.944 gen current_lnL precision last_tree_imp -250 -203.9441 0.500 245 +247 -203.9441 0.500 245 MODEL REPORT - Parameter values are FINAL Model 1 @@ -14236,6 +14269,12 @@ 170 -194.5936 0.500 168 180 -194.5926 0.500 168 190 -194.5693 0.500 168 +200 -194.2413 0.500 196 +210 -194.2413 0.500 196 +220 -194.2043 0.500 196 +230 -194.1525 0.500 196 +240 -194.0255 0.500 234 +250 -194.0104 0.500 234 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14323,16 +14362,16 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 192, seed 609337585, best lnL -194.569 +Bootstrap rep 1 (of 1) generation 253, seed 1231904052, best lnL -194.010 gen current_lnL precision last_tree_imp -192 -194.5693 0.500 168 +253 -194.0104 0.500 234 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120507 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.637, AG = 5.880, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 + AC = 1.668, AG = 5.880, AT = 0.011, CG = 4.174, CT = 2.304, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14360,15 +14399,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -194.5693 +Replicate 1 : -194.0104 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.121 1.000 1.637 5.88 0.01146 4.174 2.324 1 +rep 1: 0.121 1.000 1.668 5.88 0.01146 4.174 2.304 1 Treelengths: TL -rep 1: 10.398 +rep 1: 10.538 Saving best tree to bootstrap file ch.c.boot.tre @@ -14552,6 +14591,13 @@ 2700 -3351.1604 0.010 0 2800 -3351.1128 0.010 0 2900 -3351.1121 0.010 0 +3000 -3351.1082 0.010 0 +3100 -3351.0954 0.010 0 +3200 -3351.0723 0.010 0 +3300 -3351.0705 0.010 0 +3400 -3351.0543 0.010 0 +3500 -3351.0535 0.010 0 +3600 -3351.0529 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14655,16 +14701,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 2925, seed 1867532441, best lnL -3351.112 +Search rep 1 (of 2) generation 3644, seed 903670304, best lnL -3351.053 gen current_lnL precision last_tree_imp -2925 -3351.1121 0.010 0 -3000 -3351.1082 0.010 0 -3100 -3351.0954 0.010 0 -3200 -3351.0723 0.010 0 -3300 -3351.0705 0.010 0 -3400 -3351.0543 0.010 0 -3500 -3351.0535 0.010 0 -3600 -3351.0529 0.010 0 +3644 -3351.0529 0.010 0 3700 -3351.0214 0.010 0 3800 -3351.0091 0.010 0 3900 -3350.9559 0.010 0 @@ -14688,60 +14727,75 @@ 5700 -3350.7265 0.010 0 5800 -3350.6814 0.010 0 5900 -3350.6771 0.010 0 +6000 -3350.6716 0.010 0 +6100 -3350.6583 0.010 0 +6200 -3350.6583 0.010 0 +6300 -3350.6550 0.010 0 +6400 -3350.6535 0.010 0 +6500 -3350.6535 0.010 0 +6600 -3350.6529 0.010 0 +6700 -3350.6529 0.010 0 +6800 -3350.6473 0.010 0 +6900 -3350.6114 0.010 0 +7000 -3350.6077 0.010 0 +7100 -3350.6074 0.010 0 +7200 -3350.6071 0.010 0 +7300 -3350.6067 0.010 0 +7400 -3350.5868 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.6743 +Current score = -3350.5856 Performing final optimizations... -pass 1 : -3350.6412 (branch= 0.0067 alpha= 0.0000 pinv= 0.0211 eq freqs= 0.0001 rel rates= 0.0052 subset rates= 0.0000) -pass 2 : -3350.6026 (branch= 0.0000 alpha= 0.0230 pinv= 0.0155 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 3 : -3350.5606 (branch= 0.0015 alpha= 0.0159 pinv= 0.0145 eq freqs= 0.0049 rel rates= 0.0051 subset rates= 0.0000) -pass 4 : -3350.5274 (branch= 0.0017 alpha= 0.0150 pinv= 0.0130 eq freqs= 0.0000 rel rates= 0.0034 subset rates= 0.0000) -pass 5 : -3350.4925 (branch= 0.0042 alpha= 0.0118 pinv= 0.0121 eq freqs= 0.0011 rel rates= 0.0042 subset rates= 0.0015) -pass 6 : -3350.4637 (branch= 0.0026 alpha= 0.0103 pinv= 0.0111 eq freqs= 0.0000 rel rates= 0.0048 subset rates= 0.0000) -pass 7 : -3350.4360 (branch= 0.0005 alpha= 0.0106 pinv= 0.0100 eq freqs= 0.0002 rel rates= 0.0053 subset rates= 0.0013) -pass 8 : -3350.4120 (branch= 0.0016 alpha= 0.0094 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0039 subset rates= 0.0000) -pass 9 : -3350.3903 (branch= 0.0003 alpha= 0.0085 pinv= 0.0082 eq freqs= 0.0000 rel rates= 0.0037 subset rates= 0.0010) -pass 10: -3350.3711 (branch= 0.0010 alpha= 0.0076 pinv= 0.0074 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) -pass 11: -3350.3546 (branch= 0.0001 alpha= 0.0068 pinv= 0.0066 eq freqs= 0.0000 rel rates= 0.0030 subset rates= 0.0000) -pass 12: -3350.3394 (branch= 0.0000 alpha= 0.0065 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0000) -pass 13: -3350.3259 (branch= 0.0000 alpha= 0.0059 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0024 subset rates= 0.0000) -pass 14: -3350.3139 (branch= 0.0000 alpha= 0.0052 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0021 subset rates= 0.0000) -pass 15: -3350.3033 (branch= 0.0000 alpha= 0.0046 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0018 subset rates= 0.0000) -pass 16: -3350.2940 (branch= 0.0000 alpha= 0.0041 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0016 subset rates= 0.0000) -pass 17: -3350.2858 (branch= 0.0000 alpha= 0.0036 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0014 subset rates= 0.0000) -pass 18: -3350.2787 (branch= 0.0000 alpha= 0.0032 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0012 subset rates= 0.0000) -pass 19: -3350.2724 (branch= 0.0000 alpha= 0.0028 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) -pass 20: -3350.2670 (branch= 0.0000 alpha= 0.0024 pinv= 0.0021 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) +pass 1 : -3350.5531 (branch= 0.0000 alpha= 0.0000 pinv= 0.0253 eq freqs= 0.0071 rel rates= 0.0000 subset rates= 0.0000) +pass 2 : -3350.5160 (branch= 0.0026 alpha= 0.0166 pinv= 0.0150 eq freqs= 0.0000 rel rates= 0.0030 subset rates= 0.0000) +pass 3 : -3350.4802 (branch= 0.0000 alpha= 0.0182 pinv= 0.0135 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 4 : -3350.4506 (branch= 0.0017 alpha= 0.0131 pinv= 0.0124 eq freqs= 0.0011 rel rates= 0.0000 subset rates= 0.0011) +pass 5 : -3350.4235 (branch= 0.0024 alpha= 0.0134 pinv= 0.0110 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 6 : -3350.4018 (branch= 0.0016 alpha= 0.0097 pinv= 0.0100 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 7 : -3350.3819 (branch= 0.0003 alpha= 0.0098 pinv= 0.0089 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) +pass 8 : -3350.3630 (branch= 0.0002 alpha= 0.0090 pinv= 0.0080 eq freqs= 0.0001 rel rates= 0.0003 subset rates= 0.0013) +pass 9 : -3350.3466 (branch= 0.0013 alpha= 0.0075 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0002 subset rates= 0.0000) +pass 10: -3350.3331 (branch= 0.0002 alpha= 0.0066 pinv= 0.0065 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 11: -3350.3207 (branch= 0.0001 alpha= 0.0064 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 12: -3350.3096 (branch= 0.0000 alpha= 0.0058 pinv= 0.0051 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 13: -3350.2997 (branch= 0.0000 alpha= 0.0052 pinv= 0.0045 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 14: -3350.2910 (branch= 0.0000 alpha= 0.0045 pinv= 0.0040 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 15: -3350.2833 (branch= 0.0000 alpha= 0.0040 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 16: -3350.2766 (branch= 0.0000 alpha= 0.0035 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 17: -3350.2707 (branch= 0.0000 alpha= 0.0031 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 18: -3350.2655 (branch= 0.0000 alpha= 0.0027 pinv= 0.0024 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 19: -3350.2609 (branch= 0.0000 alpha= 0.0024 pinv= 0.0021 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 20: -3350.2571 (branch= 0.0000 alpha= 0.0020 pinv= 0.0018 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 30: -3350.2401 (branch= 0.0000 alpha= 0.0119 pinv= 0.0107 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) +pass 30: -3350.2378 (branch= 0.0000 alpha= 0.0101 pinv= 0.0089 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2343 (branch= 0.0000 alpha= 0.0025 pinv= 0.0023 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) +pass 40: -3350.2338 (branch= 0.0000 alpha= 0.0021 pinv= 0.0019 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2332 (branch= 0.0000 alpha= 0.0005 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 50: -3350.2330 (branch= 0.0000 alpha= 0.0004 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) optimization up to ... -pass 57: -3350.2330 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 53: -3350.2330 (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 = -3350.2331 +Final score = -3350.2330 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.122, AG = 10.445, AT = 2.699, CG = 0.001, CT = 21.993, GT = 1.000 + AC = 3.143, AG = 10.511, AT = 2.717, CG = 0.001, CT = 22.140, 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 - 0.5758 + 0.5744 with an invariant (invariable) site category, proportion estimated - 0.3651 + 0.3645 Substitution rate categories under this model: rate proportion - 0.0000 0.3651 - 0.0482 0.1587 - 0.2986 0.1587 - 0.8685 0.1587 - 2.7848 0.1587 + 0.0000 0.3645 + 0.0479 0.1589 + 0.2978 0.1589 + 0.8677 0.1589 + 2.7866 0.1589 Model 2 Number of states = 2 (binary data) @@ -14766,20 +14820,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2330 (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: 3.122 10.44 2.699 0.001 21.99 1 0.333 0.222 0.157 0.288 0.576 0.365 +rep 1: 3.143 10.51 2.717 0.001 22.14 1 0.333 0.222 0.157 0.288 0.574 0.365 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.789 1.821 0.179 +rep 1: 0.790 1.821 0.179 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -14944,6 +14998,7 @@ Optimizing branchlengths... improved 0.061 lnL 1200 -3320.1411 0.010 1 1300 -3320.0813 0.010 1 +1400 -3320.0722 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15044,10 +15099,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1305, seed 1068294377, best lnL -3320.081 +Search rep 1 (of 2) generation 1493, seed 803013256, best lnL -3320.024 gen current_lnL precision last_tree_imp -1305 -3320.0813 0.010 1 -1400 -3320.0722 0.010 1 +1493 -3320.0235 0.010 1 1500 -3320.0235 0.010 1 1600 -3320.0193 0.010 1 1700 -3320.0162 0.010 1 @@ -15061,63 +15115,61 @@ 2500 -3319.3301 0.010 1 2600 -3319.1283 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3319.1097 +Current score = -3319.1283 Performing final optimizations... -pass 1 : -3318.8750 (branch= 0.0079 alpha= 0.0350 pinv= 0.0129 eq freqs= 0.0158 rel rates= 0.1025 ins/del rates= 0.0605) -pass 2 : -3318.7293 (branch= 0.0306 alpha= 0.0052 pinv= 0.0146 eq freqs= 0.0000 rel rates= 0.0903 ins/del rates= 0.0050) -pass 3 : -3318.5898 (branch= 0.0325 alpha= 0.0106 pinv= 0.0138 eq freqs= 0.0020 rel rates= 0.0707 ins/del rates= 0.0099) -pass 4 : -3318.4770 (branch= 0.0204 alpha= 0.0099 pinv= 0.0127 eq freqs= 0.0000 rel rates= 0.0644 ins/del rates= 0.0053) -pass 5 : -3318.3820 (branch= 0.0135 alpha= 0.0094 pinv= 0.0121 eq freqs= 0.0015 rel rates= 0.0531 ins/del rates= 0.0053) -pass 6 : -3318.3028 (branch= 0.0084 alpha= 0.0089 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0470 ins/del rates= 0.0033) -pass 7 : -3318.2354 (branch= 0.0055 alpha= 0.0088 pinv= 0.0104 eq freqs= 0.0003 rel rates= 0.0400 ins/del rates= 0.0023) -pass 8 : -3318.1779 (branch= 0.0035 alpha= 0.0083 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0346 ins/del rates= 0.0015) -pass 9 : -3318.1280 (branch= 0.0023 alpha= 0.0078 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0301 ins/del rates= 0.0010) -pass 10: -3318.0841 (branch= 0.0015 alpha= 0.0075 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0262 ins/del rates= 0.0006) -pass 11: -3318.0461 (branch= 0.0010 alpha= 0.0070 pinv= 0.0072 eq freqs= 0.0000 rel rates= 0.0225 ins/del rates= 0.0004) -pass 12: -3318.0130 (branch= 0.0006 alpha= 0.0064 pinv= 0.0065 eq freqs= 0.0000 rel rates= 0.0193 ins/del rates= 0.0003) -pass 13: -3317.9840 (branch= 0.0004 alpha= 0.0058 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0167 ins/del rates= 0.0002) -pass 14: -3317.9585 (branch= 0.0003 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0144 ins/del rates= 0.0001) -pass 15: -3317.9364 (branch= 0.0002 alpha= 0.0048 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0124 ins/del rates= 0.0001) -pass 16: -3317.9170 (branch= 0.0001 alpha= 0.0044 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0107 ins/del rates= 0.0000) -pass 17: -3317.9000 (branch= 0.0001 alpha= 0.0039 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0092 ins/del rates= 0.0000) -pass 18: -3317.8851 (branch= 0.0000 alpha= 0.0035 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0080 ins/del rates= 0.0000) -pass 19: -3317.8722 (branch= 0.0000 alpha= 0.0031 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0068 ins/del rates= 0.0000) -pass 20: -3317.8609 (branch= 0.0000 alpha= 0.0028 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0059 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8043 (branch= 0.0000 alpha= 0.0144 pinv= 0.0133 eq freqs= 0.0001 rel rates= 0.0288 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7909 (branch= 0.0001 alpha= 0.0034 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0068 ins/del rates= 0.0000) +pass 1 : -3318.9377 (branch= 0.0070 alpha= 0.0000 pinv= 0.0128 eq freqs= 0.0201 rel rates= 0.0963 ins/del rates= 0.0544) +pass 2 : -3318.7686 (branch= 0.0457 alpha= 0.0076 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.0908 ins/del rates= 0.0088) +pass 3 : -3318.6305 (branch= 0.0300 alpha= 0.0110 pinv= 0.0151 eq freqs= 0.0033 rel rates= 0.0687 ins/del rates= 0.0099) +pass 4 : -3318.5195 (branch= 0.0154 alpha= 0.0106 pinv= 0.0142 eq freqs= 0.0007 rel rates= 0.0656 ins/del rates= 0.0045) +pass 5 : -3318.4189 (branch= 0.0139 alpha= 0.0112 pinv= 0.0134 eq freqs= 0.0006 rel rates= 0.0566 ins/del rates= 0.0049) +pass 6 : -3318.3383 (branch= 0.0081 alpha= 0.0101 pinv= 0.0125 eq freqs= 0.0000 rel rates= 0.0466 ins/del rates= 0.0032) +pass 7 : -3318.2683 (branch= 0.0052 alpha= 0.0098 pinv= 0.0117 eq freqs= 0.0004 rel rates= 0.0407 ins/del rates= 0.0022) +pass 8 : -3318.2068 (branch= 0.0037 alpha= 0.0096 pinv= 0.0107 eq freqs= 0.0002 rel rates= 0.0357 ins/del rates= 0.0015) +pass 9 : -3318.1542 (branch= 0.0023 alpha= 0.0092 pinv= 0.0098 eq freqs= 0.0001 rel rates= 0.0303 ins/del rates= 0.0010) +pass 10: -3318.1080 (branch= 0.0015 alpha= 0.0085 pinv= 0.0090 eq freqs= 0.0001 rel rates= 0.0265 ins/del rates= 0.0006) +pass 11: -3318.0677 (branch= 0.0010 alpha= 0.0080 pinv= 0.0082 eq freqs= 0.0000 rel rates= 0.0227 ins/del rates= 0.0004) +pass 12: -3318.0324 (branch= 0.0006 alpha= 0.0074 pinv= 0.0074 eq freqs= 0.0000 rel rates= 0.0196 ins/del rates= 0.0003) +pass 13: -3318.0014 (branch= 0.0004 alpha= 0.0068 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0169 ins/del rates= 0.0002) +pass 14: -3317.9743 (branch= 0.0003 alpha= 0.0062 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0145 ins/del rates= 0.0001) +pass 15: -3317.9504 (branch= 0.0002 alpha= 0.0056 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0126 ins/del rates= 0.0001) +pass 16: -3317.9294 (branch= 0.0001 alpha= 0.0051 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0109 ins/del rates= 0.0000) +pass 17: -3317.9110 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0094 ins/del rates= 0.0000) +pass 18: -3317.8950 (branch= 0.0000 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0081 ins/del rates= 0.0000) +pass 19: -3317.8809 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0069 ins/del rates= 0.0000) +pass 20: -3317.8685 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0061 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8062 (branch= 0.0000 alpha= 0.0172 pinv= 0.0158 eq freqs= 0.0001 rel rates= 0.0292 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7878 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0016 ins/del rates= 0.0000) +pass 40: -3317.7913 (branch= 0.0001 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0068 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7872 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 ins/del rates= 0.0000) +pass 50: -3317.7879 (branch= 0.0001 alpha= 0.0009 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0016 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 60: -3317.7872 (branch= 0.0000 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 ins/del rates= 0.0000) optimization up to ... -pass 72: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 69: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7870 +Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.067, AG = 10.267, AT = 2.656, CG = 0.001, CT = 21.544, GT = 1.000 + AC = 3.066, AG = 10.263, AT = 2.655, CG = 0.001, CT = 21.536, 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 - 0.5750 + 0.5742 with an invariant (invariable) site category, proportion estimated - 0.3613 + 0.3610 Substitution rate categories under this model: rate proportion - 0.0000 0.3613 - 0.0480 0.1597 - 0.2981 0.1597 - 0.8680 0.1597 - 2.7859 0.1597 + 0.0000 0.3610 + 0.0478 0.1598 + 0.2976 0.1598 + 0.8676 0.1598 + 2.7869 0.1598 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15143,13 +15195,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.067 10.27 2.656 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 0.574 0.361 Partition model subset 2: ins del @@ -15314,15 +15366,68 @@ 7800 -210.1872 0.010 1104 8000 -210.1732 0.010 1104 8200 -210.1275 0.010 1104 -NOTE: ****Specified time limit (5 seconds) reached... +8400 -210.1090 0.010 1104 +8600 -210.0887 0.010 1104 +8800 -210.0539 0.010 1104 +9000 -210.0488 0.010 1104 +9200 -209.9764 0.010 1104 +9400 -209.9612 0.010 1104 +9600 -209.9440 0.010 1104 +9800 -209.9190 0.010 1104 +10000 -209.8863 0.010 1104 + Optimizing parameters... improved 0.505 lnL + Optimizing branchlengths... improved 0.011 lnL +NOTE: ****Specified generation limit (10000) reached... -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. +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +Model 1 + Number of states = 4 (nucleotide data) + Nucleotide Relative Rate Matrix: 6 rates + AC = 5.150, AG = 9.093, AT = 0.233, CG = 9.359, CT = 14.077, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2377 0.3274 0.2094 0.2255 + Rate Heterogeneity Model: + 3 discrete gamma distributed rate categories, alpha param estimated + 4.1580 + with an invariant (invariable) site category, proportion estimated + 0.2914 + Substitution rate categories under this model: + rate proportion + 0.0000 0.2914 + 0.5191 0.2362 + 0.9259 0.2362 + 1.5550 0.2362 + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 1 branches were collapsed. + +Saving site likelihoods to file ch.n.G3.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + +####################################################### +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -209.3698 + +Parameter estimates: + r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv +rep 1: 5.15 9.093 0.2328 9.359 14.08 1 0.238 0.327 0.209 0.225 4.158 0.291 + +Treelengths: + TL +rep 1: 2.284 + +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 + +WARNING: Internal states inferred on tree from prematurely terminated search + +####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -15393,38 +15498,31 @@ STARTING RUN Restarting from checkpoint... - generation 8220, seed 1978094683, best lnL -210.124 + generation 10001, seed 991383469, best lnL -209.370 gen current_lnL precision last_tree_imp -8220 -210.1236 0.010 1104 -8300 -210.1114 0.010 1104 -8400 -210.1090 0.010 1104 -8500 -210.1074 0.010 1104 -8600 -210.0887 0.010 1104 -Reached termination condition! -last topological improvement at gen 1104 -Improvement over last 500 gen = 0.04941 +10001 -209.3698 0.010 1104 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.918, AG = 6.885, AT = 0.186, CG = 6.926, CT = 11.159, GT = 1.000 + AC = 5.150, AG = 9.093, AT = 0.233, CG = 9.359, CT = 14.077, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2363 0.3327 0.2105 0.2206 + (ACGT) 0.2377 0.3274 0.2094 0.2255 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.8479 + 4.1580 with an invariant (invariable) site category, proportion estimated - 0.1920 + 0.2914 Substitution rate categories under this model: rate proportion - 0.0000 0.1920 - 0.3352 0.2693 - 0.8372 0.2693 - 1.8275 0.2693 + 0.0000 0.2914 + 0.5191 0.2362 + 0.9259 0.2362 + 1.5550 0.2362 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.G3.sitelikes.log ... @@ -15432,15 +15530,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.0887 +Replicate 1 : -209.3698 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: 3.918 6.885 0.186 6.926 11.16 1 0.236 0.333 0.210 0.221 1.848 0.192 +rep 1: 5.15 9.093 0.2328 9.359 14.08 1 0.238 0.327 0.209 0.225 4.158 0.291 Treelengths: TL -rep 1: 2.342 +rep 1: 2.284 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 @@ -15608,58 +15706,15 @@ 9200 -163.8480 0.010 7384 9400 -163.7485 0.010 7384 9600 -163.6371 0.010 7384 -9800 -163.6002 0.010 7384 -10000 -163.5761 0.010 7384 - Optimizing parameters... improved 1.518 lnL - Optimizing branchlengths... improved 0.021 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 0.623, AG = 8.599, AT = 1.922, CG = 3.484, CT = 32.597, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.1298 0.4236 0.2357 0.2109 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 551.8391 - with an invariant (invariable) site category, proportion estimated - 0.3606 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3606 - 0.9464 0.1599 - 0.9857 0.1599 - 1.0133 0.1599 - 1.0546 0.1599 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 3 branches were collapsed. - - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -162.0374 - -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: 0.6227 8.599 1.922 3.484 32.6 1 0.130 0.424 0.236 0.211 551.839 0.361 - -Treelengths: - TL -rep 1: 3.163 +NOTE: ****Specified time limit (5 seconds) reached... -Saving best tree to bootstrap file ch.n.G4.boot.tre +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -WARNING: Tree from prematurely terminated search saved to bootstrap file -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -15731,11 +15786,17 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 10001, seed 172398639, best lnL -162.037 +Bootstrap rep 1 (of 1) generation 9783, seed 77450316, best lnL -163.600 gen current_lnL precision last_tree_imp -10001 -162.0374 0.010 7384 +9783 -163.6002 0.010 7384 +9800 -163.6002 0.010 7384 +9900 -163.5966 0.010 7384 +10000 -163.5761 0.010 7384 + Optimizing parameters... improved 1.518 lnL + Optimizing branchlengths... improved 0.021 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates @@ -15759,6 +15820,10 @@ 3 branches were collapsed. +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + ####################################################### Completed 1 replicate search(es) (of 1). @@ -15775,7 +15840,7 @@ Saving best tree to bootstrap file ch.n.G4.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf @@ -16241,68 +16306,15 @@ 9000 -210.0297 0.010 8309 9200 -209.9925 0.010 8309 9400 -209.9916 0.010 8309 -9600 -209.9835 0.010 8309 -9800 -209.9761 0.010 8309 -10000 -209.9756 0.010 8309 - Optimizing parameters... improved 0.521 lnL - Optimizing branchlengths... improved 0.003 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 2.413, AG = 4.430, AT = 0.038, CG = 4.487, CT = 8.603, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2415 0.3376 0.2132 0.2077 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 4.0676 - with an invariant (invariable) site category, proportion estimated - 0.3027 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3027 - 0.4580 0.1743 - 0.7775 0.1743 - 1.0844 0.1743 - 1.6801 0.1743 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. - - -NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with - a positive constraint, it is possible for a constrained branch itself to be collapsed. - If you care, be careful to check whether this has happened or turn off branch collapsing. - -Saving site likelihoods to file ch.n.const.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -209.4515 - -Parameter estimates: - r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.413 4.43 0.0383 4.487 8.603 1 0.242 0.338 0.213 0.208 4.068 0.303 - -Treelengths: - TL -rep 1: 2.478 - -Saving final tree from best search rep (#1) to ch.n.const.best.tre -Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -16381,11 +16393,20 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 828288349, best lnL -209.451 + generation 9477, seed 740807011, best lnL -209.984 gen current_lnL precision last_tree_imp -10001 -209.4515 0.010 8309 +9477 -209.9838 0.010 8309 +9500 -209.9835 0.010 8309 +9600 -209.9835 0.010 8309 +9700 -209.9835 0.010 8309 +9800 -209.9761 0.010 8309 +9900 -209.9756 0.010 8309 +10000 -209.9756 0.010 8309 + Optimizing parameters... improved 0.521 lnL + Optimizing branchlengths... improved 0.003 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates @@ -16414,6 +16435,11 @@ If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + ####################################################### @@ -16432,6 +16458,8 @@ Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/p.3diff.conf @@ -16772,9 +16800,9 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1610, seed 1821416504, best lnL -13370.482 +Bootstrap rep 1 (of 1) generation 1674, seed 622948917, best lnL -13370.469 gen current_lnL precision last_tree_imp -1610 -13370.4816 0.206 0 +1674 -13370.4688 0.206 0 1700 -13370.4688 0.206 0 1800 -13370.4569 0.206 0 1900 -13370.4339 