Diff of the two buildlogs: -- --- b1/build.log 2025-01-14 02:00:37.840443252 +0000 +++ b2/build.log 2025-01-14 02:05:53.750069644 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 13 13:51:54 -12 2025 -I: pbuilder-time-stamp: 1736819514 +I: Current time: Mon Feb 16 22:23:38 +14 2026 +I: pbuilder-time-stamp: 1771230218 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -23,54 +23,86 @@ dpkg-source: info: unpacking garli_2.1-9.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/55507/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/87288/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +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 Feb 16 08:23 /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/87288/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/87288/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='b71a6ad30777406fa970d9af2167be2d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='55507' - PS1='# ' - PS2='> ' + INVOCATION_ID=3b969cb1021c4d0796413ec5aa8cc4f5 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=87288 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.hqKze1JY/pbuilderrc_wnSp --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.hqKze1JY/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hqKze1JY/pbuilderrc_HuXp --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.hqKze1JY/b2 --logfile b2/build.log garli_2.1-9.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos12-i386 6.1.0-29-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.123-1 (2025-01-02) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-29-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.123-1 (2025-01-02) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/55507/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/87288/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -166,7 +198,7 @@ Get: 50 http://deb.debian.org/debian trixie/main i386 libncl-dev i386 2.1.21+git20210811.b1213a7-6 [642 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 mpi-default-dev i386 1.18 [3372 B] Get: 52 http://deb.debian.org/debian trixie/main i386 ncl-tools i386 2.1.21+git20210811.b1213a7-6 [199 kB] -Fetched 42.6 MB in 1s (38.1 MB/s) +Fetched 42.6 MB in 0s (128 MB/s) Preconfiguring packages ... 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 ... 19839 files and directories currently installed.) @@ -396,7 +428,11 @@ 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_2.1-9_source.changes +I: user script /srv/workspace/pbuilder/87288/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/87288/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_2.1-9_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-9 dpkg-buildpackage: info: source distribution unstable @@ -498,8 +534,8 @@ 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 @@ -568,7 +604,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j11 + make -j21 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' @@ -585,6 +621,16 @@ 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 -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1322 | register int nsq = n * n; @@ -617,6 +663,50 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from bipartition.cpp:20: +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++/14/string:49, + from bipartition.h:23, + from bipartition.cpp:19: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/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++/14/bits/stl_function.h:1435: +/usr/include/c++/14/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++/14/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++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ 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); @@ -634,20 +724,13 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from adaptation.cpp:25: + from optimization.cpp:19: 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++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from tree.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -685,20 +768,64 @@ /usr/include/c++/14/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{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, - from bipartition.h:23, - from bipartition.cpp:19: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from adaptation.cpp:18: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + 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++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/iomanip:42, + from individual.cpp:21: +/usr/include/c++/14/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++/14/bits/stl_function.h:1435: +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -711,6 +838,13 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +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++/14/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)); @@ -733,72 +867,23 @@ /usr/include/c++/14/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 -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp -adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': -adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 271 | fread((char *) this, 1, scalarSize, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:278:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 278 | fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:280:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 280 | fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:281:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 281 | fread((char *) randNNInum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:283:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 283 | fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:284:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 284 | fread((char *) exNNInum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:286:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:287:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 287 | fread((char *) randSPRnum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:289:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 289 | fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 290 | fread((char *) limSPRnum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:292:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 292 | fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:293:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 293 | fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:295:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 295 | fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:296:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 296 | fread((char *) randRecomnum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:298:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 298 | fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:299:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:301:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 301 | fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:302:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 302 | fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:304:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 304 | fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +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;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -839,11 +924,18 @@ /usr/include/c++/14/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++/14/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 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{ | ^~~~~~~~~~~~~~~ @@ -853,7 +945,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from population.h:23: + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -877,10 +969,6 @@ /usr/include/c++/14/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; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ 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)); @@ -888,9 +976,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -/usr/include/c++/14/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; @@ -898,20 +983,9 @@ /usr/include/c++/14/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{ | ^~~~~~~~~~~~~~~ @@ -921,7 +995,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -952,32 +1026,20 @@ /usr/include/c++/14/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++/14/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{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -993,6 +1055,13 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +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++/14/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)); @@ -1015,34 +1084,20 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': -datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from model.cpp:17: +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1081,13 +1136,16 @@ 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, - from optimization.cpp:19: + from individual.h:21, + from population.h:31, + from funcs.h:25, + from tree.cpp:33: 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++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, - from tree.h:24: + from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1125,7 +1183,28 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from population.cpp:23: +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from mpitrick.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1170,22 +1254,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-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/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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; @@ -1193,35 +1261,78 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from model.h:25, - from clamanager.h:25, - from condlike.cpp:22: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/i386-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/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -In file included from population.cpp:49: 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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6845 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6849 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6855 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6862 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6865 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6868 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6872 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6878 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from model.h:25, + from clamanager.h:25, + from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1328,8 +1485,12 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, - from /usr/include/ncl/ncl.h:27, - from garlireader.cpp:41: + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/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/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1341,7 +1502,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -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 -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1364,7 +1524,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -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 -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1385,14 +1544,22 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from rng.h:36, - from tree.h:30: + from /usr/include/c++/14/string:54: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/i386-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/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/stdio.h:970, + from /usr/lib/i386-linux-gnu/mpich/include/mpicxx.h:41, + from /usr/lib/i386-linux-gnu/mpich/include/mpi.h:977, + from mpitrick.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1404,14 +1571,13 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -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 -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from /usr/include/c++/14/string:54, + from translatetable.h:24, + from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1423,98 +1589,53 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -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 -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] - 323 | else sprintf(temp, ".run%d", rank); - | ^~ -garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] - 323 | else sprintf(temp, ".run%d", rank); - | ^~~~~~~~ +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from rng.h:36, + from tree.h:30: In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~ -garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~~~~~~~~ +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/stdio.h:970, + from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ -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 -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from tree.cpp:33: -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++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.cpp:21: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/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++/14/bits/stl_function.h:1435: -/usr/include/c++/14/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++/14/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++/14/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;idlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6845 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6849 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6855 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6862 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6865 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6868 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6872 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6878 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from mpitrick.cpp:27: -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++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from mpitrick.cpp:21: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/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++/14/bits/stl_function.h:1435: -/usr/include/c++/14/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++/14/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++/14/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{ | ^~~~~~~~~~~~~~~ @@ -2023,7 +2053,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2039,7 +2069,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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 -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp 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)); @@ -2066,7 +2095,7 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from adaptation.cpp:25: + from configreader.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2076,7 +2105,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2126,17 +2155,15 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from funcs.cpp:30: + 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from population.h:23: + from /usr/include/c++/14/iomanip:42, + from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2178,21 +2205,33 @@ 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++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from population.h:23: +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2234,15 +2273,17 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from individual.cpp:28: + from adaptation.cpp:25: 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2280,77 +2321,60 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from model.cpp:17: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/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++/14/bits/stl_function.h:1435: +/usr/include/c++/14/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++/14/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++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ 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); @@ -2358,13 +2382,10 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': -datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, - from model.cpp:26: + from population.h:31, + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2374,7 +2395,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from model.cpp:17: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2412,14 +2433,20 @@ /usr/include/c++/14/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{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, - from tree.h:24: + from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2457,56 +2484,24 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from optimization.cpp:21: +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{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, - from population.cpp:23: + from tree.