0.206 0 @@ -17179,7 +17207,6 @@ 800 -467.7328 0.010 0 900 -467.7315 0.010 0 1000 -467.7286 0.010 0 -1100 -467.7271 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17305,9 +17332,10 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1140, seed 264192760, best lnL -467.721 +Search rep 2 (of 5) generation 1000, seed 245966214, best lnL -467.729 gen current_lnL precision last_tree_imp -1140 -467.7215 0.010 0 +1000 -467.7286 0.010 0 +1100 -467.7271 0.010 0 1200 -467.7201 0.010 0 1300 -467.7189 0.010 0 1400 -467.7173 0.010 0 @@ -17471,22 +17499,30 @@ 3000 -467.7153 0.010 0 3100 -467.7148 0.010 0 3200 -467.7140 0.010 0 +3300 -467.7139 0.010 0 +3400 -467.7136 0.010 0 +3500 -467.7136 0.010 0 +3600 -467.7132 0.010 0 +3700 -467.7130 0.010 0 +3800 -467.7129 0.010 0 +3900 -467.7124 0.010 0 +4000 -467.7117 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7139 +Current score = -467.7117 Performing final optimizations... -pass 1 : -467.7139 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.7014 (branch= 0.0125 subset rates= 0.0000) -pass 3 : -467.6899 (branch= 0.0116 subset rates= 0.0000) -pass 4 : -467.6871 (branch= 0.0027 subset rates= 0.0001) -pass 5 : -467.6842 (branch= 0.0028 subset rates= 0.0000) -pass 6 : -467.6817 (branch= 0.0022 subset rates= 0.0003) -pass 7 : -467.6801 (branch= 0.0016 subset rates= 0.0000) -pass 8 : -467.6791 (branch= 0.0010 subset rates= 0.0000) -pass 9 : -467.6787 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6784 (branch= 0.0003 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 1 : -467.7117 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.7021 (branch= 0.0095 subset rates= 0.0000) +pass 3 : -467.6897 (branch= 0.0124 subset rates= 0.0000) +pass 4 : -467.6864 (branch= 0.0034 subset rates= 0.0000) +pass 5 : -467.6847 (branch= 0.0017 subset rates= 0.0000) +pass 6 : -467.6827 (branch= 0.0020 subset rates= 0.0000) +pass 7 : -467.6815 (branch= 0.0012 subset rates= 0.0000) +pass 8 : -467.6800 (branch= 0.0009 subset rates= 0.0007) +pass 9 : -467.6794 (branch= 0.0005 subset rates= 0.0000) +pass 10: -467.6787 (branch= 0.0004 subset rates= 0.0003) +pass 11: -467.6784 (branch= 0.0003 subset rates= 0.0000) +pass 12: -467.6783 (branch= 0.0001 subset rates= 0.0000) +pass 13: -467.6782 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... @@ -17555,7 +17591,7 @@ TL R(1) R(2) R(3) rep 1: 3.838 0.789 1.477 2.150 rep 2: 3.842 0.786 1.478 2.181 -rep 3: 3.844 0.786 1.480 2.183 +rep 3: 3.843 0.786 1.480 2.183 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -17771,7 +17807,7 @@ pass 14: -477.2119 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2119 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17865,6 +17901,25 @@ 1300 -477.2708 0.010 510 1400 -477.2690 0.010 510 1500 -477.2686 0.010 510 +1600 -477.2682 0.010 510 +1700 -477.2659 0.010 510 +1800 -477.2652 0.010 510 +1900 -477.2634 0.010 510 +2000 -477.2631 0.010 510 +2100 -477.2605 0.010 510 +2200 -477.2601 0.010 510 +2300 -477.2592 0.010 510 +2400 -477.2590 0.010 510 +2500 -477.2586 0.010 510 +2600 -477.2586 0.010 510 +2700 -477.2584 0.010 510 +2800 -477.2581 0.010 510 +2900 -477.2571 0.010 510 +3000 -477.2519 0.010 510 +3100 -477.2510 0.010 510 +3200 -477.2508 0.010 510 +3300 -477.2504 0.010 510 +3400 -477.2503 0.010 510 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17990,28 +18045,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1530, seed 26361542, best lnL -477.269 +Search rep 2 (of 5) generation 3477, seed 1262367632, best lnL -477.250 gen current_lnL precision last_tree_imp -1530 -477.2686 0.010 510 -1600 -477.2682 0.010 510 -1700 -477.2659 0.010 510 -1800 -477.2652 0.010 510 -1900 -477.2634 0.010 510 -2000 -477.2631 0.010 510 -2100 -477.2605 0.010 510 -2200 -477.2601 0.010 510 -2300 -477.2592 0.010 510 -2400 -477.2590 0.010 510 -2500 -477.2586 0.010 510 -2600 -477.2586 0.010 510 -2700 -477.2584 0.010 510 -2800 -477.2581 0.010 510 -2900 -477.2571 0.010 510 -3000 -477.2519 0.010 510 -3100 -477.2510 0.010 510 -3200 -477.2508 0.010 510 -3300 -477.2504 0.010 510 -3400 -477.2503 0.010 510 +3477 -477.2501 0.010 510 3500 -477.2501 0.010 510 3600 -477.2490 0.010 510 3700 -477.2490 0.010 510 @@ -18041,7 +18077,7 @@ pass 13: -477.2121 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2121 -Time used so far = 0 hours, 0 minutes and 8 seconds +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18163,25 +18199,155 @@ 4400 -477.4619 0.010 223 4500 -477.4609 0.010 223 4600 -477.4598 0.010 223 -NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.4598 +4700 -477.4598 0.010 223 +4800 -477.4597 0.010 223 +4900 -477.4588 0.010 223 +5000 -477.4588 0.010 223 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +5100 -477.4588 0.010 223 +5200 -477.4587 0.010 223 +5300 -477.4587 0.010 223 +5400 -477.4587 0.010 223 +Reached termination condition! +last topological improvement at gen 223 +Improvement over last 500 gen = 0.00011 +Current score = -477.4587 Performing final optimizations... -pass 1 : -477.4593 (branch= 0.0000 subset rates= 0.0005) -pass 2 : -477.4473 (branch= 0.0120 subset rates= 0.0000) -pass 3 : -477.4408 (branch= 0.0065 subset rates= 0.0000) -pass 4 : -477.4359 (branch= 0.0049 subset rates= 0.0000) -pass 5 : -477.4344 (branch= 0.0015 subset rates= 0.0000) -pass 6 : -477.4334 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -477.4325 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -477.4322 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -477.4318 (branch= 0.0004 subset rates= 0.0000) -pass 10: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.4316 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.4582 (branch= 0.0000 subset rates= 0.0005) +pass 2 : -477.4462 (branch= 0.0120 subset rates= 0.0000) +pass 3 : -477.4398 (branch= 0.0064 subset rates= 0.0000) +pass 4 : -477.4355 (branch= 0.0042 subset rates= 0.0000) +pass 5 : -477.4341 (branch= 0.0014 subset rates= 0.0000) +pass 6 : -477.4336 (branch= 0.0005 subset rates= 0.0000) +pass 7 : -477.4328 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -477.4325 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -477.4321 (branch= 0.0002 subset rates= 0.0002) +pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.4317 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0000) pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4316 +Time used so far = 0 hours, 0 minutes and 10 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.63 1.91 2.75 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 7 branches were collapsed. + +>>>Completed Search rep 3 (of 5)<<< + +>>>Search rep 4 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=1474313403 + +Initial ln Likelihood: -617.2472 +optimizing: starting branch lengths, subset rates... +pass 1:+ 122.395 (branch= 110.80 scale= 1.82 subset rates= 9.78) +pass 2:+ 12.603 (branch= 8.56 scale= 0.00 subset rates= 4.05) +pass 3:+ 3.457 (branch= 2.23 scale= 0.04 subset rates= 1.18) +pass 4:+ 0.792 (branch= 0.50 scale= 0.02 subset rates= 0.27) +pass 5:+ 0.108 (branch= 0.11 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.024 (branch= 0.01 scale= 0.00 subset rates= 0.01) +pass 7:+ 0.024 (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: -477.8447 +gen current_lnL precision last_tree_imp +0 -477.8447 0.010 0 +100 -477.7601 0.010 42 +200 -477.7377 0.010 42 +300 -477.7206 0.010 42 +400 -477.5657 0.010 324 +500 -477.5326 0.010 417 +600 -477.5291 0.010 417 +700 -477.5243 0.010 417 +800 -477.5166 0.010 417 +900 -477.5080 0.010 417 +1000 -477.5038 0.010 417 +1100 -477.5010 0.010 417 +1200 -477.4982 0.010 417 +1300 -477.4970 0.010 417 +1400 -477.4967 0.010 417 +1500 -477.4935 0.010 417 +1600 -477.4915 0.010 417 +1700 -477.4905 0.010 417 +1800 -477.4881 0.010 417 +1900 -477.4874 0.010 417 +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -477.4868 +Performing final optimizations... +pass 1 : -477.4735 (branch= 0.0133 subset rates= 0.0000) +pass 2 : -477.4664 (branch= 0.0071 subset rates= 0.0000) +pass 3 : -477.4524 (branch= 0.0140 subset rates= 0.0000) +pass 4 : -477.4460 (branch= 0.0064 subset rates= 0.0000) +pass 5 : -477.4404 (branch= 0.0056 subset rates= 0.0000) +pass 6 : -477.4363 (branch= 0.0041 subset rates= 0.0000) +pass 7 : -477.4348 (branch= 0.0015 subset rates= 0.0000) +pass 8 : -477.4337 (branch= 0.0007 subset rates= 0.0004) +pass 9 : -477.4328 (branch= 0.0010 subset rates= 0.0000) +pass 10: -477.4324 (branch= 0.0004 subset rates= 0.0000) +pass 11: -477.4321 (branch= 0.0001 subset rates= 0.0001) +pass 12: -477.4321 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.4320 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4320 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4320 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -477.4320 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18210,11 +18376,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.74 + 0.63 1.91 2.72 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 4 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -18222,14 +18388,15 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 4 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -477.2119 (best) Replicate 2 : -477.2121 (same topology as 1) -Replicate 3 : -477.4316 (TERMINATED PREMATURELY) +Replicate 3 : -477.4316 +Replicate 4 : -477.4320 (same topology as 3) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18246,7 +18413,8 @@ TL R(1) R(2) R(3) rep 1: 4.671 0.643 1.908 2.618 rep 2: 4.668 0.644 1.904 2.619 -rep 3: 4.928 0.632 1.915 2.738 +rep 3: 4.930 0.631 1.914 2.747 +rep 4: 4.923 0.634 1.911 2.724 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### @@ -18443,6 +18611,210 @@ 2700 -425.5888 0.010 365 2800 -425.5883 0.010 365 2900 -425.5869 0.010 365 +3000 -425.5868 0.010 365 +3100 -425.5859 0.010 365 +3200 -425.5858 0.010 365 +3300 -425.5850 0.010 365 +3400 -425.5843 0.010 365 +3500 -425.5843 0.010 365 +3600 -425.5841 0.010 365 +3700 -425.5839 0.010 365 +3800 -425.5839 0.010 365 +3900 -425.5839 0.010 365 +Reached termination condition! +last topological improvement at gen 365 +Improvement over last 500 gen = 0.00044 +Current score = -425.5839 +Performing final optimizations... +pass 1 : -425.5730 (branch= 0.0000 subset rates= 0.0109) +pass 2 : -425.5586 (branch= 0.0144 subset rates= 0.0000) +pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0000) +pass 4 : -425.5509 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -425.5505 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -425.5498 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -425.5494 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.5488 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -425.5486 +Time used so far = 0 hours, 0 minutes and 2 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.87 1.53 1.12 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 10 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=222492842 + +Initial ln Likelihood: -586.0233 +optimizing: starting branch lengths, subset rates... +pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) +pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) +pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) +pass 4:+ 1.686 (branch= 1.66 scale= 0.02 subset rates= 0.01) +pass 5:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.031 (branch= 0.03 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 9:+ 0.043 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass10:+ 0.052 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass11:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass12:+ 0.042 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass13:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass14:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.2276 +gen current_lnL precision last_tree_imp +0 -439.2276 0.010 0 +100 -428.8676 0.010 98 +200 -428.0499 0.010 164 +300 -427.6003 0.010 249 +400 -427.5649 0.010 249 +500 -427.4911 0.010 499 +600 -427.3864 0.010 511 +700 -425.7188 0.010 668 +800 -425.6951 0.010 722 +900 -425.6795 0.010 722 +1000 -425.6689 0.010 722 +1100 -425.6640 0.010 722 +1200 -425.6430 0.010 722 +1300 -425.6381 0.010 722 +1400 -425.6345 0.010 722 +1500 -425.6341 0.010 722 +1600 -425.6274 0.010 722 +1700 -425.6239 0.010 722 +1800 -425.6235 0.010 722 +1900 -425.6225 0.010 722 +2000 -425.6202 0.010 722 +2100 -425.6196 0.010 722 +2200 -425.6174 0.010 722 +2300 -425.6146 0.010 722 +2400 -425.6135 0.010 722 +2500 -425.6104 0.010 722 +2600 -425.6099 0.010 722 +2700 -425.6088 0.010 722 +2800 -425.6077 0.010 722 +2900 -425.6073 0.010 722 +3000 -425.6058 0.010 722 +3100 -425.6056 0.010 722 +3200 -425.6055 0.010 722 +3300 -425.6051 0.010 722 +3400 -425.6049 0.010 722 +3500 -425.6048 0.010 722 +3600 -425.6048 0.010 722 +Reached termination condition! +last topological improvement at gen 722 +Improvement over last 500 gen = 0.00084 +Current score = -425.6048 +Performing final optimizations... +pass 1 : -425.5797 (branch= 0.0000 subset rates= 0.0251) +pass 2 : -425.5576 (branch= 0.0188 subset rates= 0.0032) +pass 3 : -425.5535 (branch= 0.0041 subset rates= 0.0000) +pass 4 : -425.5523 (branch= 0.0012 subset rates= 0.0000) +pass 5 : -425.5511 (branch= 0.0012 subset rates= 0.0000) +pass 6 : -425.5503 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -425.5497 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -425.5495 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -425.5493 (branch= 0.0002 subset rates= 0.0000) +pass 10: -425.5493 (branch= 0.0000 subset rates= 0.0000) +pass 11: -425.5492 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5492 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.5492 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -425.5492 +Time used so far = 0 hours, 0 minutes and 4 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.87 1.53 1.11 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 9 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=2129292874 + +Initial ln Likelihood: -588.2493 +optimizing: starting branch lengths, subset rates... +pass 1:+ 141.031 (branch= 140.49 scale= 0.38 subset rates= 0.17) +pass 2:+ 6.536 (branch= 6.52 scale= 0.00 subset rates= 0.02) +pass 3:+ 1.051 (branch= 1.03 scale= 0.00 subset rates= 0.02) +pass 4:+ 0.060 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.5715 +gen current_lnL precision last_tree_imp +0 -439.5715 0.010 0 +100 -431.1392 0.010 95 +200 -428.6587 0.010 167 +300 -427.6515 0.010 295 +400 -427.2438 0.010 295 +500 -427.2137 0.010 295 +600 -427.1679 0.010 568 +700 -427.1487 0.010 568 +800 -425.4816 0.010 762 +900 -425.4263 0.010 803 +1000 -425.4085 0.010 803 +1100 -425.4058 0.010 803 +1200 -425.3915 0.010 803 +1300 -425.3912 0.010 803 +1400 -425.3887 0.010 803 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18571,38 +18943,59 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 2990, seed 1652369306, best lnL -425.587 +Bootstrap rep 1 (of 1) Search rep 3 (of 5) generation 1480, seed 956589356, best lnL -425.387 gen current_lnL precision last_tree_imp -2990 -425.5868 0.010 365 -3000 -425.5868 0.010 365 -3100 -425.5859 0.010 365 -3200 -425.5858 0.010 365 -3300 -425.5850 0.010 365 -3400 -425.5843 0.010 365 -3500 -425.5843 0.010 365 -3600 -425.5841 0.010 365 -3700 -425.5839 0.010 365 -3800 -425.5839 0.010 365 -3900 -425.5839 0.010 365 +1480 -425.3865 0.010 803 +1500 -425.3865 0.010 803 +1600 -425.3820 0.010 803 +1700 -425.3760 0.010 803 +1800 -425.3759 0.010 803 +1900 -425.3750 0.010 803 +2000 -425.3712 0.010 803 +2100 -425.3702 0.010 803 +2200 -425.3666 0.010 803 +2300 -425.3654 0.010 803 +2400 -425.3635 0.010 803 +2500 -425.3630 0.010 803 +2600 -425.3623 0.010 803 +2700 -425.3620 0.010 803 +2800 -425.3614 0.010 803 +2900 -425.3593 0.010 803 +3000 -425.3584 0.010 803 +3100 -425.3582 0.010 803 +3200 -425.3573 0.010 803 +3300 -425.3569 0.010 803 +3400 -425.3569 0.010 803 +3500 -425.3566 0.010 803 +3600 -425.3560 0.010 803 +3700 -425.3555 0.010 803 +3800 -425.3551 0.010 803 +3900 -425.3542 0.010 803 +4000 -425.3542 0.010 803 +4100 -425.3538 0.010 803 +4200 -425.3536 0.010 803 +4300 -425.3535 0.010 803 +4400 -425.3534 0.010 803 Reached termination condition! -last topological improvement at gen 365 -Improvement over last 500 gen = 0.00044 -Current score = -425.5839 +last topological improvement at gen 803 +Improvement over last 500 gen = 0.00083 +Current score = -425.3534 Performing final optimizations... -pass 1 : -425.5730 (branch= 0.0000 subset rates= 0.0109) -pass 2 : -425.5586 (branch= 0.0144 subset rates= 0.0000) -pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0000) -pass 4 : -425.5509 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -425.5505 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -425.5498 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -425.5494 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5488 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -425.5487 (branch= 