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2544,19 +2539,207 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6845 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6849 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6855 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6862 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6865 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6868 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6872 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6878 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': +datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from model.h:25, - from clamanager.h:25, - from condlike.cpp:22: + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2568,11 +2751,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from population.cpp:49: -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++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.cpp:21: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/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++/14/bits/stl_function.h:1435: -/usr/include/c++/14/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++/14/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++/14/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;idlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6845 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6849 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6855 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6862 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6865 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6868 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6872 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6878 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from translatetable.h:24, - from translatetable.cpp:19: + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2916,9 +2948,13 @@ from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from rng.h:36, + from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2930,22 +2966,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-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 9 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, 536870911] - 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/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 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:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2956,7 +2976,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from treenode.cpp:21: + from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2987,6 +3007,22 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-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 9 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, 536870911] + 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/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 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 ()); + | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests @@ -3003,7 +3039,7 @@ # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1\nbootstrapseed = 42/' \{\} \; dh_auto_test - make -j11 check "TESTSUITEFLAGS=-j11 --verbose" VERBOSE=1 + make -j21 check "TESTSUITEFLAGS=-j21 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making check in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' @@ -5523,7 +5559,7 @@ 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 ... ####################################################### @@ -5970,7 +6006,7 @@ 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 26 seconds +Time used = 0 hours, 0 minutes and 13 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6122,7 +6158,7 @@ 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 18 seconds +Time used = 0 hours, 0 minutes and 9 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6307,11 +6343,11 @@ pass 13: -3350.7072 (branch= 0.0019 alpha= 0.0093 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0577 subset rates= 0.0000) pass 14: -3350.6389 (branch= 0.0005 alpha= 0.0090 pinv= 0.0090 eq freqs= 0.0001 rel rates= 0.0486 subset rates= 0.0012) pass 15: -3350.5822 (branch= 0.0009 alpha= 0.0082 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0392 subset rates= 0.0000) -pass 16: -3350.5338 (branch= 0.0003 alpha= 0.0075 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0333 subset rates= 0.0000) -pass 17: -3350.4923 (branch= 0.0001 alpha= 0.0072 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0275 subset rates= 0.0000) +pass 16: -3350.5337 (branch= 0.0003 alpha= 0.0075 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0333 subset rates= 0.0000) +pass 17: -3350.4923 (branch= 0.0001 alpha= 0.0072 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0274 subset rates= 0.0000) pass 18: -3350.4567 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0231 subset rates= 0.0000) -pass 19: -3350.4262 (branch= 0.0000 alpha= 0.0058 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0193 subset rates= 0.0000) -pass 20: -3350.3998 (branch= 0.0000 alpha= 0.0052 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0165 subset rates= 0.0000) +pass 19: -3350.4262 (branch= 0.0000 alpha= 0.0059 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0193 subset rates= 0.0000) +pass 20: -3350.3998 (branch= 0.0000 alpha= 0.0052 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0164 subset rates= 0.0000) optimization up to ... pass 30: -3350.2717 (branch= 0.0000 alpha= 0.0276 pinv= 0.0250 eq freqs= 0.0002 rel rates= 0.0754 subset rates= 0.0000) optimization up to ... @@ -6321,12 +6357,14 @@ optimization up to ... pass 60: -3350.2340 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0011 subset rates= 0.0000) optimization up to ... -pass 70: -3350.2337 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 70: -3350.2338 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) + optimization up to ... +pass 80: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 77: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 82: -3350.2336 (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 = -3350.2336 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6339,7 +6377,7 @@ Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.11 10.4 2.687 0.001 21.85 1 0.333 0.222 0.157 0.288 0.579 0.366 +rep 1: 3.114 10.41 2.689 0.001 21.88 1 0.333 0.222 0.157 0.288 0.580 0.366 Partition model subset 2: Model contains no estimated parameters @@ -6352,9 +6390,9 @@ Writing optimized trees and models to scr.g.dnaBnoZ.best.all.tre ***********TEST************** -***Score is 3350.23362 +***Score is 3350.23358 ***Expected is 3350.2345 -***SCORE DIFFERENCE IS -.00088 +***SCORE DIFFERENCE IS -.00092 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaBnoZ.conf *** Running scoring test ./scoring/g.dnaMix.conf @@ -6534,7 +6572,7 @@ pass 75: -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 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6851,7 +6889,7 @@ 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 ... ####################################################### @@ -7018,7 +7056,7 @@ pass 15: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 -Time used = 0 hours, 0 minutes and 12 seconds +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7272,7 +7310,7 @@ 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 7 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8333,7 +8371,7 @@ pass 14: -472.3906 (branch= 0.0000) Looking for minimum length branches... Final score = -472.3906 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9124,53 +9162,53 @@ 3000 -210.5163 0.010 1215 Reached termination condition! last topological improvement at gen 1215 -Improvement over last 500 gen = 0.03351 -Current score = -210.5119 +Improvement over last 500 gen = 0.03350 +Current score = -210.5120 Performing final optimizations... -pass 1 : -210.1432 (branch= 0.0000 alpha= 0.0976 pinv= 0.2252 eq freqs= 0.0000 rel rates= 0.0459) -pass 2 : -209.5398 (branch= 0.0000 alpha= 0.3289 pinv= 0.2490 eq freqs= 0.0028 rel rates= 0.0227) -pass 3 : -209.3300 (branch= 0.0346 alpha= 0.1445 pinv= 0.0169 eq freqs= 0.0069 rel rates= 0.0069) -pass 4 : -209.2583 (branch= 0.0471 alpha= 0.0154 pinv= 0.0019 eq freqs= 0.0011 rel rates= 0.0061) -pass 5 : -209.2211 (branch= 0.0234 alpha= 0.0069 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) -pass 6 : -209.1987 (branch= 0.0105 alpha= 0.0024 pinv= 0.0009 eq freqs= 0.0002 rel rates= 0.0084) -pass 7 : -209.1782 (branch= 0.0070 alpha= 0.0024 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0104) -pass 8 : -209.1601 (branch= 0.0044 alpha= 0.0012 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0117) -pass 9 : -209.1461 (branch= 0.0023 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0111) -pass 10: -209.1349 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) -pass 11: -209.1252 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0089) -pass 12: -209.1165 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) -pass 13: -209.1087 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) -pass 14: -209.1016 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) -pass 15: -209.0948 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) -pass 16: -209.0886 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) -pass 17: -209.0827 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) -pass 18: -209.0772 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) -pass 19: -209.0719 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) -pass 20: -209.0671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) - optimization up to ... -pass 30: -208.9998 (branch= 0.0075 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0583) - optimization up to ... -pass 40: -208.8391 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1218) - optimization up to ... -pass 50: -208.6974 (branch= 0.0133 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1212) - optimization up to ... -pass 60: -208.6231 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0722) - optimization up to ... -pass 70: -208.5738 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0488) +pass 1 : -210.1425 (branch= 0.0000 alpha= 0.0977 pinv= 0.2257 eq freqs= 0.0000 rel rates= 0.0461) +pass 2 : -209.5279 (branch= 0.0000 alpha= 0.3286 pinv= 0.2607 eq freqs= 0.0029 rel rates= 0.0224) +pass 3 : -209.3296 (branch= 0.0362 alpha= 0.1346 pinv= 0.0139 eq freqs= 0.0068 rel rates= 0.0067) +pass 4 : -209.2592 (branch= 0.0438 alpha= 0.0174 pinv= 0.0020 eq freqs= 0.0011 rel rates= 0.0061) +pass 5 : -209.2221 (branch= 0.0231 alpha= 0.0072 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) +pass 6 : -209.1992 (branch= 0.0107 alpha= 0.0026 pinv= 0.0009 eq freqs= 0.0002 rel rates= 0.0084) +pass 7 : -209.1783 (branch= 0.0076 alpha= 0.0022 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0105) +pass 8 : -209.1601 (branch= 0.0045 alpha= 0.0012 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0118) +pass 9 : -209.1460 (branch= 0.0023 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0111) +pass 10: -209.1347 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) +pass 11: -209.1251 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0088) +pass 12: -209.1164 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) +pass 13: -209.1085 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) +pass 14: -209.1014 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) +pass 15: -209.0947 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) +pass 16: -209.0885 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) +pass 17: -209.0826 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) +pass 18: -209.0771 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) +pass 19: -209.0718 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) +pass 20: -209.0670 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) + optimization up to ... +pass 30: -208.9995 (branch= 0.0076 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0584) + optimization up to ... +pass 40: -208.8390 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1217) + optimization up to ... +pass 50: -208.6976 (branch= 0.0132 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1211) + optimization up to ... +pass 60: -208.6234 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0722) + optimization up to ... +pass 70: -208.5739 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0489) optimization up to ... -pass 80: -208.5378 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0356) +pass 80: -208.5380 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0356) optimization up to ... -pass 90: -208.5107 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) +pass 90: -208.5108 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0270) optimization up to ... -pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) +pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0211) optimization up to ... -pass 110: -208.4726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) +pass 110: -208.4727 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0168) optimization up to ... pass 120: -208.4588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... -pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) +pass 130: -208.4473 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) optimization up to ... -pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) +pass 140: -208.4376 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) optimization up to ... pass 150: -208.4292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... @@ -9186,27 +9224,27 @@ optimization up to ... pass 210: -208.3981 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) optimization up to ... -pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) optimization up to ... -pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) +pass 230: -208.3917 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 240: -208.3889 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... -pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) +pass 250: -208.3864 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... -pass 260: -208.3840 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) +pass 260: -208.3841 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... -pass 270: -208.3819 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) +pass 270: -208.3820 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 290: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +pass 290: -208.3782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3765 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 310: -208.3750 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3735 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... @@ -9222,38 +9260,40 @@ optimization up to ... pass 390: -208.3655 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 400: -208.3646 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 400: -208.3647 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3630 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3609 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 470: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 480: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 480: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) + optimization up to ... +pass 490: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 490: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 500: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 500: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 510: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) optimization up to ... -pass 509: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 512: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... -Final score = -208.3584 -Time used = 0 hours, 0 minutes and 6 seconds +Final score = -208.3583 +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.311, AG = 188.753, AT = 6.967, CG = 