0.0001 subset rates= 0.0000) -pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.3485 (branch= 0.0000 subset rates= 0.0049) +pass 2 : -425.3321 (branch= 0.0164 subset rates= 0.0000) +pass 3 : -425.3250 (branch= 0.0071 subset rates= 0.0000) +pass 4 : -425.3223 (branch= 0.0027 subset rates= 0.0000) +pass 5 : -425.3220 (branch= 0.0003 subset rates= 0.0000) +pass 6 : -425.3220 (branch= 0.0000 subset rates= 0.0000) +pass 7 : -425.3215 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -425.3208 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -425.3207 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3206 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3205 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.5486 +Final score = -425.3205 Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL @@ -18631,87 +19024,183 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.53 1.12 + 0.86 1.55 1.15 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 10 branches were collapsed. + 9 branches were collapsed. ->>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< ->>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< Obtained starting tree 1 from Nexus -Starting with seed=222492842 +Starting with seed=1573911897 -Initial ln Likelihood: -586.0233 +Initial ln Likelihood: -585.3657 optimizing: starting branch lengths, subset rates... -pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) -pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) -pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) -pass 4:+ 1.686 (branch= 1.66 scale= 0.02 subset rates= 0.01) -pass 5:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.031 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 9:+ 0.043 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass10:+ 0.052 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass11:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) -pass12:+ 0.042 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass13:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass14:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.2276 +pass 1:+ 128.924 (branch= 128.21 scale= 0.69 subset rates= 0.02) +pass 2:+ 11.959 (branch= 11.78 scale= 0.03 subset rates= 0.15) +pass 3:+ 4.421 (branch= 4.33 scale= 0.00 subset rates= 0.09) +pass 4:+ 0.779 (branch= 0.76 scale= 0.00 subset rates= 0.01) +pass 5:+ 0.057 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.2135 gen current_lnL precision last_tree_imp -0 -439.2276 0.010 0 -100 -428.8676 0.010 98 -200 -428.0499 0.010 164 -300 -427.6003 0.010 249 -400 -427.5649 0.010 249 -500 -427.4911 0.010 499 -600 -427.3864 0.010 511 -700 -425.7188 0.010 668 -800 -425.6951 0.010 722 -900 -425.6795 0.010 722 -1000 -425.6689 0.010 722 -1100 -425.6640 0.010 722 -1200 -425.6430 0.010 722 -1300 -425.6381 0.010 722 -1400 -425.6345 0.010 722 -1500 -425.6341 0.010 722 -1600 -425.6274 0.010 722 -1700 -425.6239 0.010 722 -1800 -425.6235 0.010 722 -1900 -425.6225 0.010 722 -2000 -425.6202 0.010 722 -2100 -425.6196 0.010 722 -2200 -425.6174 0.010 722 -2300 -425.6146 0.010 722 -2400 -425.6135 0.010 722 -2500 -425.6104 0.010 722 -2600 -425.6099 0.010 722 -2700 -425.6088 0.010 722 -2800 -425.6077 0.010 722 -2900 -425.6073 0.010 722 -3000 -425.6058 0.010 722 -3100 -425.6056 0.010 722 -3200 -425.6055 0.010 722 -3300 -425.6051 0.010 722 +0 -439.2135 0.010 0 +100 -428.1779 0.010 67 +200 -427.4638 0.010 189 +300 -427.4437 0.010 226 +400 -427.1435 0.010 393 +500 -427.1285 0.010 393 +600 -427.1120 0.010 393 +700 -427.1022 0.010 393 +800 -427.1003 0.010 393 +900 -427.0977 0.010 393 +1000 -427.0972 0.010 393 +1100 -427.0948 0.010 393 +1200 -427.0919 0.010 393 +1300 -427.0909 0.010 393 +1400 -427.0892 0.010 393 +1500 -427.0880 0.010 393 +1600 -427.0868 0.010 393 +1700 -427.0861 0.010 393 +1800 -427.0846 0.010 393 +1900 -425.5433 0.010 1890 +2000 -425.5081 0.010 1942 +2100 -425.3789 0.010 2010 +2200 -425.3685 0.010 2010 +2300 -425.3666 0.010 2010 +2400 -425.3610 0.010 2010 +2500 -425.3592 0.010 2010 +2600 -425.3552 0.010 2010 +2700 -425.3536 0.010 2010 +2800 -425.3506 0.010 2010 +2900 -425.3506 0.010 2010 +3000 -425.3501 0.010 2010 +3100 -425.3496 0.010 2010 +3200 -425.3490 0.010 2010 +3300 -425.3485 0.010 2010 +3400 -425.3474 0.010 2010 +3500 -425.3470 0.010 2010 +3600 -425.3468 0.010 2010 +3700 -425.3464 0.010 2010 +3800 -425.3463 0.010 2010 +3900 -425.3463 0.010 2010 +4000 -425.3463 0.010 2010 +Reached termination condition! +last topological improvement at gen 2010 +Improvement over last 500 gen = 0.00068 +Current score = -425.3463 +Performing final optimizations... +pass 1 : -425.3462 (branch= 0.0000 subset rates= 0.0001) +pass 2 : -425.3287 (branch= 0.0175 subset rates= 0.0000) +pass 3 : -425.3239 (branch= 0.0048 subset rates= 0.0000) +pass 4 : -425.3232 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -425.3227 (branch= 0.0005 subset rates= 0.0000) +pass 6 : -425.3212 (branch= 0.0015 subset rates= 0.0000) +pass 7 : -425.3208 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.3204 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -425.3201 (branch= 0.0002 subset rates= 0.0000) +pass 10: -425.3201 (branch= 0.0000 subset rates= 0.0000) +pass 11: -425.3201 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3200 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3200 (branch= 0.0000 subset rates= 0.0000) +pass 14: -425.3200 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -425.3200 +Time used so far = 0 hours, 0 minutes and 10 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate 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: + 0.86 1.54 1.15 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 9 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 5 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=1327400645 + +Initial ln Likelihood: -651.2869 +optimizing: starting branch lengths, subset rates... +pass 1:+ 192.214 (branch= 190.29 scale= 1.86 subset rates= 0.06) +pass 2:+ 17.187 (branch= 17.07 scale= 0.02 subset rates= 0.10) +pass 3:+ 2.448 (branch= 2.39 scale= 0.03 subset rates= 0.03) +pass 4:+ 0.139 (branch= 0.14 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.071 (branch= 0.07 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.2266 +gen current_lnL precision last_tree_imp +0 -439.2266 0.010 0 +100 -433.0025 0.010 78 +200 -428.0919 0.010 168 +300 -427.2239 0.010 259 +400 -425.5959 0.010 327 +500 -425.4273 0.010 444 +600 -425.4204 0.010 444 +700 -425.4191 0.010 444 +800 -425.4084 0.010 444 +900 -425.4010 0.010 444 +1000 -425.3956 0.010 444 +1100 -425.3930 0.010 444 +1200 -425.3870 0.010 444 +1300 -425.3843 0.010 444 +1400 -425.3837 0.010 444 +1500 -425.3818 0.010 444 +1600 -425.3794 0.010 444 +1700 -425.3782 0.010 444 +1800 -425.3769 0.010 444 +1900 -425.3760 0.010 444 +2000 -425.3756 0.010 444 +2100 -425.3741 0.010 444 +2200 -425.3735 0.010 444 +2300 -425.3720 0.010 444 +2400 -425.3713 0.010 444 +2500 -425.3709 0.010 444 +2600 -425.3708 0.010 444 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.6051 +Current score = -425.3706 Performing final optimizations... -pass 1 : -425.5768 (branch= 0.0000 subset rates= 0.0283) -pass 2 : -425.5577 (branch= 0.0191 subset rates= 0.0000) -pass 3 : -425.5524 (branch= 0.0053 subset rates= 0.0000) -pass 4 : -425.5524 (branch= 0.0000 subset rates= 0.0000) -pass 5 : -425.5519 (branch= 0.0005 subset rates= 0.0000) -pass 6 : -425.5508 (branch= 0.0010 subset rates= 0.0000) -pass 7 : -425.5495 (branch= 0.0009 subset rates= 0.0004) -pass 8 : -425.5491 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -425.5489 (branch= 0.0002 subset rates= 0.0000) -pass 10: -425.5488 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.5488 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.5487 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0001) +pass 1 : -425.3669 (branch= 0.0000 subset rates= 0.0037) +pass 2 : -425.3364 (branch= 0.0200 subset rates= 0.0105) +pass 3 : -425.3276 (branch= 0.0087 subset rates= 0.0000) +pass 4 : -425.3247 (branch= 0.0023 subset rates= 0.0007) +pass 5 : -425.3228 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -425.3216 (branch= 0.0013 subset rates= 0.0000) +pass 7 : -425.3211 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.3208 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -425.3207 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3207 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3206 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.5486 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -425.3206 +Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -18739,11 +19228,11 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.53 1.12 + 0.87 1.53 1.15 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. + 10 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) Search rep 5 (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!*** @@ -18751,13 +19240,16 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 5 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -425.5486 (best) -Replicate 2 : -425.5486 (TERMINATED PREMATURELY) +Replicate 1 : -425.5486 +Replicate 2 : -425.5492 +Replicate 3 : -425.3205 +Replicate 4 : -425.3200 (best) (same topology as 3) +Replicate 5 : -425.3206 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18773,9 +19265,12 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.038 0.868 1.530 1.121 -rep 2: 3.040 0.869 1.528 1.119 +rep 2: 3.039 0.868 1.535 1.108 +rep 3: 2.976 0.862 1.548 1.149 +rep 4: 2.978 0.864 1.541 1.149 +rep 5: 2.981 0.866 1.534 1.150 -Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#4) to bootstrap file ch.p.mkv.ssr.boot.tre ####################################################### TREEFILES PASS @@ -18960,6 +19455,251 @@ 1800 -473.9877 0.010 653 1900 -473.9867 0.010 653 2000 -473.9852 0.010 653 +2100 -473.9830 0.010 653 +2200 -473.9824 0.010 653 +2300 -473.9816 0.010 653 +2400 -473.9807 0.010 653 +2500 -473.9801 0.010 653 +2600 -473.9795 0.010 653 +2700 -473.9790 0.010 653 +2800 -473.9779 0.010 653 +2900 -473.9776 0.010 653 +3000 -473.9775 0.010 653 +3100 -473.9771 0.010 653 +3200 -473.9769 0.010 653 +3300 -473.9766 0.010 653 +3400 -473.9762 0.010 653 +3500 -473.9761 0.010 653 +3600 -473.9761 0.010 653 +3700 -473.9759 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00096 +Current score = -473.9759 +Performing final optimizations... +pass 1 : -473.9758 (branch= 0.0001 subset rates= 0.0000) +pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0016) +pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9550 (branch= 0.0009 subset rates= 0.0000) +pass 5 : -473.9525 (branch= 0.0007 subset rates= 0.0018) +pass 6 : -473.9521 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -473.9516 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9508 +Time used so far = 0 hours, 0 minutes and 2 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 2.81 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=74284197 + +Initial ln Likelihood: -646.1143 +optimizing: starting branch lengths, subset rates... +pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) +pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) +pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) +pass 4:+ 2.490 (branch= 1.89 scale= 0.00 subset rates= 0.60) +pass 5:+ 0.684 (branch= 0.61 scale= 0.02 subset rates= 0.05) +pass 6:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8185 +gen current_lnL precision last_tree_imp +0 -474.8185 0.010 0 +100 -474.7244 0.010 55 +200 -474.7128 0.010 55 +300 -474.7037 0.010 55 +400 -474.6654 0.010 339 +500 -474.5695 0.010 496 +600 -474.0703 0.010 585 +700 -474.0481 0.010 585 +800 -474.0412 0.010 585 +900 -474.0316 0.010 585 +1000 -474.0282 0.010 585 +1100 -474.0225 0.010 585 +1200 -474.0142 0.010 585 +1300 -474.0116 0.010 585 +1400 -474.0080 0.010 585 +1500 -474.0041 0.010 585 +1600 -474.0016 0.010 585 +1700 -474.0010 0.010 585 +1800 -473.9994 0.010 585 +1900 -473.9983 0.010 585 +2000 -473.9971 0.010 585 +2100 -473.9968 0.010 585 +2200 -473.9964 0.010 585 +2300 -473.9963 0.010 585 +2400 -473.9952 0.010 585 +2500 -473.9949 0.010 585 +2600 -473.9933 0.010 585 +2700 -473.9932 0.010 585 +2800 -473.9932 0.010 585 +2900 -473.9930 0.010 585 +3000 -473.9930 0.010 585 +3100 -473.9925 0.010 585 +Reached termination condition! +last topological improvement at gen 585 +Improvement over last 500 gen = 0.00079 +Current score = -473.9925 +Performing final optimizations... +pass 1 : -473.9818 (branch= 0.0000 subset rates= 0.0107) +pass 2 : -473.9604 (branch= 0.0189 subset rates= 0.0025) +pass 3 : -473.9545 (branch= 0.0058 subset rates= 0.0000) +pass 4 : -473.9538 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -473.9535 (branch= 0.0003 subset rates= 0.0000) +pass 6 : -473.9521 (branch= 0.0014 subset rates= 0.0000) +pass 7 : -473.9516 (branch= 0.0003 subset rates= 0.0002) +pass 8 : -473.9513 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -473.9511 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9510 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0001) +Looking for minimum length branches... +Final score = -473.9508 +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 2.06 2.81 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 2 (of 5)<<< + +>>>Search rep 3 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=663269721 + +Initial ln Likelihood: -659.0351 +optimizing: starting branch lengths, subset rates... +pass 1:+ 164.999 (branch= 154.40 scale= 0.48 subset rates= 10.12) +pass 2:+ 14.317 (branch= 9.49 scale= 0.03 subset rates= 4.79) +pass 3:+ 3.819 (branch= 2.06 scale= 0.02 subset rates= 1.74) +pass 4:+ 0.906 (branch= 0.30 scale= 0.00 subset rates= 0.60) +pass 5:+ 0.122 (branch= 0.09 scale= 0.00 subset rates= 0.03) +pass 6:+ 0.038 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8340 +gen current_lnL precision last_tree_imp +0 -474.8340 0.010 0 +100 -474.7919 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -19085,48 +19825,194 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 2030, seed 565002103, best lnL -473.984 +Search rep 3 (of 5) generation 192, seed 1900073578, best lnL -474.731 gen current_lnL precision last_tree_imp -2030 -473.9844 0.010 653 -2100 -473.9830 0.010 653 -2200 -473.9824 0.010 653 -2300 -473.9816 0.010 653 -2400 -473.9807 0.010 653 -2500 -473.9801 0.010 653 -2600 -473.9795 0.010 653 -2700 -473.9790 0.010 653 -2800 -473.9779 0.010 653 -2900 -473.9776 0.010 653 -3000 -473.9775 0.010 653 -3100 -473.9771 0.010 653 -3200 -473.9769 0.010 653 -3300 -473.9766 0.010 653 -3400 -473.9762 0.010 653 -3500 -473.9761 0.010 653 -3600 -473.9761 0.010 653 -3700 -473.9759 0.010 653 +192 -474.7307 0.010 183 +200 -474.7307 0.010 183 +300 -474.7187 0.010 183 +400 -474.7036 0.010 183 +500 -474.6871 0.010 183 +600 -474.5395 0.010 535 +700 -474.5271 0.010 535 +800 -474.5227 0.010 535 +900 -474.5120 0.010 535 +1000 -474.5077 0.010 535 +1100 -474.5053 0.010 535 +1200 -474.5039 0.010 535 +1300 -474.5013 0.010 535 +1400 -474.4986 0.010 535 +1500 -474.4981 0.010 535 +1600 -474.4956 0.010 535 +1700 -474.4907 0.010 535 +1800 -474.4796 0.010 535 +1900 -474.4760 0.010 535 +2000 -474.4747 0.010 535 +2100 -474.4733 0.010 535 +2200 -474.4720 0.010 535 +2300 -474.4709 0.010 535 +2400 -474.4703 0.010 535 +2500 -474.4697 0.010 535 +2600 -474.4676 0.010 535 +2700 -474.4670 0.010 535 +2800 -474.4665 0.010 535 +2900 -474.4661 0.010 535 +3000 -474.4649 0.010 535 +3100 -474.4642 0.010 535 +3200 -474.4636 0.010 535 +3300 -474.4636 0.010 535 +3400 -474.4619 0.010 535 +3500 -474.4614 0.010 535 +3600 -474.4611 0.010 535 +3700 -474.4608 0.010 535 +3800 -474.4608 0.010 535 +3900 -474.4607 0.010 535 +4000 -474.4607 0.010 535 Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00096 -Current score = -473.9759 +last topological improvement at gen 535 +Improvement over last 500 gen = 0.00071 +Current score = -474.4607 Performing final optimizations... -pass 1 : -473.9758 (branch= 0.0001 subset rates= 0.0000) -pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0016) -pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9550 (branch= 0.0009 subset rates= 0.0000) -pass 5 : -473.9525 (branch= 0.0007 subset rates= 0.0018) -pass 6 : -473.9521 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -473.9516 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4602 (branch= 0.0000 subset rates= 0.0005) +pass 2 : -474.4430 (branch= 0.0172 subset rates= 0.0000) +pass 3 : -474.4430 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -474.4383 (branch= 0.0047 subset rates= 0.0000) +pass 5 : -474.4338 (branch= 0.0046 subset rates= 0.0000) +pass 6 : -474.4316 (branch= 0.0021 subset rates= 0.0000) +pass 7 : -474.4301 (branch= 0.0016 subset rates= 0.0000) +pass 8 : -474.4294 (branch= 0.0006 subset rates= 0.0001) +pass 9 : -474.4289 (branch= 0.0005 subset rates= 0.0000) +pass 10: -474.4285 (branch= 0.0003 subset rates= 0.0000) +pass 11: -474.4283 (branch= 0.0002 subset rates= 0.0001) +pass 12: -474.4282 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4281 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -474.4281 +Time used so far = 0 hours, 0 minutes and 8 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.59 2.03 2.92 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 7 branches were collapsed. + +>>>Completed Search rep 3 (of 5)<<< + +>>>Search rep 4 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=17311967 + +Initial ln Likelihood: -692.6191 +optimizing: starting branch lengths, subset rates... +pass 1:+ 190.070 (branch= 177.15 scale= 2.85 subset rates= 10.07) +pass 2:+ 19.411 (branch= 14.64 scale= 0.00 subset rates= 4.77) +pass 3:+ 6.755 (branch= 5.00 scale= 0.00 subset rates= 1.76) +pass 4:+ 1.362 (branch= 0.80 scale= 0.00 subset rates= 0.57) +pass 5:+ 0.119 (branch= 0.09 scale= 0.00 subset rates= 0.03) +pass 6:+ 0.055 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.014 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8346 +gen current_lnL precision last_tree_imp +0 -474.8346 0.010 0 +100 -474.7468 0.010 62 +200 -474.1733 0.010 145 +300 -474.1512 0.010 145 +400 -474.1334 0.010 145 +500 -474.0520 0.010 463 +600 -474.0182 0.010 523 +700 -474.0118 0.010 523 +800 -474.0048 0.010 523 +900 -474.0037 0.010 523 +1000 -473.9971 0.010 523 +1100 -473.9952 0.010 523 +1200 -473.9905 0.010 523 +1300 -473.9889 0.010 523 +1400 -473.9874 0.010 523 +1500 -473.9858 0.010 523 +1600 -473.9833 0.010 523 +1700 -473.9805 0.010 523 +1800 -473.9803 0.010 523 +1900 -473.9793 0.010 523 +2000 -473.9793 0.010 523 +2100 -473.9792 0.010 523 +2200 -473.9790 0.010 523 +2300 -473.9788 0.010 523 +2400 -473.9787 0.010 523 +Reached termination condition! +last topological improvement at gen 523 +Improvement over last 500 gen = 0.00068 +Current score = -473.9787 +Performing final optimizations... +pass 1 : -473.9772 (branch= 0.0000 subset rates= 0.0015) +pass 2 : -473.9618 (branch= 0.0154 subset rates= 0.0000) +pass 3 : -473.9579 (branch= 0.0039 subset rates= 0.0000) +pass 4 : -473.9570 (branch= 0.0009 subset rates= 0.0000) +pass 5 : -473.9566 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -473.9553 (branch= 0.0014 subset rates= 0.0000) +pass 7 : -473.9547 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -473.9542 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -473.9540 (branch= 0.0001 subset rates= 0.0000) +pass 10: -473.9521 (branch= 0.0000 subset rates= 0.0019) +pass 11: -473.9509 (branch= 0.0007 subset rates= 0.0005) +pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 8 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19154,13 +20040,13 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.81 + 0.59 2.06 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 1 (of 5)<<< +>>>Completed Search rep 4 (of 5)<<< ->>>Search rep 2 (of 5)<<< +>>>Search rep 5 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -19189,52 +20075,62 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=74284197 +Starting with seed=956020669 -Initial ln Likelihood: -646.1143 +Initial ln Likelihood: -624.6851 optimizing: starting branch lengths, subset rates... -pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) -pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) -pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) -pass 4:+ 2.490 (branch= 1.89 scale= 0.00 subset rates= 0.60) -pass 5:+ 0.684 (branch= 0.61 scale= 0.02 subset rates= 0.05) -pass 6:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 1:+ 131.117 (branch= 120.44 scale= 0.58 subset rates= 10.09) +pass 2:+ 13.135 (branch= 8.63 scale= 0.00 subset rates= 4.50) +pass 3:+ 3.192 (branch= 1.64 scale= 0.00 subset rates= 1.56) +pass 4:+ 1.951 (branch= 1.36 scale= 0.00 subset rates= 0.59) +pass 5:+ 0.359 (branch= 0.32 scale= 0.00 subset rates= 0.04) +pass 6:+ 0.103 (branch= 0.10 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8185 +lnL after optimization: -474.8284 gen current_lnL precision last_tree_imp -0 -474.8185 0.010 0 -100 -474.7244 0.010 55 -200 -474.7128 0.010 55 -300 -474.7037 0.010 55 -400 -474.6654 0.010 339 -500 -474.5695 0.010 496 -600 -474.0703 0.010 585 -700 -474.0481 0.010 585 -800 -474.0412 0.010 585 -900 -474.0316 0.010 585 -1000 -474.0282 0.010 585 -1100 -474.0225 0.010 585 -1200 -474.0142 0.010 585 -1300 -474.0116 0.010 585 -1400 -474.0080 0.010 585 +0 -474.8284 0.010 0 +100 -474.7589 0.010 25 +200 -474.7224 0.010 109 +300 -474.2174 0.010 295 +400 -474.1962 0.010 295 +500 -474.0193 0.010 437 +600 -474.0174 0.010 437 +700 -474.0106 0.010 437 +800 -474.0060 0.010 437 +900 -474.0058 0.010 437 +1000 -474.0014 0.010 437 +1100 -474.0008 0.010 437 +1200 -473.9993 0.010 437 +1300 -473.9971 0.010 437 +1400 -473.9960 0.010 437 +1500 -473.9933 0.010 437 +1600 -473.9931 0.010 437 +1700 -473.9916 0.010 437 +1800 -473.9909 0.010 437 +1900 -473.9899 0.010 437 +2000 -473.9895 0.010 437 +2100 -473.9889 0.010 437 +2200 -473.9889 0.010 437 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.0068 +Current score = -473.9881 Performing final optimizations... -pass 1 : -474.0009 (branch= 0.0000 subset rates= 0.0059) -pass 2 : -473.9724 (branch= 0.0207 subset rates= 0.0078) -pass 3 : -473.9576 (branch= 0.0143 subset rates= 0.0005) -pass 4 : -473.9568 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -473.9542 (branch= 0.0027 subset rates= 0.0000) -pass 6 : -473.9534 (branch= 0.0008 subset rates= 0.0000) -pass 7 : -473.9514 (branch= 0.0019 subset rates= 0.0000) -pass 8 : -473.9510 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9835 (branch= 0.0000 subset rates= 0.0046) +pass 2 : -473.9616 (branch= 0.0167 subset rates= 0.0051) +pass 3 : -473.9558 (branch= 0.0058 subset rates= 0.0000) +pass 4 : -473.9540 (branch= 0.0018 subset rates= 0.0000) +pass 5 : -473.9525 (branch= 0.0016 subset rates= 0.0000) +pass 6 : -473.9517 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -473.9497 (branch= 0.0013 subset rates= 0.0008) +pass 8 : -473.9491 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -473.9487 (branch= 0.0004 subset rates= 0.0000) +pass 10: -473.9486 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9484 (branch= 0.0000 subset rates= 0.0002) +pass 12: -473.9484 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9483 (branch= 0.0000 subset rates= 0.0001) +pass 14: -473.9483 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -473.9483 +Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -19262,11 +20158,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.06 2.81 + 0.59 2.07 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. ->>>Terminated Search rep 2 (of 5)<<< +>>>Terminated Search rep 5 (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!*** @@ -19274,13 +20170,16 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 5 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9508 -Replicate 2 : -473.9508 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -473.9508 (same topology as 1) +Replicate 3 : -474.4281 +Replicate 4 : -473.9508 (same topology as 1) +Replicate 5 : -473.9483 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19297,8 +20196,11 @@ TL R(1) R(2) R(3) rep 1: 4.351 0.587 2.066 2.813 rep 2: 4.349 0.588 2.064 2.806 +rep 3: 4.601 0.587 2.035 2.918 +rep 4: 4.349 0.588 2.062 2.810 +rep 5: 4.348 0.588 2.066 2.807 -Saving final tree from best search rep (#2) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#5) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -19363,11 +20265,11 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli' in '../garli_2.1-7_amd64.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-7_amd64.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-7_amd64.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_amd64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-7_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-7_amd64.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-7_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -19375,12 +20277,14 @@ 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/3069313/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3069313/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/28240 and its subdirectories -I: Current time: Sun May 5 11:28:38 -12 2024 -I: pbuilder-time-stamp: 1714951718 +I: removing directory /srv/workspace/pbuilder/3069313 and its subdirectories +I: Current time: Sun Jun 8 19:58:19 +14 2025 +I: pbuilder-time-stamp: 1749362299