204.934, CT = 194.972, GT = 1.000 + AC = 123.075, AG = 189.929, AT = 7.010, CG = 206.213, CT = 196.176, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: @@ -9277,11 +9317,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3584 +Replicate 1 : -208.3583 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: 122.3 188.8 6.967 204.9 195 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 123.1 189.9 7.01 206.2 196.2 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -9418,43 +9458,43 @@ Current score = -211.2855 Performing final optimizations... pass 1 : -208.9741 (branch= 0.0000 alpha= 0.7616 pinv= 1.4574 eq freqs= 0.0064 rel rates= 0.0860) -pass 2 : -208.5660 (branch= 0.0406 alpha= 0.3181 pinv= 0.0098 eq freqs= 0.0118 rel rates= 0.0278) -pass 3 : -208.5065 (branch= 0.0302 alpha= 0.0021 pinv= 0.0000 eq freqs= 0.0017 rel rates= 0.0254) -pass 4 : -208.4811 (branch= 0.0032 alpha= 0.0000 pinv= 0.0017 eq freqs= 0.0000 rel rates= 0.0206) -pass 5 : -208.4602 (branch= 0.0023 alpha= 0.0007 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0175) -pass 6 : -208.4415 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0178) -pass 7 : -208.4245 (branch= 0.0009 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0158) -pass 8 : -208.4098 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0145) -pass 9 : -208.3958 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0136) -pass 10: -208.3830 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0126) -pass 11: -208.3715 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) -pass 12: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) -pass 13: -208.3514 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) -pass 14: -208.3425 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) -pass 15: -208.3343 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) -pass 16: -208.3268 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) -pass 17: -208.3195 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0073) -pass 18: -208.3129 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) -pass 19: -208.3065 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) -pass 20: -208.3007 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) +pass 2 : -208.5667 (branch= 0.0405 alpha= 0.3178 pinv= 0.0097 eq freqs= 0.0118 rel rates= 0.0276) +pass 3 : -208.5070 (branch= 0.0301 alpha= 0.0023 pinv= 0.0000 eq freqs= 0.0017 rel rates= 0.0256) +pass 4 : -208.4820 (branch= 0.0032 alpha= 0.0000 pinv= 0.0016 eq freqs= 0.0000 rel rates= 0.0202) +pass 5 : -208.4605 (branch= 0.0022 alpha= 0.0010 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0177) +pass 6 : -208.4419 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0177) +pass 7 : -208.4248 (branch= 0.0009 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0160) +pass 8 : -208.4101 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0143) +pass 9 : -208.3962 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0137) +pass 10: -208.3835 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0125) +pass 11: -208.3722 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0113) +pass 12: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0106) +pass 13: -208.3518 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) +pass 14: -208.3429 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) +pass 15: -208.3346 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) +pass 16: -208.3271 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) +pass 17: -208.3198 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0073) +pass 18: -208.3132 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 19: -208.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) +pass 20: -208.3009 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... -pass 30: -208.2567 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0439) +pass 30: -208.2568 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0440) optimization up to ... -pass 40: -208.2293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0273) +pass 40: -208.2294 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0273) optimization up to ... -pass 50: -208.2105 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0187) +pass 50: -208.2105 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) optimization up to ... -pass 60: -208.1969 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0136) +pass 60: -208.1968 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... pass 70: -208.1864 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... -pass 90: -208.1715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) +pass 90: -208.1716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) optimization up to ... pass 100: -208.1661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... -pass 110: -208.1614 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) +pass 110: -208.1615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) optimization up to ... pass 120: -208.1575 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... @@ -9464,7 +9504,7 @@ optimization up to ... pass 150: -208.1485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 160: -208.1461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) +pass 160: -208.1461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 170: -208.1440 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... @@ -9500,7 +9540,7 @@ optimization up to ... pass 330: -208.1265 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 340: -208.1259 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 340: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 350: -208.1254 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... @@ -9508,16 +9548,16 @@ optimization up to ... pass 370: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) +pass 372: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 7 seconds +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 22.244, AG = 32.321, AT = 0.001, CG = 36.409, CT = 80.319, GT = 1.000 + AC = 22.239, AG = 32.314, AT = 0.001, CG = 36.402, CT = 80.320, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: @@ -9545,7 +9585,7 @@ 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: 22.24 32.32 0.001 36.41 80.32 1 0.221 0.344 0.216 0.218 999.900 0.338 +rep 1: 22.24 32.31 0.001 36.4 80.32 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL @@ -9673,148 +9713,158 @@ Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL -2000 -210.9689 0.010 1502 +2000 -210.9688 0.010 1502 2500 -210.8711 0.010 1502 -3000 -210.7511 0.010 2883 -3500 -210.7006 0.010 2883 -4000 -210.6776 0.010 2883 -4500 -210.6528 0.010 2883 -5000 -210.5910 0.010 4692 -5500 -210.5256 0.010 4692 -6000 -210.4351 0.010 4692 -6500 -210.4174 0.010 4692 +3000 -210.7510 0.010 2883 +3500 -210.7005 0.010 2883 +4000 -210.6775 0.010 2883 +4500 -210.6526 0.010 2883 +5000 -210.5940 0.010 4692 +5500 -210.5367 0.010 5207 +6000 -210.4081 0.010 5812 +6500 -210.3701 0.010 5812 +7000 -210.3450 0.010 5812 +7500 -210.3290 0.010 5812 +8000 -210.1893 0.010 7789 +8500 -210.0964 0.010 7789 +9000 -210.0080 0.010 7789 +9500 -209.9339 0.010 7789 +10000 -209.8869 0.010 9713 + Optimizing parameters... improved 0.477 lnL + Optimizing branchlengths... improved 0.000 lnL +10500 -209.3800 0.010 9713 +11000 -209.3651 0.010 9713 +11500 -209.3535 0.010 9713 Reached termination condition! -last topological improvement at gen 4692 -Improvement over last 500 gen = 0.02291 -Current score = -210.4049 +last topological improvement at gen 9713 +Improvement over last 500 gen = 0.01208 +Current score = -209.3469 Performing final optimizations... -pass 1 : -209.9406 (branch= 0.0001 alpha= 0.0823 pinv= 0.2856 eq freqs= 0.0000 rel rates= 0.0962) -pass 2 : -209.3924 (branch= 0.0062 alpha= 0.3452 pinv= 0.1692 eq freqs= 0.0000 rel rates= 0.0276) -pass 3 : -209.2775 (branch= 0.0331 alpha= 0.0616 pinv= 0.0125 eq freqs= 0.0043 rel rates= 0.0032) -pass 4 : -209.2277 (branch= 0.0299 alpha= 0.0092 pinv= 0.0000 eq freqs= 0.0031 rel rates= 0.0077) -pass 5 : -209.1812 (branch= 0.0279 alpha= 0.0113 pinv= 0.0007 eq freqs= 0.0008 rel rates= 0.0058) -pass 6 : -209.1484 (branch= 0.0164 alpha= 0.0062 pinv= 0.0006 eq freqs= 0.0007 rel rates= 0.0089) -pass 7 : -209.1265 (branch= 0.0077 alpha= 0.0037 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0100) -pass 8 : -209.1126 (branch= 0.0038 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0092) -pass 9 : -209.1029 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0080) -pass 10: -209.0949 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0071) -pass 11: -209.0879 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0064) -pass 12: -209.0819 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) -pass 13: -209.0762 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) -pass 14: -209.0710 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) -pass 15: -209.0658 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) -pass 16: -209.0606 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) -pass 17: -209.0550 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) -pass 18: -209.0489 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) -pass 19: -209.0423 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0055) -pass 20: -209.0349 (branch= 0.0013 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) +pass 1 : -209.2605 (branch= 0.0000 alpha= 0.0678 pinv= 0.0119 eq freqs= 0.0000 rel rates= 0.0066) +pass 2 : -209.2247 (branch= 0.0171 alpha= 0.0188 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 3 : -209.1584 (branch= 0.0447 alpha= 0.0139 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0029) +pass 4 : -209.1042 (branch= 0.0278 alpha= 0.0139 pinv= 0.0006 eq freqs= 0.0040 rel rates= 0.0079) +pass 5 : -209.0705 (branch= 0.0171 alpha= 0.0065 pinv= 0.0000 eq freqs= 0.0014 rel rates= 0.0088) +pass 6 : -209.0535 (branch= 0.0083 alpha= 0.0003 pinv= 0.0000 eq freqs= 0.0012 rel rates= 0.0071) +pass 7 : -209.0438 (branch= 0.0023 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0012 rel rates= 0.0062) +pass 8 : -209.0357 (branch= 0.0020 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0056) +pass 9 : -209.0274 (branch= 0.0020 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0059) +pass 10: -209.0185 (branch= 0.0023 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0062) +pass 11: -209.0085 (branch= 0.0028 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0068) +pass 12: -208.9981 (branch= 0.0025 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0075) +pass 13: -208.9862 (branch= 0.0029 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0005 rel rates= 0.0084) +pass 14: -208.9729 (branch= 0.0033 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0006 rel rates= 0.0093) +pass 15: -208.9583 (branch= 0.0036 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0007 rel rates= 0.0102) +pass 16: -208.9425 (branch= 0.0038 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0008 rel rates= 0.0111) +pass 17: -208.9255 (branch= 0.0039 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0009 rel rates= 0.0120) +pass 18: -208.9075 (branch= 0.0038 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0130) +pass 19: -208.8892 (branch= 0.0037 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0135) +pass 20: -208.8700 (branch= 0.0036 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0143) optimization up to ... -pass 30: -208.9078 (branch= 0.0251 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0049 rel rates= 0.0960) +pass 30: -208.7099 (branch= 0.0200 alpha= 0.0000 pinv= 0.0018 eq freqs= 0.0077 rel rates= 0.1306) optimization up to ... -pass 40: -208.7374 (branch= 0.0228 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0081 rel rates= 0.1377) +pass 40: -208.6301 (branch= 0.0017 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0768) optimization up to ... -pass 50: -208.6461 (branch= 0.0028 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0016 rel rates= 0.0865) +pass 50: -208.5785 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0510) optimization up to ... -pass 60: -208.5898 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0556) +pass 60: -208.5414 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0367) optimization up to ... -pass 70: -208.5497 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0397) +pass 70: -208.5134 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0278) optimization up to ... -pass 80: -208.5198 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0297) +pass 80: -208.4917 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0215) optimization up to ... -pass 90: -208.4966 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0230) +pass 90: -208.4743 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0173) optimization up to ... -pass 100: -208.4783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0182) +pass 100: -208.4602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0140) optimization up to ... -pass 110: -208.4635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0147) +pass 110: -208.4485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0117) optimization up to ... -pass 120: -208.4511 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) +pass 120: -208.4386 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) optimization up to ... -pass 130: -208.4408 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0102) +pass 130: -208.4301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0084) optimization up to ... -pass 140: -208.4321 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0087) +pass 140: -208.4229 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0071) optimization up to ... -pass 150: -208.4246 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) +pass 150: -208.4167 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0062) optimization up to ... -pass 160: -208.4181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) +pass 160: -208.4112 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) optimization up to ... -pass 170: -208.4125 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) +pass 170: -208.4065 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... -pass 180: -208.4076 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) +pass 180: -208.4022 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0042) optimization up to ... -pass 190: -208.4033 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0043) +pass 190: -208.3984 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0038) optimization up to ... -pass 200: -208.3994 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) +pass 200: -208.3950 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... -pass 210: -208.3959 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 210: -208.3919 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... -pass 220: -208.3928 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) +pass 220: -208.3892 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... -pass 230: -208.3898 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) +pass 230: -208.3866 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 240: -208.3872 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) +pass 240: -208.3843 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... -pass 250: -208.3848 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 250: -208.3821 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 260: -208.3826 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) +pass 260: -208.3801 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 270: -208.3806 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) +pass 270: -208.3783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... -pass 280: -208.3788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3766 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 290: -208.3771 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) +pass 290: -208.3751 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 300: -208.3754 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 300: -208.3736 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... -pass 310: -208.3740 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) +pass 310: -208.3722 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 320: -208.3726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3710 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 330: -208.3713 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) +pass 330: -208.3698 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 340: -208.3700 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 340: -208.3686 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 350: -208.3689 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 350: -208.3676 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 360: -208.3678 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 360: -208.3666 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 370: -208.3668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 370: -208.3656 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 380: -208.3659 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 380: -208.3647 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 390: -208.3650 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 390: -208.3639 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 400: -208.3641 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 400: -208.3631 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 410: -208.3633 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 410: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 420: -208.3625 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 420: -208.3616 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 430: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 430: -208.3609 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 440: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 440: -208.3603 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 450: -208.3604 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 450: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 460: -208.3598 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 460: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 470: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 470: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) +pass 480: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) - optimization up to ... -pass 491: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 490: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... -Final score = -208.3584 -Time used = 0 hours, 0 minutes and 7 seconds +Final score = -208.3583 +Time used = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.675, AG = 189.304, AT = 6.999, CG = 205.533, CT = 195.564, GT = 1.000 + AC = 122.734, AG = 189.877, AT = 7.006, CG = 205.815, CT = 195.714, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2035 0.2835 + (ACGT) 0.2225 0.2906 0.2034 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 @@ -9841,11 +9891,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3584 +Replicate 1 : -208.3583 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: 122.7 189.3 6.999 205.5 195.6 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.7 189.9 7.006 205.8 195.7 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -9972,73 +10022,73 @@ Optimization precision reduced Optimizing parameters... improved 1.494 lnL Optimizing branchlengths... improved 0.350 lnL -1500 -210.9424 0.010 1230 +1500 -210.9425 0.010 1230 2000 -210.7769 0.010 1230 2500 -210.6534 0.010 1230 3000 -210.6127 0.010 1230 Reached termination condition! last topological improvement at gen 1230 -Improvement over last 500 gen = 0.03865 +Improvement over last 500 gen = 0.03867 Current score = -210.5968 Performing final optimizations... -pass 1 : -210.1948 (branch= 0.0000 alpha= 0.1301 pinv= 0.2110 eq freqs= 0.0000 rel rates= 0.0609) -pass 2 : -209.5704 (branch= 0.0039 alpha= 0.3419 pinv= 0.2425 eq freqs= 0.0034 rel rates= 0.0327) -pass 3 : -209.3335 (branch= 0.0544 alpha= 0.1398 pinv= 0.0224 eq freqs= 0.0092 rel rates= 0.0111) -pass 4 : -209.2507 (branch= 0.0578 alpha= 0.0172 pinv= 0.0013 eq freqs= 0.0022 rel rates= 0.0042) -pass 5 : -209.2005 (branch= 0.0351 alpha= 0.0090 pinv= 0.0011 eq freqs= 0.0004 rel rates= 0.0046) -pass 6 : -209.1719 (branch= 0.0156 alpha= 0.0050 pinv= 0.0004 eq freqs= 0.0005 rel rates= 0.0072) -pass 7 : -209.1457 (branch= 0.0098 alpha= 0.0033 pinv= 0.0002 eq freqs= 0.0013 rel rates= 0.0115) -pass 8 : -209.1242 (branch= 0.0072 alpha= 0.0015 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0117) -pass 9 : -209.1104 (branch= 0.0030 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0098) -pass 10: -209.1003 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0084) -pass 11: -209.0921 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0074) -pass 12: -209.0851 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065) -pass 13: -209.0788 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0059) -pass 14: -209.0733 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) -pass 15: -209.0680 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) -pass 16: -209.0632 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 17: -209.0583 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 18: -209.0534 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 19: -209.0481 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) -pass 20: -209.0424 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) - optimization up to ... -pass 30: -208.9333 (branch= 0.0198 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0039 rel rates= 0.0847) - optimization up to ... -pass 40: -208.7577 (branch= 0.0266 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1383) - optimization up to ... -pass 50: -208.6571 (branch= 0.0041 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0023 rel rates= 0.0936) - optimization up to ... -pass 60: -208.5973 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0589) +pass 1 : -210.1949 (branch= 0.0000 alpha= 0.1301 pinv= 0.2109 eq freqs= 0.0000 rel rates= 0.0609) +pass 2 : -209.5752 (branch= 0.0039 alpha= 0.3416 pinv= 0.2382 eq freqs= 0.0034 rel rates= 0.0327) +pass 3 : -209.3362 (branch= 0.0533 alpha= 0.1441 pinv= 0.0218 eq freqs= 0.0090 rel rates= 0.0108) +pass 4 : -209.2540 (branch= 0.0528 alpha= 0.0215 pinv= 0.0016 eq freqs= 0.0022 rel rates= 0.0041) +pass 5 : -209.2037 (branch= 0.0351 alpha= 0.0090 pinv= 0.0010 eq freqs= 0.0004 rel rates= 0.0048) +pass 6 : -209.1737 (branch= 0.0170 alpha= 0.0052 pinv= 0.0003 eq freqs= 0.0005 rel rates= 0.0070) +pass 7 : -209.1473 (branch= 0.0104 alpha= 0.0033 pinv= 0.0002 eq freqs= 0.0012 rel rates= 0.0111) +pass 8 : -209.1252 (branch= 0.0071 alpha= 0.0022 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0118) +pass 9 : -209.1109 (branch= 0.0034 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0099) +pass 10: -209.1007 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0084) +pass 11: -209.0923 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0074) +pass 12: -209.0852 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) +pass 13: -209.0790 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) +pass 14: -209.0734 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) +pass 15: -209.0681 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) +pass 16: -209.0633 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 17: -209.0584 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 18: -209.0535 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 19: -209.0482 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 20: -209.0425 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) + optimization up to ... +pass 30: -208.9336 (branch= 0.0198 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0039 rel rates= 0.0846) + optimization up to ... +pass 40: -208.7570 (branch= 0.0268 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0088 rel rates= 0.1390) + optimization up to ... +pass 50: -208.6569 (branch= 0.0042 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0023 rel rates= 0.0931) + optimization up to ... +pass 60: -208.5971 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0588) optimization up to ... -pass 70: -208.5553 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0416) +pass 70: -208.5550 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0417) optimization up to ... -pass 80: -208.5239 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0311) +pass 80: -208.5239 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0309) optimization up to ... -pass 90: -208.4999 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0238) +pass 90: -208.4998 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0239) optimization up to ... -pass 100: -208.4809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0189) +pass 100: -208.4809 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0188) optimization up to ... pass 110: -208.4656 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0152) optimization up to ... pass 120: -208.4529 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0126) optimization up to ... -pass 130: -208.4423 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 130: -208.4424 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... -pass 140: -208.4334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) +pass 140: -208.4333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) optimization up to ... -pass 150: -208.4257 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) +pass 150: -208.4256 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) optimization up to ... -pass 160: -208.4191 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 160: -208.4191 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... pass 170: -208.4134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... -pass 180: -208.4083 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 180: -208.4084 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4039 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... -pass 200: -208.3999 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) +pass 200: -208.4000 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... -pass 210: -208.3963 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) +pass 210: -208.3964 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3932 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... @@ -10052,7 +10102,7 @@ optimization up to ... pass 270: -208.3809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 280: -208.3790 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3791 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3773 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... @@ -10092,22 +10142,20 @@ optimization up to ... pass 470: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) - optimization up to ... -pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 480: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 492: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 490: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... -Final score = -208.3584 -Time used = 0 hours, 0 minutes and 7 seconds +Final score = -208.3585 +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.522, AG = 189.082, AT = 6.990, CG = 205.290, CT = 195.326, GT = 1.000 + AC = 121.995, AG = 188.263, AT = 6.960, CG = 204.402, CT = 194.488, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2035 0.2835 + (ACGT) 0.2225 0.2905 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 @@ -10134,11 +10182,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3584 +Replicate 1 : -208.3585 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: 122.5 189.1 6.99 205.3 195.3 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122 188.3 6.96 204.4 194.5 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -12810,6 +12858,14 @@ 500 -90.3850 0.500 215 600 -90.2906 0.500 215 700 -90.2169 0.500 215 +800 -90.1648 0.500 215 +Optimization precision reduced + Optimizing parameters... improved 0.159 lnL + Optimizing branchlengths... improved 0.317 lnL +900 -88.9507 0.010 879 +1000 -88.8871 0.010 879 +1100 -88.8475 0.010 879 +1200 -88.8463 0.010 879 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12906,18 +12962,11 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 761, seed 807911389, best lnL -90.178 +Bootstrap rep 1 (of 1) generation 1200, seed 1726644519, best lnL -88.846 gen current_lnL precision last_tree_imp -761 -90.1775 0.500 215 -800 -90.1648 0.500 215 -Optimization precision reduced - Optimizing parameters... improved 0.159 lnL - Optimizing branchlengths... improved 0.317 lnL -900 -88.9507 0.010 879 -1000 -88.8871 0.010 879 -NOTE: ****Specified generation limit (1000) reached... +1200 -88.8463 0.010 879 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -12929,41 +12978,37 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.9045 + 0.9578 with an invariant (invariable) site category, proportion estimated - 0.1355 + 0.1284 Substitution rate categories under this model: rate proportion - 0.0000 0.1355 - 0.1669 0.2882 - 0.6855 0.2882 - 2.1476 0.2882 + 0.0000 0.1284 + 0.1794 0.2905 + 0.7011 0.2905 + 2.1195 0.2905 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -88.8871 +Replicate 1 : -88.8463 Parameter estimates: alpha pinv -rep 1: 0.904 0.136 +rep 1: 0.958 0.128 Treelengths: TL -rep 1: 2.441 +rep 1: 2.338 Saving best tree to bootstrap file ch.a.G3.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf @@ -13086,6 +13131,12 @@ 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 +600 -111.7788 0.500 84 +Optimization precision reduced + Optimizing parameters... improved 0.386 lnL + Optimizing branchlengths... improved 0.390 lnL +700 -110.8142 0.010 615 +800 -110.5642 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13172,15 +13223,9 @@ STARTING RUN Restarting from checkpoint... - generation 515, seed 235243732, best lnL -111.804 + generation 864, seed 1964287180, best lnL -110.559 gen current_lnL precision last_tree_imp -515 -111.8042 0.500 84 -600 -111.7788 0.500 84 -Optimization precision reduced - Optimizing parameters... improved 0.386 lnL - Optimizing branchlengths... improved 0.390 lnL -700 -110.8142 0.010 615 -800 -110.5642 0.010 707 +864 -110.5588 0.010 707 900 -110.5555 0.010 707 1000 -110.5065 0.010 707 NOTE: ****Specified generation limit (1000) reached... @@ -13365,6 +13410,20 @@ 1400 -111.6821 0.010 563 1500 -111.6819 0.010 563 1600 -111.6818 0.010 563 +1700 -111.6818 0.010 563 +1800 -111.6818 0.010 563 +1900 -111.6818 0.010 563 +2000 -111.6817 0.010 563 +2100 -111.6817 0.010 563 +2200 -111.6817 0.010 563 +2300 -111.6817 0.010 563 +2400 -111.6817 0.010 563 +2500 -111.6817 0.010 563 +2600 -111.6816 0.010 563 +2700 -111.6816 0.010 563 +2800 -111.6816 0.010 563 +2900 -111.6815 0.010 563 +3000 -111.6815 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13450,9 +13509,9 @@ STARTING RUN Restarting from checkpoint... - generation 1613, seed 1448343071, best lnL -111.682 + generation 3048, seed 1405670355, best lnL -111.682 gen current_lnL precision last_tree_imp -1613 -111.6818 0.010 563 +3048 -111.6815 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13476,14 +13535,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6818 +Replicate 1 : -111.6815 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.606 +rep 1: 2.607 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log @@ -13614,6 +13673,13 @@ 20 -205.6892 0.500 18 30 -205.6499 0.500 18 40 -205.6371 0.500 18 +50 -205.6175 0.500 18 +60 -205.5990 0.500 53 +70 -205.5741 0.500 53 +80 -205.4022 0.500 76 +90 -205.3871 0.500 76 +100 -205.3829 0.500 76 +110 -205.3431 0.500 106 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13700,18 +13766,11 @@ STARTING RUN Restarting from checkpoint... - generation 47, seed 270655128, best lnL -205.637 + generation 119, seed 612438734, best lnL -205.343 gen current_lnL precision last_tree_imp -47 -205.6368 0.500 18 -50 -205.6175 0.500 18 -60 -205.5990 0.500 53 -70 -205.5741 0.500 53 -80 -205.4022 0.500 76 -90 -205.3871 0.500 76 -100 -205.3829 0.500 76 -NOTE: ****Specified generation limit (100) reached... +119 -205.3431 0.500 106 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates @@ -13743,17 +13802,12 @@ No branches were short enough to be collapsed. Saving site likelihoods to file ch.c.M3x2.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 : -205.3829 +Replicate 1 : -205.3431 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) @@ -13761,13 +13815,11 @@ Treelengths: TL -rep 1: 7.371 +rep 1: 7.779 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/c.conf @@ -13896,6 +13948,13 @@ 10 -195.3553 0.500 0 20 -195.3340 0.500 0 30 -195.2776 0.500 0 +40 -195.2555 0.500 0 +50 -195.2137 0.500 0 +60 -195.1629 0.500 0 +70 -195.0043 0.500 0 +80 -194.9478 0.500 0 +90 -194.9092 0.500 0 +100 -194.9092 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13983,19 +14042,11 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 34, seed 1396138699, best lnL -195.278 +Bootstrap rep 1 (of 1) generation 106, seed 1626872889, best lnL -194.909 gen current_lnL precision last_tree_imp -34 -195.2776 0.500 0 -40 -195.2555 0.500 0 -50 -195.2137 0.500 0 -60 -195.1629 0.500 0 -70 -195.0043 0.500 0 -80 -194.9478 0.500 0 -90 -194.9092 0.500 0 -100 -194.9092 0.500 0 -NOTE: ****Specified generation limit (100) reached... +106 -194.9092 0.500 0 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120505 @@ -14024,10 +14075,6 @@ No branches were short enough to be collapsed. -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - ####################################################### Completed 1 replicate search(es) (of 1). @@ -14044,7 +14091,7 @@ Saving best tree to bootstrap file ch.c.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -14208,6 +14255,19 @@ 1100 -3352.7219 0.010 0 1200 -3352.6779 0.010 0 1300 -3352.5564 0.010 0 +1400 -3352.3174 0.010 0 +1500 -3352.2778 0.010 0 +1600 -3352.1759 0.010 0 +1700 -3352.1636 0.010 0 +1800 -3352.0841 0.010 0 +1900 -3351.7369 0.010 0 +2000 -3351.6702 0.010 0 +2100 -3351.4829 0.010 0 +2200 -3351.2993 0.010 0 +2300 -3351.2513 0.010 0 +2400 -3351.2155 0.010 0 +2500 -3351.1237 0.010 0 +2600 -3351.0612 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14311,75 +14371,88 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1324, seed 969983281, best lnL -3352.545 +Search rep 1 (of 2) generation 2663, seed 1185916086, best lnL -3351.061 gen current_lnL precision last_tree_imp -1324 -3352.5453 0.010 0 -1400 -3352.3174 0.010 0 -1500 -3352.2778 0.010 0 -1600 -3352.1759 0.010 0 -1700 -3352.1636 0.010 0 -1800 -3352.0841 0.010 0 -1900 -3351.7369 0.010 0 -2000 -3351.6702 0.010 0 -2100 -3351.4829 0.010 0 -2200 -3351.2993 0.010 0 -2300 -3351.2513 0.010 0 +2663 -3351.0612 0.010 0 +2700 -3351.0610 0.010 0 +2800 -3351.0554 0.010 0 +2900 -3351.0122 0.010 0 +3000 -3351.0122 0.010 0 +3100 -3350.9995 0.010 0 +3200 -3350.9822 0.010 0 +3300 -3350.9797 0.010 0 +3400 -3350.9771 0.010 0 +3500 -3350.9769 0.010 0 +3600 -3350.9764 0.010 0 +3700 -3350.9432 0.010 0 +3800 -3350.9290 0.010 0 +3900 -3350.8687 0.010 0 +4000 -3350.8687 0.010 0 +4100 -3350.8589 0.010 0 +4200 -3350.8534 0.010 0 +4300 -3350.8532 0.010 0 +4400 -3350.8506 0.010 0 +4500 -3350.8506 0.010 0 +4600 -3350.8163 0.010 0 +4700 -3350.8150 0.010 0 +4800 -3350.8148 0.010 0 +4900 -3350.8148 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.2511 +Current score = -3350.8148 Performing final optimizations... -pass 1 : -3351.0980 (branch= 0.0000 alpha= 0.0293 pinv= 0.0165 eq freqs= 0.0245 rel rates= 0.0701 subset rates= 0.0127) -pass 2 : -3350.9809 (branch= 0.0105 alpha= 0.0099 pinv= 0.0177 eq freqs= 0.0000 rel rates= 0.0777 subset rates= 0.0013) -pass 3 : -3350.8827 (branch= 0.0109 alpha= 0.0148 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.0545 subset rates= 0.0021) -pass 4 : -3350.8009 (branch= 0.0077 alpha= 0.0136 pinv= 0.0148 eq freqs= 0.0007 rel rates= 0.0434 subset rates= 0.0016) -pass 5 : -3350.7309 (branch= 0.0052 alpha= 0.0117 pinv= 0.0137 eq freqs= 0.0000 rel rates= 0.0380 subset rates= 0.0012) -pass 6 : -3350.6702 (branch= 0.0032 alpha= 0.0119 pinv= 0.0126 eq freqs= 0.0004 rel rates= 0.0326 subset rates= 0.0000) -pass 7 : -3350.6151 (branch= 0.0008 alpha= 0.0115 pinv= 0.0114 eq freqs= 0.0000 rel rates= 0.0298 subset rates= 0.0016) -pass 8 : -3350.5677 (branch= 0.0015 alpha= 0.0105 pinv= 0.0104 eq freqs= 0.0002 rel rates= 0.0248 subset rates= 0.0000) -pass 9 : -3350.5252 (branch= 0.0002 alpha= 0.0097 pinv= 0.0094 eq freqs= 0.0000 rel rates= 0.0221 subset rates= 0.0011) -pass 10: -3350.4879 (branch= 0.0011 alpha= 0.0088 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0182 subset rates= 0.0000) -pass 11: -3350.4560 (branch= 0.0002 alpha= 0.0079 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0162 subset rates= 0.0000) -pass 12: -3350.4273 (branch= 0.0000 alpha= 0.0075 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0142 subset rates= 0.0000) -pass 13: -3350.4021 (branch= 0.0000 alpha= 0.0068 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0122 subset rates= 0.0000) -pass 14: -3350.3800 (branch= 0.0000 alpha= 0.0061 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0104 subset rates= 0.0000) -pass 15: -3350.3607 (branch= 0.0000 alpha= 0.0055 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0089 subset rates= 0.0000) -pass 16: -3350.3438 (branch= 0.0000 alpha= 0.0049 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0077 subset rates= 0.0000) -pass 17: -3350.3291 (branch= 0.0000 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0065 subset rates= 0.0000) -pass 18: -3350.3163 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0056 subset rates= 0.0000) -pass 19: -3350.3051 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0048 subset rates= 0.0000) -pass 20: -3350.2954 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2472 (branch= 0.0000 alpha= 0.0147 pinv= 0.0133 eq freqs= 0.0001 rel rates= 0.0200 subset rates= 0.0000) +pass 1 : -3350.7629 (branch= 0.0000 alpha= 0.0000 pinv= 0.0239 eq freqs= 0.0001 rel rates= 0.0280 subset rates= 0.0000) +pass 2 : -3350.7186 (branch= 0.0000 alpha= 0.0109 pinv= 0.0167 eq freqs= 0.0000 rel rates= 0.0156 subset rates= 0.0011) +pass 3 : -3350.6627 (branch= 0.0082 alpha= 0.0168 pinv= 0.0145 eq freqs= 0.0000 rel rates= 0.0153 subset rates= 0.0011) +pass 4 : -3350.6102 (branch= 0.0070 alpha= 0.0124 pinv= 0.0138 eq freqs= 0.0015 rel rates= 0.0169 subset rates= 0.0010) +pass 5 : -3350.5655 (branch= 0.0053 alpha= 0.0117 pinv= 0.0127 eq freqs= 0.0000 rel rates= 0.0139 subset rates= 0.0010) +pass 6 : -3350.5270 (branch= 0.0035 alpha= 0.0110 pinv= 0.0116 eq freqs= 0.0000 rel rates= 0.0125 subset rates= 0.0000) +pass 7 : -3350.4917 (branch= 0.0006 alpha= 0.0106 pinv= 0.0105 eq freqs= 0.0000 rel rates= 0.0120 subset rates= 0.0016) +pass 8 : -3350.4610 (branch= 0.0016 alpha= 0.0097 pinv= 0.0095 eq freqs= 0.0001 rel rates= 0.0099 subset rates= 0.0000) +pass 9 : -3350.4340 (branch= 0.0002 alpha= 0.0089 pinv= 0.0085 eq freqs= 0.0000 rel rates= 0.0093 subset rates= 0.0000) +pass 10: -3350.4093 (branch= 0.0001 alpha= 0.0086 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0084 subset rates= 0.0000) +pass 11: -3350.3864 (branch= 0.0001 alpha= 0.0077 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0072 subset rates= 0.0010) +pass 12: -3350.3672 (branch= 0.0008 alpha= 0.0065 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) +pass 13: -3350.3506 (branch= 0.0001 alpha= 0.0057 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0052 subset rates= 0.0000) +pass 14: -3350.3356 (branch= 0.0000 alpha= 0.0054 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0047 subset rates= 0.0000) +pass 15: -3350.3222 (branch= 0.0000 alpha= 0.0049 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 16: -3350.3105 (branch= 0.0000 alpha= 0.0043 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) +pass 17: -3350.3001 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) +pass 18: -3350.2911 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0027 subset rates= 0.0000) +pass 19: -3350.2832 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) +pass 20: -3350.2763 (branch= 0.0000 alpha= 0.0026 pinv= 0.0023 eq freqs= 0.0000 rel rates= 0.0020 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2424 (branch= 0.0000 alpha= 0.0127 pinv= 0.0115 eq freqs= 0.0000 rel rates= 0.0097 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2363 (branch= 0.0000 alpha= 0.0032 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0047 subset rates= 0.0000) +pass 40: -3350.2349 (branch= 0.0000 alpha= 0.0027 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2339 (branch= 0.0000 alpha= 0.0006 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0012 subset rates= 0.0000) +pass 50: -3350.2334 (branch= 0.0000 alpha= 0.0005 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 60: -3350.2331 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 69: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 64: -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 = -3350.2334 -Time used so far = 0 hours, 0 minutes and 13 seconds +Final score = -3350.2331 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.113, AG = 10.404, AT = 2.686, CG = 0.001, CT = 21.876, GT = 1.000 + AC = 3.116, AG = 10.423, AT = 2.692, CG = 0.001, CT = 21.943, 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 - 0.5784 + 0.5768 with an invariant (invariable) site category, proportion estimated - 0.3659 + 0.3654 Substitution rate categories under this model: rate proportion - 0.0000 0.3659 - 0.0487 0.1585 - 0.3001 0.1585 - 0.8699 0.1585 - 2.7814 0.1585 + 0.0000 0.3654 + 0.0484 0.1586 + 0.2991 0.1586 + 0.8690 0.1586 + 2.7835 0.1586 Model 2 Number of states = 2 (binary data) @@ -14404,20 +14477,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2334 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.113 10.4 2.686 0.001 21.88 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.116 10.42 2.692 0.001 21.94 1 0.333 0.222 0.157 0.288 0.577 0.365 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.788 1.820 0.180 +rep 1: 0.789 1.821 0.179 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -14567,6 +14640,13 @@ 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 +500 -3323.6818 0.500 1 +600 -3323.3459 0.500 1 +Optimization precision reduced + Optimizing parameters... improved 1.812 lnL + Optimizing branchlengths... improved 0.023 lnL +700 -3321.3649 0.255 1 +800 -3321.0294 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14667,74 +14747,77 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 434, seed 234137079, best lnL -3323.902 +Search rep 1 (of 2) generation 858, seed 758392478, best lnL -3321.014 gen current_lnL precision last_tree_imp -434 -3323.9019 0.500 1 -500 -3323.6818 0.500 1 -600 -3323.3459 0.500 1 +858 -3321.0142 0.255 1 +900 -3321.0142 0.255 1 +1000 -3320.9667 0.255 1 +1100 -3320.8654 0.255 1 Optimization precision reduced - Optimizing parameters... improved 1.812 lnL - Optimizing branchlengths... improved 0.023 lnL -700 -3321.3649 0.255 1 -800 -3321.0294 0.255 1 + Optimizing parameters... improved 0.576 lnL + Optimizing branchlengths... improved 0.057 lnL +1200 -3320.1587 0.010 1 +1300 -3320.0989 0.010 1 +1400 -3320.0706 0.010 1 +1500 -3320.0213 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3321.0142 +Current score = -3320.0123 Performing final optimizations... -pass 1 : -3320.3940 (branch= 0.0389 alpha= 0.0000 pinv= 0.0127 eq freqs= 0.0124 rel rates= 0.5392 ins/del rates= 0.0170) -pass 2 : -3319.9303 (branch= 0.0587 alpha= 0.0040 pinv= 0.0163 eq freqs= 0.0045 rel rates= 0.3634 ins/del rates= 0.0168) -pass 3 : -3319.5727 (branch= 0.0425 alpha= 0.0109 pinv= 0.0156 eq freqs= 0.0060 rel rates= 0.2688 ins/del rates= 0.0138) -pass 4 : -3319.2837 (branch= 0.0315 alpha= 0.0099 pinv= 0.0153 eq freqs= 0.0018 rel rates= 0.2191 ins/del rates= 0.0115) -pass 5 : -3319.0435 (branch= 0.0214 alpha= 0.0087 pinv= 0.0147 eq freqs= 0.0009 rel rates= 0.1856 ins/del rates= 0.0087) -pass 6 : -3318.8454 (branch= 0.0132 alpha= 0.0111 pinv= 0.0138 eq freqs= 0.0010 rel rates= 0.1538 ins/del rates= 0.0053) -pass 7 : -3318.6809 (branch= 0.0094 alpha= 0.0094 pinv= 0.0132 eq freqs= 0.0007 rel rates= 0.1278 ins/del rates= 0.0039) -pass 8 : -3318.5458 (branch= 0.0061 alpha= 0.0102 pinv= 0.0122 eq freqs= 0.0003 rel rates= 0.1036 ins/del rates= 0.0026) -pass 9 : -3318.4330 (branch= 0.0040 alpha= 0.0099 pinv= 0.0113 eq freqs= 0.0003 rel rates= 0.0856 ins/del rates= 0.0017) -pass 10: -3318.3375 (branch= 0.0026 alpha= 0.0095 pinv= 0.0110 eq freqs= 0.0002 rel rates= 0.0709 ins/del rates= 0.0011) -pass 11: -3318.2590 (branch= 0.0017 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0574 ins/del rates= 0.0007) -pass 12: -3318.1931 (branch= 0.0011 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0470 ins/del rates= 0.0005) -pass 13: -3318.1370 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0392 ins/del rates= 0.0003) -pass 14: -3318.0890 (branch= 0.0005 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0327 ins/del rates= 0.0002) -pass 15: -3318.0485 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0268 ins/del rates= 0.0001) -pass 16: -3318.0137 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0225 ins/del rates= 0.0001) -pass 17: -3317.9836 (branch= 0.0001 alpha= 0.0055 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0191 ins/del rates= 0.0000) -pass 18: -3317.9574 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0163 ins/del rates= 0.0000) -pass 19: -3317.9347 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0139 ins/del rates= 0.0000) -pass 20: -3317.9151 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0119 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8172 (branch= 0.0001 alpha= 0.0216 pinv= 0.0199 eq freqs= 0.0001 rel rates= 0.0562 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7939 (branch= 0.0001 alpha= 0.0054 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0129 ins/del rates= 0.0000) +pass 1 : -3319.5850 (branch= 0.0156 alpha= 0.0000 pinv= 0.0136 eq freqs= 0.0000 rel rates= 0.3437 ins/del rates= 0.0543) +pass 2 : -3319.2796 (branch= 0.0317 alpha= 0.0164 pinv= 0.0158 eq freqs= 0.0097 rel rates= 0.2223 ins/del rates= 0.0095) +pass 3 : -3319.0488 (branch= 0.0289 alpha= 0.0140 pinv= 0.0153 eq freqs= 0.0000 rel rates= 0.1665 ins/del rates= 0.0061) +pass 4 : -3318.8659 (branch= 0.0166 alpha= 0.0108 pinv= 0.0148 eq freqs= 0.0022 rel rates= 0.1332 ins/del rates= 0.0054) +pass 5 : -3318.7048 (branch= 0.0129 alpha= 0.0113 pinv= 0.0140 eq freqs= 0.0011 rel rates= 0.1173 ins/del rates= 0.0045) +pass 6 : -3318.5751 (branch= 0.0079 alpha= 0.0112 pinv= 0.0131 eq freqs= 0.0005 rel rates= 0.0936 ins/del rates= 0.0033) +pass 7 : -3318.4652 (branch= 0.0052 alpha= 0.0104 pinv= 0.0123 eq freqs= 0.0006 rel rates= 0.0793 ins/del rates= 0.0022) +pass 8 : -3318.3708 (branch= 0.0034 alpha= 0.0103 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0677 ins/del rates= 0.0015) +pass 9 : -3318.2900 (branch= 0.0027 alpha= 0.0092 pinv= 0.0105 eq freqs= 0.0001 rel rates= 0.0572 ins/del rates= 0.0011) +pass 10: -3318.2209 (branch= 0.0017 alpha= 0.0090 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0480 ins/del rates= 0.0008) +pass 11: -3318.1619 (branch= 0.0011 alpha= 0.0085 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0401 ins/del rates= 0.0005) +pass 12: -3318.1113 (branch= 0.0007 alpha= 0.0079 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0336 ins/del rates= 0.0003) +pass 13: -3318.0684 (branch= 0.0004 alpha= 0.0074 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0275 ins/del rates= 0.0002) +pass 14: -3318.0315 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0232 ins/del rates= 0.0001) +pass 15: -3317.9994 (branch= 0.0002 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0198 ins/del rates= 0.0001) +pass 16: -3317.9715 (branch= 0.0001 alpha= 0.0055 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0169 ins/del rates= 0.0000) +pass 17: -3317.9472 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0145 ins/del rates= 0.0000) +pass 18: -3317.9261 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0123 ins/del rates= 0.0000) +pass 19: -3317.9077 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0106 ins/del rates= 0.0000) +pass 20: -3317.8917 (branch= 0.0000 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0090 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8117 (branch= 0.0001 alpha= 0.0190 pinv= 0.0175 eq freqs= 0.0001 rel rates= 0.0434 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7926 (branch= 0.0001 alpha= 0.0047 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0100 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7886 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0031 ins/del rates= 0.0000) +pass 50: -3317.7882 (branch= 0.0001 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0024 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) +pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0005 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... -pass 75: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 73: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 14 seconds +Final score = -3317.7870 +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 = 3.064, AG = 10.256, AT = 2.653, CG = 0.001, CT = 21.521, GT = 1.000 + AC = 3.068, AG = 10.268, AT = 2.657, CG = 0.001, CT = 21.552, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3328 0.2223 0.1566 0.2882 + (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5748 + 0.5750 with an invariant (invariable) site category, proportion estimated 0.3613 Substitution rate categories under this model: rate proportion 0.0000 0.3613 0.0480 0.1597 - 0.2980 0.1597 - 0.8679 0.1597 - 2.7862 0.1597 + 0.2981 0.1597 + 0.8680 0.1597 + 2.7859 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -14760,13 +14843,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.064 10.26 2.653 0.001 21.52 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.068 10.27 2.657 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -14914,6 +14997,21 @@ 4400 -210.6493 0.010 1104 4600 -210.6258 0.010 1104 4800 -210.5949 0.010 1104 +5000 -210.5740 0.010 1104 +5200 -210.5694 0.010 1104 +5400 -210.5461 0.010 1104 +5600 -210.5152 0.010 1104 +5800 -210.4823 0.010 1104 +6000 -210.4633 0.010 1104 +6200 -210.4596 0.010 1104 +6400 -210.4468 0.010 1104 +6600 -210.4214 0.010 1104 +6800 -210.3965 0.010 1104 +7000 -210.3383 0.010 1104 +7200 -210.3217 0.010 1104 +7400 -210.2807 0.010 1104 +7600 -210.2625 0.010 1104 +7800 -210.1873 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14993,37 +15091,41 @@ STARTING RUN Restarting from checkpoint... - generation 4909, seed 1433938782, best lnL -210.578 + generation 7948, seed 1271509165, best lnL -210.176 gen current_lnL precision last_tree_imp -4909 -210.5781 0.010 1104 -5000 -210.5740 0.010 1104 -5100 -210.5711 0.010 1104 -5200 -210.5694 0.010 1104 +7948 -210.1765 0.010 1104 +8000 -210.1732 0.010 1104 +8100 -210.1384 0.010 1104 +8200 -210.1282 0.010 1104 +8300 -210.1126 0.010 1104 +8400 -210.1102 0.010 1104 +8500 -210.1087 0.010 1104 +8600 -210.0895 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.04047 +Improvement over last 500 gen = 0.04891 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.798, AG = 5.231, AT = 0.196, CG = 4.937, CT = 7.821, GT = 1.000 + AC = 3.918, AG = 6.882, AT = 0.186, CG = 6.998, CT = 11.153, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2331 0.3366 0.2107 0.2196 + (ACGT) 0.2363 0.3327 0.2105 0.2206 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.2338 + 1.8479 with an invariant (invariable) site category, proportion estimated - 0.1337 + 0.1921 Substitution rate categories under this model: rate proportion - 0.0000 0.1337 - 0.2378 0.2888 - 0.7622 0.2888 - 1.9999 0.2888 + 0.0000 0.1921 + 0.3353 0.2693 + 0.8372 0.2693 + 1.8275 0.2693 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... @@ -15031,15 +15133,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.5694 +Replicate 1 : -210.0895 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: 2.798 5.231 0.1964 4.937 7.821 1 0.233 0.337 0.211 0.220 1.234 0.134 +rep 1: 3.918 6.882 0.186 6.998 11.15 1 0.236 0.333 0.210 0.221 1.848 0.192 Treelengths: TL -rep 1: 2.254 +rep 1: 2.358 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 @@ -15162,27 +15264,49 @@ 800 -169.9099 0.500 296 Optimization precision reduced Optimizing parameters... improved 2.192 lnL - Optimizing branchlengths... improved 0.321 lnL -1000 -167.2062 0.010 843 -1200 -167.1470 0.010 843 -1400 -167.0481 0.010 843 -1600 -166.9636 0.010 843 -1800 -166.8217 0.010 843 -2000 -166.6783 0.010 843 -2200 -166.5883 0.010 843 -2400 -166.4575 0.010 843 -2600 -166.3858 0.010 843 -2800 -166.3653 0.010 843 -3000 -166.3065 0.010 843 -3200 -166.2781 0.010 843 -3400 -166.2093 0.010 843 -3600 -166.0613 0.010 843 -3800 -165.9516 0.010 843 -4000 -165.8994 0.010 843 -4200 -165.8521 0.010 843 -4400 -165.7753 0.010 843 -4600 -165.6384 0.010 843 -4800 -165.6163 0.010 843 + Optimizing branchlengths... improved 0.320 lnL +1000 -167.2074 0.010 843 +1200 -167.1480 0.010 843 +1400 -167.0491 0.010 843 +1600 -166.9644 0.010 843 +1800 -166.8226 0.010 843 +2000 -166.6791 0.010 843 +2200 -166.5890 0.010 843 +2400 -166.4580 0.010 843 +2600 -166.3863 0.010 843 +2800 -166.3659 0.010 843 +3000 -166.3073 0.010 843 +3200 -166.2790 0.010 843 +3400 -166.2102 0.010 843 +3600 -166.0622 0.010 843 +3800 -165.9523 0.010 843 +4000 -165.9343 0.010 843 +4200 -165.8879 0.010 843 +4400 -165.8803 0.010 843 +4600 -165.7812 0.010 843 +4800 -165.7686 0.010 843 +5000 -165.6811 0.010 843 +5200 -165.6633 0.010 843 +5400 -165.5975 0.010 843 +5600 -165.4766 0.010 843 +5800 -165.3724 0.010 843 +6000 -165.3454 0.010 843 +6200 -165.2645 0.010 843 +6400 -165.1352 0.010 843 +6600 -165.0587 0.010 843 +6800 -165.0560 0.010 843 +7000 -164.9213 0.010 843 +7200 -164.8005 0.010 843 +7400 -164.7206 0.010 7384 +7600 -164.6623 0.010 7384 +7800 -164.5214 0.010 7384 +8000 -164.4386 0.010 7384 +8200 -164.2994 0.010 7384 +8400 -164.1764 0.010 7384 +8600 -164.1247 0.010 7384 +8800 -163.9566 0.010 7384 +9000 -163.8544 0.010 7384 +9200 -163.8481 0.010 7384 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15263,59 +15387,65 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 4984, seed 992040394, best lnL -165.579 +Bootstrap rep 1 (of 1) generation 9340, seed 100441632, best lnL -163.751 gen current_lnL precision last_tree_imp -4984 -165.5789 0.010 843 -5000 -165.5786 0.010 843 -5100 -165.5692 0.010 843 -5200 -165.5685 0.010 843 -5300 -165.5354 0.010 843 -5400 -165.5324 0.010 843 -Reached termination condition! -last topological improvement at gen 843 -Improvement over last 500 gen = 0.04861 +9340 -163.7508 0.010 7384 +9400 -163.7486 0.010 7384 +9500 -163.7091 0.010 7384 +9600 -163.6371 0.010 7384 +9700 -163.6121 0.010 7384 +9800 -163.6002 0.010 7384 +9900 -163.5966 0.010 7384 +10000 -163.5762 0.010 7384 + Optimizing parameters... improved 1.517 lnL + Optimizing branchlengths... improved 0.024 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 - AC = 0.564, AG = 6.915, AT = 0.931, CG = 2.640, CT = 13.907, GT = 1.000 + AC = 0.623, AG = 8.556, AT = 1.923, CG = 3.484, CT = 32.886, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1330 0.4081 0.2343 0.2246 + (ACGT) 0.1298 0.4236 0.2357 0.2109 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 2.0867 + 526.3244 with an invariant (invariable) site category, proportion estimated - 0.2365 + 0.3606 Substitution rate categories under this model: rate proportion - 0.0000 0.2365 - 0.3034 0.1909 - 0.6639 0.1909 - 1.0720 0.1909 - 1.9606 0.1909 + 0.0000 0.3606 + 0.9452 0.1599 + 0.9853 0.1599 + 1.0136 0.1599 + 1.0559 0.1599 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 2 branches were collapsed. + 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 : -165.5324 +Replicate 1 : -162.0354 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: 0.564 6.915 0.9307 2.64 13.91 1 0.133 0.408 0.234 0.225 2.087 0.236 +rep 1: 0.6227 8.556 1.923 3.484 32.89 1 0.130 0.424 0.236 0.211 526.324 0.361 Treelengths: TL -rep 1: 2.283 +rep 1: 3.168 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 @@ -15453,15 +15583,63 @@ 7000 -212.7024 0.010 3769 7200 -212.7024 0.010 3769 7400 -212.6754 0.010 3769 -NOTE: ****Specified time limit (5 seconds) reached... +7600 -212.6692 0.010 3769 +7800 -212.6655 0.010 3769 +8000 -212.6638 0.010 3769 +8200 -212.6580 0.010 3769 +8400 -212.6570 0.010 3769 +8600 -212.6363 0.010 3769 +8800 -212.5814 0.010 3769 +9000 -212.5438 0.010 3769 +9200 -212.5311 0.010 3769 +9400 -212.5139 0.010 3769 +9600 -212.5123 0.010 3769 +9800 -212.5095 0.010 3769 +10000 -212.5014 0.010 3769 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 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 = 7.821, AG = 15.066, AT = 0.614, CG = 15.029, CT = 9.551, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2189 0.2871 0.1831 0.3108 + Rate Heterogeneity Model: + no rate heterogeneity + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 1 branches were collapsed. + +Saving site likelihoods to file ch.n.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + +####################################################### +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -212.5014 + +Parameter estimates: + r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) +rep 1: 7.821 15.07 0.6138 15.03 9.551 1 0.219 0.287 0.183 0.311 + +Treelengths: + TL +rep 1: 1.722 + +Saving final tree from best search rep (#1) to ch.n.best.tre +Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log + +WARNING: Internal states inferred on tree from prematurely terminated search + +####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -15532,21 +15710,17 @@ STARTING RUN Restarting from checkpoint... - generation 7569, seed 1973931830, best lnL -212.673 + generation 10001, seed 1459438551, best lnL -212.501 gen current_lnL precision last_tree_imp -7569 -212.6728 0.010 3769 -7600 -212.6692 0.010 3769 -Reached termination condition! -last topological improvement at gen 3769 -Improvement over last 500 gen = 0.03320 +10001 -212.5014 0.010 3769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.421, AG = 10.376, AT = 0.430, CG = 10.583, CT = 6.839, GT = 1.000 + AC = 7.821, AG = 15.066, AT = 0.614, CG = 15.029, CT = 9.551, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2213 0.2878 0.1825 0.3084 + (ACGT) 0.2189 0.2871 0.1831 0.3108 Rate Heterogeneity Model: no rate heterogeneity @@ -15559,15 +15733,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.6692 +Replicate 1 : -212.5014 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 5.421 10.38 0.4295 10.58 6.839 1 0.221 0.288 0.182 0.308 +rep 1: 7.821 15.07 0.6138 15.03 9.551 1 0.219 0.287 0.183 0.311 Treelengths: TL -rep 1: 1.726 +rep 1: 1.722 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log @@ -15697,41 +15871,108 @@ Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL -1600 -211.2008 0.010 1502 -1800 -211.0870 0.010 1502 -2000 -210.9689 0.010 1502 +1600 -211.2006 0.010 1502 +1800 -211.0868 0.010 1502 +2000 -210.9688 0.010 1502 2200 -210.8961 0.010 1502 2400 -210.8906 0.010 1502 -2600 -210.8174 0.010 1502 -2800 -210.7848 0.010 1502 -3000 -210.7511 0.010 2883 -3200 -210.7244 0.010 2883 -3400 -210.7007 0.010 2883 -3600 -210.6994 0.010 2883 -3800 -210.6779 0.010 2883 -4000 -210.6776 0.010 2883 -4200 -210.6762 0.010 2883 -4400 -210.6528 0.010 2883 -4600 -210.6398 0.010 2883 -4800 -210.5994 0.010 4692 -5000 -210.5910 0.010 4692 -5200 -210.5711 0.010 4692 -5400 -210.5437 0.010 4692 -5600 -210.5248 0.010 4692 -5800 -210.4688 0.010 4692 -6000 -210.4351 0.010 4692 -6200 -210.4278 0.010 4692 -6400 -210.4185 0.010 4692 -6600 -210.4167 0.010 4692 -NOTE: ****Specified time limit (5 seconds) reached... +2600 -210.8172 0.010 1502 +2800 -210.7846 0.010 1502 +3000 -210.7510 0.010 2883 +3200 -210.7242 0.010 2883 +3400 -210.7005 0.010 2883 +3600 -210.6992 0.010 2883 +3800 -210.6778 0.010 2883 +4000 -210.6775 0.010 2883 +4200 -210.6761 0.010 2883 +4400 -210.6526 0.010 2883 +4600 -210.6396 0.010 2883 +4800 -210.6026 0.010 4692 +5000 -210.5940 0.010 4692 +5200 -210.5720 0.010 4692 +5400 -210.5439 0.010 5207 +5600 -210.5367 0.010 5207 +5800 -210.4677 0.010 5207 +6000 -210.4081 0.010 5812 +6200 -210.4005 0.010 5812 +6400 -210.3714 0.010 5812 +6600 -210.3661 0.010 5812 +6800 -210.3533 0.010 5812 +7000 -210.3450 0.010 5812 +7200 -210.3444 0.010 5812 +7400 -210.3290 0.010 5812 +7600 -210.3233 0.010 5812 +7800 -210.2350 0.010 7789 +8000 -210.1893 0.010 7789 +8200 -210.1873 0.010 7789 +8400 -210.1348 0.010 7789 +8600 -210.0952 0.010 7789 +8800 -210.0512 0.010 7789 +9000 -210.0080 0.010 7789 +9200 -209.9885 0.010 7789 +9400 -209.9480 0.010 7789 +9600 -209.9338 0.010 7789 +9800 -209.8897 0.010 9713 +10000 -209.8869 0.010 9713 + Optimizing parameters... improved 0.477 lnL + Optimizing branchlengths... improved 0.000 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 = 2.658, AG = 4.802, AT = 0.044, CG = 4.939, CT = 9.263, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2412 0.3354 0.2106 0.2128 + Rate Heterogeneity Model: + 4 discrete gamma distributed rate categories, alpha param estimated + 4.4382 + with an invariant (invariable) site category, proportion estimated + 0.3025 + Substitution rate categories under this model: + rate proportion + 0.0000 0.3025 + 0.4769 0.1744 + 0.7891 0.1744 + 1.0841 0.1744 + 1.6498 0.1744 + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + No branches were short enough to be 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 : -209.4100 + +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: 2.658 4.802 0.04398 4.939 9.263 1 0.241 0.335 0.211 0.213 4.438 0.302 + +Treelengths: + TL +rep 1: 2.411 + +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 + +####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -15810,36 +16051,32 @@ STARTING RUN Restarting from checkpoint... - generation 6673, seed 799091323, best lnL -210.405 + generation 10001, seed 1730967105, best lnL -209.410 gen current_lnL precision last_tree_imp -6673 -210.4049 0.010 4692 -6700 -210.4049 0.010 4692 -Reached termination condition! -last topological improvement at gen 4692 -Improvement over last 500 gen = 0.02291 +10001 -209.4100 0.010 9713 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.132, AG = 3.982, AT = 0.204, CG = 3.820, CT = 6.941, GT = 1.000 + AC = 2.658, AG = 4.802, AT = 0.044, CG = 4.939, CT = 9.263, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2412 0.3365 0.2130 0.2093 + (ACGT) 0.2412 0.3354 0.2106 0.2128 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 1.4069 + 4.4382 with an invariant (invariable) site category, proportion estimated - 0.1702 + 0.3025 Substitution rate categories under this model: rate proportion - 0.0000 0.1702 - 0.2106 0.2075 - 0.5723 0.2075 - 1.0445 0.2075 - 2.1727 0.2075 + 0.0000 0.3025 + 0.4769 0.1744 + 0.7891 0.1744 + 1.0841 0.1744 + 1.6498 0.1744 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with @@ -15852,15 +16089,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.4049 +Replicate 1 : -209.4100 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: 2.132 3.982 0.2037 3.82 6.941 1 0.241 0.336 0.213 0.209 1.407 0.170 +rep 1: 2.658 4.802 0.04398 4.939 9.263 1 0.241 0.335 0.211 0.213 4.438 0.302 Treelengths: TL -rep 1: 2.400 +rep 1: 2.411 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 @@ -16069,6 +16306,22 @@ 600 -13371.2064 0.402 0 700 -13371.0754 0.402 0 800 -13370.9489 0.402 0 +900 -13370.7802 0.402 0 +1000 -13370.6791 0.402 0 +Optimization precision reduced + Optimizing parameters... improved 0.037 lnL + Optimizing branchlengths... improved 0.000 lnL +1100 -13370.5869 0.304 0 +1200 -13370.5240 0.304 0 +1300 -13370.5103 0.304 0 +1400 -13370.5063 0.304 0 +1500 -13370.4967 0.304 0 +Optimization precision reduced + Optimizing parameters... improved 0.015 lnL + Optimizing branchlengths... improved 0.000 lnL +1600 -13370.4816 0.206 0 +1700 -13370.4688 0.206 0 +1800 -13370.4569 0.206 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16191,77 +16444,76 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 817, seed 2014270363, best lnL -13370.906 +Bootstrap rep 1 (of 1) generation 1847, seed 830528658, best lnL -13370.441 gen current_lnL precision last_tree_imp -817 -13370.9059 0.402 0 -900 -13370.7802 0.402 0 -1000 -13370.6791 0.402 0 +1847 -13370.4411 0.206 0 +1900 -13370.4339 0.206 0 +2000 -13370.4174 0.206 0 Optimization precision reduced - Optimizing parameters... improved 0.037 lnL + Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified time limit (1 seconds) reached... +NOTE: ****Specified generation limit (2000) reached... -MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.545, AG = 2.495, AT = 1.160, CG = 1.160, CT = 4.035, GT = 1.000 + AC = 1.663, AG = 2.558, AT = 1.235, CG = 1.235, CT = 4.221, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3110 0.1818 0.3061 0.2010 + (ACGT) 0.3082 0.1810 0.3087 0.2020 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3640 + 0.3662 Substitution rate categories under this model: rate proportion - 0.0119 0.2500 - 0.1544 0.2500 - 0.6892 0.2500 - 3.1446 0.2500 + 0.0122 0.2500 + 0.1561 0.2500 + 0.6919 0.2500 + 3.1398 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 2.627, AG = 4.239, AT = 0.821, CG = 4.239, CT = 2.627, GT = 1.000 + AC = 2.621, AG = 4.245, AT = 0.820, CG = 4.245, CT = 2.621, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2791 0.1777 0.1601 0.3830 + (ACGT) 0.2814 0.1768 0.1593 0.3825 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2460 + 0.2457 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0638 0.2500 - 0.4929 0.2500 - 3.4413 0.2500 + 0.0636 0.2500 + 0.4923 0.2500 + 3.4422 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.382, AT = 4.304, CG = 0.635, CT = 5.382, GT = 1.000 + AC = 1.000, AG = 5.311, AT = 4.291, CG = 0.629, CT = 5.311, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1555 0.3460 0.2769 0.2216 + (ACGT) 0.1554 0.3464 0.2763 0.2219 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1101 + 4.1264 with an invariant (invariable) site category, proportion estimated - 0.0486 + 0.0487 Substitution rate categories under this model: rate proportion - 0.0000 0.0486 - 0.4603 0.2379 - 0.7789 0.2379 - 1.0844 0.2379 - 1.6764 0.2379 + 0.0000 0.0487 + 0.4612 0.2378 + 0.7795 0.2378 + 1.0844 0.2378 + 1.6750 0.2378 Subset rate multipliers: 0.53 0.29 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. ->>>Terminated Bootstrap rep 1 (of 1) <<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -16271,25 +16523,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.5950 (TERMINATED PREMATURELY) +Replicate 1 : -13370.4112 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 1.545 2.495 1.16 1.16 4.035 1 0.311 0.182 0.306 0.201 0.364 +rep 1: 1.663 2.558 1.235 1.235 4.221 1 0.308 0.181 0.309 0.202 0.366 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.279 0.178 0.160 0.383 0.246 +rep 1: 2.621 4.245 0.8204 4.245 2.621 1 0.281 0.177 0.159 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 5.382 4.304 0.6346 5.382 1 0.156 0.346 0.277 0.222 4.110 0.049 +rep 1: 1 5.311 4.291 0.6292 5.311 1 0.155 0.346 0.276 0.222 4.126 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.772 0.530 0.285 2.185 +rep 1: 1.762 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -16487,6 +16739,117 @@ 3000 -467.7192 0.010 76 3100 -467.7187 0.010 76 3200 -467.7186 0.010 76 +3300 -467.7184 0.010 76 +3400 -467.7184 0.010 76 +Reached termination condition! +last topological improvement at gen 76 +Improvement over last 500 gen = 0.00087 +Current score = -467.7184 +Performing final optimizations... +pass 1 : -467.7136 (branch= 0.0000 subset rates= 0.0048) +pass 2 : -467.6950 (branch= 0.0186 subset rates= 0.0000) +pass 3 : -467.6931 (branch= 0.0019 subset rates= 0.0000) +pass 4 : -467.6915 (branch= 0.0015 subset rates= 0.0000) +pass 5 : -467.6847 (branch= 0.0020 subset rates= 0.0048) +pass 6 : -467.6822 (branch= 0.0024 subset rates= 0.0000) +pass 7 : -467.6815 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -467.6798 (branch= 0.0003 subset rates= 0.0013) +pass 9 : -467.6793 (branch= 0.0006 subset rates= 0.0000) +pass 10: -467.6791 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6790 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6790 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6790 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -467.6789 +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 Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.79 1.48 2.16 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=1713359200 + +Initial ln Likelihood: -593.3879 +optimizing: starting branch lengths, subset rates... +pass 1:+ 107.964 (branch= 101.79 scale= 1.42 subset rates= 4.75) +pass 2:+ 11.667 (branch= 10.49 scale= 0.04 subset rates= 1.14) +pass 3:+ 5.232 (branch= 5.12 scale= 0.00 subset rates= 0.11) +pass 4:+ 0.672 (branch= 0.66 scale= 0.01 subset rates= 0.00) +pass 5:+ 0.009 (branch= 0.01 scale= 0.00 subset rates= 0.00) +lnL after optimization: -467.8445 +gen current_lnL precision last_tree_imp +0 -467.8445 0.010 0 +100 -467.8198 0.010 0 +200 -467.8068 0.010 0 +300 -467.7949 0.010 0 +400 -467.7826 0.010 0 +500 -467.7787 0.010 0 +600 -467.7743 0.010 0 +700 -467.7597 0.010 0 +800 -467.7573 0.010 0 +900 -467.7534 0.010 0 +1000 -467.7459 0.010 0 +1100 -467.7436 0.010 0 +1200 -467.7413 0.010 0 +1300 -467.7398 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16612,121 +16975,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 3278, seed 1726912652, best lnL -467.718 -gen current_lnL precision last_tree_imp -3278 -467.7184 0.010 76 -3300 -467.7184 0.010 76 -3400 -467.7184 0.010 76 -Reached termination condition! -last topological improvement at gen 76 -Improvement over last 500 gen = 0.00087 -Current score = -467.7184 -Performing final optimizations... -pass 1 : -467.7136 (branch= 0.0000 subset rates= 0.0048) -pass 2 : -467.6950 (branch= 0.0186 subset rates= 0.0000) -pass 3 : -467.6931 (branch= 0.0019 subset rates= 0.0000) -pass 4 : -467.6915 (branch= 0.0015 subset rates= 0.0000) -pass 5 : -467.6847 (branch= 0.0020 subset rates= 0.0048) -pass 6 : -467.6822 (branch= 0.0024 subset rates= 0.0000) -pass 7 : -467.6815 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -467.6798 (branch= 0.0003 subset rates= 0.0013) -pass 9 : -467.6793 (branch= 0.0006 subset rates= 0.0000) -pass 10: -467.6791 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0004) -pass 12: -467.6783 (branch= 0.0003 subset rates= 0.0000) -pass 13: -467.6782 (branch= 0.0001 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... -Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 6 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.79 1.48 2.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=1713359200 - -Initial ln Likelihood: -593.3879 -optimizing: starting branch lengths, subset rates... -pass 1:+ 107.964 (branch= 101.79 scale= 1.42 subset rates= 4.75) -pass 2:+ 11.667 (branch= 10.49 scale= 0.04 subset rates= 1.14) -pass 3:+ 5.232 (branch= 5.12 scale= 0.00 subset rates= 0.11) -pass 4:+ 0.672 (branch= 0.66 scale= 0.01 subset rates= 0.00) -pass 5:+ 0.009 (branch= 0.01 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8445 +Search rep 2 (of 5) generation 1370, seed 359782712, best lnL -467.739 gen current_lnL precision last_tree_imp -0 -467.8445 0.010 0 -100 -467.8198 0.010 0 -200 -467.8068 0.010 0 -300 -467.7949 0.010 0 -400 -467.7826 0.010 0 -500 -467.7787 0.010 0 -600 -467.7743 0.010 0 -700 -467.7597 0.010 0 -800 -467.7573 0.010 0 -900 -467.7534 0.010 0 -1000 -467.7459 0.010 0 -1100 -467.7436 0.010 0 -1200 -467.7413 0.010 0 -1300 -467.7398 0.010 0 +1370 -467.7390 0.010 0 1400 -467.7386 0.010 0 1500 -467.7376 0.010 0 1600 -467.7371 0.010 0 @@ -16766,7 +17017,7 @@ pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 11 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16842,25 +17093,59 @@ lnL after optimization: -467.8625 gen current_lnL precision last_tree_imp 0 -467.8625 0.010 0 +100 -467.8011 0.010 75 +200 -467.7933 0.010 75 +300 -467.7853 0.010 75 +400 -467.7712 0.010 75 +500 -467.7598 0.010 75 +600 -467.7543 0.010 75 +700 -467.7490 0.010 75 +800 -467.7446 0.010 75 +900 -467.7384 0.010 75 +1000 -467.7309 0.010 75 +1100 -467.7251 0.010 75 +1200 -467.7223 0.010 75 +1300 -467.7207 0.010 75 +1400 -467.7202 0.010 75 +1500 -467.7181 0.010 75 +1600 -467.7176 0.010 75 +1700 -467.7164 0.010 75 +1800 -467.7139 0.010 75 +1900 -467.7123 0.010 75 +2000 -467.7117 0.010 75 +2100 -467.7106 0.010 75 +2200 -467.7093 0.010 75 +2300 -467.7084 0.010 75 +2400 -467.7070 0.010 75 +2500 -467.7068 0.010 75 +2600 -467.7054 0.010 75 +2700 -467.7045 0.010 75 +2800 -467.7041 0.010 75 +2900 -467.7040 0.010 75 +3000 -467.7029 0.010 75 +3100 -467.7026 0.010 75 +3200 -467.7026 0.010 75 +3300 -467.7023 0.010 75 +3400 -467.7015 0.010 75 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.8048 +Current score = -467.7014 Performing final optimizations... -pass 1 : -467.7886 (branch= 0.0142 subset rates= 0.0020) -pass 2 : -467.7189 (branch= 0.0698 subset rates= 0.0000) -pass 3 : -467.7000 (branch= 0.0184 subset rates= 0.0004) -pass 4 : -467.6890 (branch= 0.0110 subset rates= 0.0000) -pass 5 : -467.6833 (branch= 0.0057 subset rates= 0.0000) -pass 6 : -467.6814 (branch= 0.0019 subset rates= 0.0000) -pass 7 : -467.6803 (branch= 0.0011 subset rates= 0.0000) -pass 8 : -467.6798 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -467.6794 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6791 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6791 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6790 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6789 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7003 (branch= 0.0000 subset rates= 0.0011) +pass 2 : -467.6878 (branch= 0.0125 subset rates= 0.0000) +pass 3 : -467.6822 (branch= 0.0056 subset rates= 0.0000) +pass 4 : -467.6813 (branch= 0.0009 subset rates= 0.0000) +pass 5 : -467.6806 (branch= 0.0007 subset rates= 0.0000) +pass 6 : -467.6803 (branch= 0.0003 subset rates= 0.0000) +pass 7 : -467.6797 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -467.6788 (branch= 0.0006 subset rates= 0.0003) +pass 9 : -467.6786 (branch= 0.0002 subset rates= 0.0000) +pass 10: -467.6785 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6784 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6789 +Final score = -467.6784 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16889,7 +17174,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.47 2.18 + 0.79 1.47 2.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -16906,9 +17191,9 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -467.6782 +Replicate 1 : -467.6789 Replicate 2 : -467.6782 (best) (same topology as 1) -Replicate 3 : -467.6789 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 3 : -467.6784 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16923,9 +17208,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.843 0.786 1.480 2.181 +rep 1: 3.841 0.787 1.482 2.160 rep 2: 3.843 0.786 1.477 2.187 -rep 3: 3.840 0.789 1.469 2.182 +rep 3: 3.842 0.787 1.473 2.189 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -17144,7 +17429,7 @@ pass 16: -477.4317 (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 5 seconds +Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17222,6 +17507,27 @@ lnL after optimization: -477.8517 gen current_lnL precision last_tree_imp 0 -477.8517 0.010 0 +100 -477.7860 0.010 74 +200 -477.7643 0.010 74 +300 -477.7463 0.010 74 +400 -477.7402 0.010 74 +500 -477.7271 0.010 74 +600 -477.7244 0.010 74 +700 -477.7189 0.010 74 +800 -477.7180 0.010 74 +900 -477.7173 0.010 74 +1000 -477.7111 0.010 74 +1100 -477.7093 0.010 74 +1200 -477.7091 0.010 74 +1300 -477.7049 0.010 74 +1400 -477.7022 0.010 74 +1500 -477.6989 0.010 74 +1600 -477.6967 0.010 74 +1700 -477.6956 0.010 74 +1800 -477.6946 0.010 74 +1900 -477.6945 0.010 74 +2000 -477.6902 0.010 74 +2100 -477.6899 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17347,30 +17653,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 61, seed 1574185769, best lnL -477.832 +Search rep 2 (of 5) generation 2109, seed 1457716791, best lnL -477.690 gen current_lnL precision last_tree_imp -61 -477.8319 0.010 0 -100 -477.7860 0.010 74 -200 -477.7643 0.010 74 -300 -477.7463 0.010 74 -400 -477.7402 0.010 74 -500 -477.7271 0.010 74 -600 -477.7244 0.010 74 -700 -477.7189 0.010 74 -800 -477.7180 0.010 74 -900 -477.7173 0.010 74 -1000 -477.7111 0.010 74 -1100 -477.7093 0.010 74 -1200 -477.7091 0.010 74 -1300 -477.7049 0.010 74 -1400 -477.7022 0.010 74 -1500 -477.6989 0.010 74 -1600 -477.6967 0.010 74 -1700 -477.6956 0.010 74 -1800 -477.6946 0.010 74 -1900 -477.6945 0.010 74 -2000 -477.6902 0.010 74 -2100 -477.6899 0.010 74 +2109 -477.6899 0.010 74 2200 -477.6898 0.010 74 2300 -477.6894 0.010 74 2400 -477.6889 0.010 74 @@ -17386,30 +17671,163 @@ 3400 -477.6806 0.010 74 3500 -477.6782 0.010 74 3600 -477.6776 0.010 74 +3700 -477.5167 0.010 3640 +3800 -477.5121 0.010 3640 +3900 -477.5087 0.010 3640 +4000 -477.5077 0.010 3640 +4100 -477.5055 0.010 3640 +4200 -477.5046 0.010 3640 +4300 -477.4990 0.010 3640 +4400 -477.4985 0.010 3640 +4500 -477.4959 0.010 3640 +4600 -477.4934 0.010 3640 +4700 -477.4934 0.010 3640 +4800 -477.4928 0.010 3640 +4900 -477.4905 0.010 3640 +5000 -477.4897 0.010 3640 + Optimizing parameters... improved 0.012 lnL + Optimizing branchlengths... improved 0.000 lnL +5100 -477.4735 0.010 3640 +5200 -477.4721 0.010 3640 +5300 -477.4710 0.010 3640 +5400 -477.4705 0.010 3640 +5500 -477.4701 0.010 3640 +5600 -477.4700 0.010 3640 +5700 -477.4688 0.010 3640 +5800 -477.4676 0.010 3640 +5900 -477.4659 0.010 3640 +6000 -477.4654 0.010 3640 +6100 -477.4651 0.010 3640 +6200 -477.4651 0.010 3640 +6300 -477.4647 0.010 3640 +6400 -477.4646 0.010 3640 +6500 -477.4638 0.010 3640 +6600 -477.4637 0.010 3640 +6700 -477.4633 0.010 3640 +6800 -477.4633 0.010 3640 +6900 -477.4630 0.010 3640 +7000 -477.4630 0.010 3640 +Reached termination condition! +last topological improvement at gen 3640 +Improvement over last 500 gen = 0.00082 +Current score = -477.4630 +Performing final optimizations... +pass 1 : -477.4630 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.4568 (branch= 0.0063 subset rates= 0.0000) +pass 3 : -477.4423 (branch= 0.0145 subset rates= 0.0000) +pass 4 : -477.4394 (branch= 0.0029 subset rates= 0.0000) +pass 5 : -477.4375 (branch= 0.0019 subset rates= 0.0000) +pass 6 : -477.4357 (branch= 0.0017 subset rates= 0.0000) +pass 7 : -477.4351 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -477.4343 (branch= 0.0008 subset rates= 0.0000) +pass 9 : -477.4339 (branch= 0.0004 subset rates= 0.0000) +pass 10: -477.4337 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.4336 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4335 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.4335 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4335 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4334 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.4334 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -477.4334 +Time used so far = 0 hours, 0 minutes and 11 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate 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 1.90 2.79 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 7 branches were collapsed. + +>>>Completed Search rep 2 (of 5)<<< + +>>>Search rep 3 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate 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=142730073 + +Initial ln Likelihood: -629.9190 +optimizing: starting branch lengths, subset rates... +pass 1:+ 130.937 (branch= 120.28 scale= 1.19 subset rates= 9.47) +pass 2:+ 17.167 (branch= 13.05 scale= 0.01 subset rates= 4.10) +pass 3:+ 3.157 (branch= 1.89 scale= 0.00 subset rates= 1.27) +pass 4:+ 0.670 (branch= 0.38 scale= 0.01 subset rates= 0.28) +pass 5:+ 0.070 (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: -477.9174 +gen current_lnL precision last_tree_imp +0 -477.9174 0.010 0 +100 -477.8787 0.010 0 +200 -477.8578 0.010 0 +300 -477.8324 0.010 0 +400 -477.5256 0.010 400 +500 -477.3126 0.010 461 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.6776 +Current score = -477.3061 Performing final optimizations... -pass 1 : -477.6634 (branch= 0.0051 subset rates= 0.0091) -pass 2 : -477.6437 (branch= 0.0149 subset rates= 0.0048) -pass 3 : -477.6305 (branch= 0.0132 subset rates= 0.0000) -pass 4 : -477.6248 (branch= 0.0057 subset rates= 0.0000) -pass 5 : -477.6233 (branch= 0.0015 subset rates= 0.0000) -pass 6 : -477.6210 (branch= 0.0022 subset rates= 0.0000) -pass 7 : -477.6192 (branch= 0.0019 subset rates= 0.0000) -pass 8 : -477.6184 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -477.6180 (branch= 0.0004 subset rates= 0.0000) -pass 10: -477.6178 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.6177 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.6176 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.6176 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.6170 (branch= 0.0000 subset rates= 0.0006) -pass 15: -477.6168 (branch= 0.0001 subset rates= 0.0000) -pass 16: -477.6168 (branch= 0.0000 subset rates= 0.0000) -pass 17: -477.6167 (branch= 0.0000 subset rates= 0.0000) -pass 18: -477.6167 (branch= 0.0000 subset rates= 0.0000) -pass 19: -477.6167 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2818 (branch= 0.0192 subset rates= 0.0050) +pass 2 : -477.2455 (branch= 0.0331 subset rates= 0.0033) +pass 3 : -477.2291 (branch= 0.0145 subset rates= 0.0018) +pass 4 : -477.2155 (branch= 0.0136 subset rates= 0.0000) +pass 5 : -477.2079 (branch= 0.0076 subset rates= 0.0000) +pass 6 : -477.2056 (branch= 0.0019 subset rates= 0.0004) +pass 7 : -477.2049 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -477.2047 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -477.2045 (branch= 0.0002 subset rates= 0.0000) +pass 10: -477.2044 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2044 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2044 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.6167 +Final score = -477.2044 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17438,11 +17856,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.74 + 0.64 1.93 2.63 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 2 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -17450,13 +17868,14 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -477.4316 (best) -Replicate 2 : -477.6167 (TERMINATED PREMATURELY) +Replicate 1 : -477.4316 +Replicate 2 : -477.4334 (same topology as 1) +Replicate 3 : -477.2044 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17472,9 +17891,10 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.918 2.736 -rep 2: 4.894 0.633 1.910 2.739 +rep 2: 4.933 0.631 1.902 2.786 +rep 3: 4.695 0.635 1.934 2.627 -Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre +Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf @@ -17677,6 +18097,101 @@ 3500 -425.5842 0.010 365 3600 -425.5840 0.010 365 3700 -425.5839 0.010 365 +3800 -425.5838 0.010 365 +3900 -425.5838 0.010 365 +Reached termination condition! +last topological improvement at gen 365 +Improvement over last 500 gen = 0.00044 +Current score = -425.5838 +Performing final optimizations... +pass 1 : -425.5746 (branch= 0.0000 subset rates= 0.0092) +pass 2 : -425.5588 (branch= 0.0144 subset rates= 0.0014) +pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0002) +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 : -425.5490 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5487 (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 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 1.12 +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:+ 1.685 (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: -439.2273 +gen current_lnL precision last_tree_imp +0 -439.2273 0.010 0 +100 -428.8676 0.010 98 +200 -428.0498 0.010 164 +300 -427.6002 0.010 249 +400 -427.5648 0.010 249 +500 -427.4910 0.010 499 +600 -427.3863 0.010 511 +700 -425.7187 0.010 668 +800 -425.6950 0.010 722 +900 -425.6794 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 -425.6342 0.010 722 +1600 -425.6274 0.010 722 +1700 -425.6240 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17805,31 +18320,48 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3795, seed 1768444270, best lnL -425.584 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1702, seed 608470576, best lnL -425.624 gen current_lnL precision last_tree_imp -3795 -425.5838 0.010 365 -3800 -425.5838 0.010 365 -3900 -425.5838 0.010 365 +1702 -425.6240 0.010 722 +1800 -425.6236 0.010 722 +1900 -425.6226 0.010 722 +2000 -425.6202 0.010 722 +2100 -425.6197 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 -425.6074 0.010 722 +3000 -425.6059 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 365 -Improvement over last 500 gen = 0.00044 -Current score = -425.5838 +last topological improvement at gen 722 +Improvement over last 500 gen = 0.00085 +Current score = -425.6048 Performing final optimizations... -pass 1 : -425.5804 (branch= 0.0000 subset rates= 0.0033) -pass 2 : -425.5633 (branch= 0.0144 subset rates= 0.0027) -pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0047) -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 : -425.5490 (branch= 0.0004 subset rates= 0.0000) +pass 1 : -425.5761 (branch= 0.0000 subset rates= 0.0286) +pass 2 : -425.5574 (branch= 0.0188 subset rates= 0.0000) +pass 3 : -425.5532 (branch= 0.0041 subset rates= 0.0000) +pass 4 : -425.5520 (branch= 0.0012 subset rates= 0.0000) +pass 5 : -425.5503 (branch= 0.0016 subset rates= 0.0000) +pass 6 : -425.5498 (branch= 0.0005 subset rates= 0.0000) +pass 7 : -425.5490 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -425.5490 (branch= 0.0000 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) -pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.5486 (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 6 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17859,85 +18391,76 @@ Subset rate multipliers: 0.87 1.53 1.12 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 2 (of 5)<<< ->>>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=222492842 +Starting with seed=2129292874 -Initial ln Likelihood: -586.0233 +Initial ln Likelihood: -588.2493 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:+ 1.685 (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: -439.2273 +pass 1:+ 141.030 (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:+ 0.061 (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: -439.5713 gen current_lnL precision last_tree_imp -0 -439.2273 0.010 0 -100 -428.8676 0.010 98 -200 -428.0498 0.010 164 -300 -427.6002 0.010 249 -400 -427.5648 0.010 249 -500 -427.4910 0.010 499 -600 -427.3863 0.010 511 -700 -425.7187 0.010 668 -800 -425.6950 0.010 722 -900 -425.6794 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 -425.6342 0.010 722 -1600 -425.6274 0.010 722 -1700 -425.6240 0.010 722 -1800 -425.6236 0.010 722 -1900 -425.6226 0.010 722 -2000 -425.6202 0.010 722 -2100 -425.6197 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 -425.6074 0.010 722 -3000 -425.6059 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 +0 -439.5713 0.010 0 +100 -431.1390 0.010 95 +200 -428.6585 0.010 167 +300 -427.6515 0.010 295 +400 -427.2440 0.010 295 +500 -427.2139 0.010 295 +600 -427.1679 0.010 568 +700 -427.1487 0.010 568 +800 -425.4818 0.010 762 +900 -425.4264 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 +1500 -425.3865 0.010 803 +1600 -425.3820 0.010 803 +1700 -425.3760 0.010 803 +1800 -425.3758 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 -425.3629 0.010 803 +2600 -425.3622 0.010 803 +2700 -425.3619 0.010 803 +2800 -425.3613 0.010 803 +2900 -425.3592 0.010 803 +3000 -425.3583 0.010 803 +3100 -425.3581 0.010 803 +3200 -425.3571 0.010 803 +3300 -425.3567 0.010 803 +3400 -425.3566 0.010 803 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.6049 +Current score = -425.3565 Performing final optimizations... -pass 1 : -425.5764 (branch= 0.0000 subset rates= 0.0284) -pass 2 : -425.5576 (branch= 0.0188 subset rates= 0.0000) -pass 3 : -425.5535 (branch= 0.0041 subset rates= 0.0000) -pass 4 : -425.5523 (branch= 0.0012 subset rates= 0.0000) -pass 5 : -425.5506 (branch= 0.0017 subset rates= 0.0000) -pass 6 : -425.5502 (branch= 0.0005 subset rates= 0.0000) -pass 7 : -425.5494 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -425.5491 (branch= 0.0003 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: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.3525 (branch= 0.0000 subset rates= 0.0040) +pass 2 : -425.3313 (branch= 0.0200 subset rates= 0.0012) +pass 3 : -425.3251 (branch= 0.0062 subset rates= 0.0000) +pass 4 : -425.3232 (branch= 0.0019 subset rates= 0.0000) +pass 5 : -425.3228 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -425.3221 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -425.3211 (branch= 0.0010 subset rates= 0.0000) +pass 8 : -425.3207 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -425.3205 (branch= 0.0002 subset rates= 0.0000) +pass 10: -425.3204 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.3204 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3204 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3204 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.5487 +Final score = -425.3204 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17966,11 +18489,11 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.53 1.12 + 0.86 1.54 1.16 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -17978,13 +18501,14 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -425.5486 (best) -Replicate 2 : -425.5487 (TERMINATED PREMATURELY) +Replicate 1 : -425.5486 +Replicate 2 : -425.5486 +Replicate 3 : -425.3204 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17999,11 +18523,13 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.038 0.868 1.529 1.123 -rep 2: 3.039 0.869 1.525 1.121 +rep 1: 3.039 0.869 1.528 1.122 +rep 2: 3.037 0.868 1.532 1.121 +rep 3: 2.978 0.865 1.536 1.156 -Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf @@ -18197,6 +18723,114 @@ 2800 -473.9779 0.010 653 2900 -473.9777 0.010 653 3000 -473.9777 0.010 653 +3100 -473.9773 0.010 653 +3200 -473.9772 0.010 653 +3300 -473.9771 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00088 +Current score = -473.9771 +Performing final optimizations... +pass 1 : -473.9742 (branch= 0.0000 subset rates= 0.0029) +pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9548 (branch= 0.0011 subset rates= 0.0000) +pass 5 : -473.9529 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -473.9525 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -473.9517 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -473.9513 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -473.9511 (branch= 0.0003 subset rates= 0.0000) +pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9510 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9509 +Time used so far = 0 hours, 0 minutes and 4 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate 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 2.82 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=2125680066 + +Initial ln Likelihood: -649.8224 +optimizing: starting branch lengths, subset rates... +pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) +pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) +pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) +pass 4:+ 2.344 (branch= 1.67 scale= 0.00 subset rates= 0.67) +pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) +pass 6:+ 0.135 (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: -474.8070 +gen current_lnL precision last_tree_imp +0 -474.8070 0.010 0 +100 -474.7912 0.010 0 +200 -474.7022 0.010 123 +300 -474.5643 0.010 272 +400 -474.5191 0.010 272 +500 -474.5075 0.010 272 +600 -474.5034 0.010 272 +700 -474.4997 0.010 272 +800 -474.4937 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18322,117 +18956,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 3057, seed 1295128740, best lnL -473.977 +Search rep 2 (of 5) generation 889, seed 392123304, best lnL -474.492 gen current_lnL precision last_tree_imp -3057 -473.9773 0.010 653 -3100 -473.9773 0.010 653 -3200 -473.9772 0.010 653 -3300 -473.9771 0.010 653 -Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00088 -Current score = -473.9771 -Performing final optimizations... -pass 1 : -473.9742 (branch= 0.0000 subset rates= 0.0029) -pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0000) -pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9548 (branch= 0.0011 subset rates= 0.0000) -pass 5 : -473.9529 (branch= 0.0018 subset rates= 0.0000) -pass 6 : -473.9525 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -473.9517 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -473.9513 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9511 (branch= 0.0003 subset rates= 0.0000) -pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9510 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9509 -Time used so far = 0 hours, 0 minutes and 6 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 2.82 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=2125680066 - -Initial ln Likelihood: -649.8224 -optimizing: starting branch lengths, subset rates... -pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) -pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) -pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) -pass 4:+ 2.344 (branch= 1.67 scale= 0.00 subset rates= 0.67) -pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) -pass 6:+ 0.135 (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: -474.8070 -gen current_lnL precision last_tree_imp -0 -474.8070 0.010 0 -100 -474.7912 0.010 0 -200 -474.7022 0.010 123 -300 -474.5643 0.010 272 -400 -474.5191 0.010 272 -500 -474.5075 0.010 272 -600 -474.5034 0.010 272 -700 -474.4997 0.010 272 -800 -474.4937 0.010 272 +889 -474.4918 0.010 272 900 -474.4914 0.010 272 1000 -474.4880 0.010 272 1100 -474.4855 0.010 272 @@ -18451,26 +18977,53 @@ 2400 -474.4765 0.010 272 2500 -474.4765 0.010 272 2600 -474.4747 0.010 272 +2700 -474.4737 0.010 272 +2800 -474.4721 0.010 272 +2900 -474.4720 0.010 272 +3000 -474.4653 0.010 272 +3100 -474.4597 0.010 272 +3200 -474.4561 0.010 272 +3300 -474.4551 0.010 272 +3400 -474.4539 0.010 272 +3500 -474.4525 0.010 272 +3600 -474.4522 0.010 272 +3700 -474.4507 0.010 272 +3800 -474.4505 0.010 272 +3900 -474.4501 0.010 272 +4000 -474.4501 0.010 272 +4100 -474.4499 0.010 272 +4200 -474.4490 0.010 272 +4300 -474.4489 0.010 272 +4400 -474.4484 0.010 272 +4500 -474.4482 0.010 272 +4600 -474.4481 0.010 272 +4700 -474.4472 0.010 272 +4800 -474.4468 0.010 272 +4900 -474.4462 0.010 272 +5000 -474.4461 0.010 272 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +5100 -474.4451 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4737 +Current score = -474.4451 Performing final optimizations... -pass 1 : -474.4671 (branch= 0.0066 subset rates= 0.0000) -pass 2 : -474.4468 (branch= 0.0204 subset rates= 0.0000) -pass 3 : -474.4359 (branch= 0.0108 subset rates= 0.0000) -pass 4 : -474.4352 (branch= 0.0008 subset rates= 0.0000) -pass 5 : -474.4333 (branch= 0.0018 subset rates= 0.0000) -pass 6 : -474.4311 (branch= 0.0022 subset rates= 0.0000) -pass 7 : -474.4304 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -474.4293 (branch= 0.0012 subset rates= 0.0000) -pass 9 : -474.4288 (branch= 0.0004 subset rates= 0.0000) -pass 10: -474.4286 (branch= 0.0002 subset rates= 0.0000) -pass 11: -474.4285 (branch= 0.0001 subset rates= 0.0000) -pass 12: -474.4284 (branch= 0.0000 subset rates= 0.0000) -pass 13: -474.4284 (branch= 0.0000 subset rates= 0.0000) -pass 14: -474.4284 (branch= 0.0000 subset rates= 0.0000) -pass 15: -474.4284 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4451 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -474.4337 (branch= 0.0114 subset rates= 0.0000) +pass 3 : -474.4320 (branch= 0.0017 subset rates= 0.0000) +pass 4 : -474.4313 (branch= 0.0008 subset rates= 0.0000) +pass 5 : -474.4303 (branch= 0.0010 subset rates= 0.0000) +pass 6 : -474.4299 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -474.4291 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -474.4288 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -474.4285 (branch= 0.0003 subset rates= 0.0000) +pass 10: -474.4283 (branch= 0.0002 subset rates= 0.0000) +pass 11: -474.4282 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 13: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4281 (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 = -474.4284 +Final score = -474.4281 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18499,7 +19052,7 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.04 2.91 + 0.59 2.03 2.93 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. @@ -18517,7 +19070,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9509 (best) -Replicate 2 : -474.4284 (TERMINATED PREMATURELY) +Replicate 2 : -474.4281 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18533,7 +19086,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.351 0.587 2.065 2.818 -rep 2: 4.602 0.586 2.040 2.913 +rep 2: 4.602 0.587 2.031 2.930 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -18551,7 +19104,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j11 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j21 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/garli-2.1' Making install in src make[2]: Entering directory '/build/reproducible-path/garli-2.1/src' @@ -18601,9 +19154,9 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_i386.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_i386.deb'. -dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_i386.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-9_i386.deb'. +dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_i386.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_i386.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_i386.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_i386.changes @@ -18612,12 +19165,14 @@ 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/87288/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/87288/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/55507 and its subdirectories -I: Current time: Mon Jan 13 14:00:37 -12 2025 -I: pbuilder-time-stamp: 1736820037 +I: removing directory /srv/workspace/pbuilder/87288 and its subdirectories +I: Current time: Mon Feb 16 22:28:51 +14 2026 +I: pbuilder-time-stamp: 1771230531