Diff of the two buildlogs: -- --- b1/build.log 2025-01-10 05:31:44.226041997 +0000 +++ b2/build.log 2025-01-10 05:51:24.632106116 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 11 23:39:07 -12 2026 -I: pbuilder-time-stamp: 1770896347 +I: Current time: Fri Jan 10 19:31:49 +14 2025 +I: pbuilder-time-stamp: 1736487109 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ 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/3778595/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/128431/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 10 05:32 /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/128431/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/128431/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6e50f19ab9574441a32af298150b7f54' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3778595' - PS1='# ' - PS2='> ' + INVOCATION_ID=9ba529f41a6c461886ac8bd4555a0b80 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=128431 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.SBY6ynWv/pbuilderrc_Nfxe --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.SBY6ynWv/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.SBY6ynWv/pbuilderrc_skGW --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.SBY6ynWv/b2 --logfile b2/build.log garli_2.1-9.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3778595/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/128431/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -268,7 +300,7 @@ Get: 155 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 5.0.6-3 [1088 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] -Fetched 127 MB in 17s (7253 kB/s) +Fetched 127 MB in 6s (20.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19853 files and directories currently installed.) @@ -785,8 +817,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Feb 12 11:41:53 UTC 2026. -Universal Time is now: Thu Feb 12 11:41:53 UTC 2026. +Local time is now: Fri Jan 10 05:36:13 UTC 2025. +Universal Time is now: Fri Jan 10 05:36:13 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -940,7 +972,11 @@ 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/128431/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/128431/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 @@ -1042,8 +1078,8 @@ 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 @@ -1112,7 +1148,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j42 + make -j20 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' @@ -1138,6 +1174,10 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.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; + | ^~~ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); @@ -1145,10 +1185,6 @@ garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ -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; - | ^~~ 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, @@ -1215,37 +1251,19 @@ /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); - | ^~ -configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] - 337 | sprintf(modName, "model%d", modelNum); - | ^~~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 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 tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from adaptation.cpp: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/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: + 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 | ^~~~~~~~~~~~~~~ @@ -1283,18 +1301,16 @@ /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 | ^~~~~~~~~~~~~~~ @@ -1332,11 +1348,36 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -1346,7 +1387,7 @@ 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 adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1388,16 +1429,11 @@ 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{ | ^~~~~~~~~~~~~~~ @@ -1407,7 +1443,7 @@ 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: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1449,15 +1485,17 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from individual.cpp:28: + from configreader.cpp:30: 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 configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1495,21 +1533,22 @@ /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/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: +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 | ^~~~~~~~~~~~~~~ @@ -1525,10 +1564,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -1551,10 +1586,7 @@ /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.cpp:21: +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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1657,24 +1716,17 @@ /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/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, - from population.cpp:23: + from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1687,67 +1739,6 @@ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1773,15 +1764,11 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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{ | ^~~~~~~~~~~~~~~ @@ -1791,7 +1778,7 @@ 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 mpitrick.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1829,11 +1816,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from 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{ @@ -2548,9 +2562,49 @@ /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 configoptions.cpp:20: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': +configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 337 | sprintf(modName, "model%d", modelNum); + | ^~ +configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 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 tree.h:35, from individual.h:21, - from model.cpp:26: + from population.h:31, + from funcs.h:25, + from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2560,7 +2614,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -2598,26 +2652,9 @@ /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); - | ^~ -configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] - 337 | sprintf(modName, "model%d", modelNum); - | ^~~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 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 tree.h:35, from individual.h:21, - from population.h:31, - from garlimain.cpp:40: + from model.cpp:26: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2627,7 +2664,7 @@ 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 model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2665,26 +2702,18 @@ /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 population.h:23: +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 | ^~~~~~~~~~~~~~~ @@ -2725,18 +2754,13 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from configreader.cpp:30: + from population.cpp:45: 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 configreader.cpp:21: +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 | ^~~~~~~~~~~~~~~ @@ -2756,6 +2780,11 @@ 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 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 tree.h:24: + from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2884,18 +2913,21 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from adaptation.cpp:25: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.cpp:21: +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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2986,6 +3017,7 @@ /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/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 configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -3041,15 +3078,14 @@ /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); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': -reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 388 | fread(&unique, scalarSize, 1, in); +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 602 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In constructor 'Swap::Swap(FILE*&)': -reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 264 | fread(&count, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from treenode.h:30, - from tree.h:31: -bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': -bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': -population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1880 | fread((char *) &seed, sizeof(seed), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1887 | fread((char *) &t, sizeof(t), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(this, scalarSize, 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -3266,7 +3302,13 @@ 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 treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3282,7 +3324,14 @@ 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 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3304,7 +3353,9 @@ 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 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3320,15 +3371,7 @@ 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3341,7 +3384,16 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from configreader.cpp:18: + 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 datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3371,12 +3423,8 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h: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 datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: + from /usr/include/ncl/ncl.h:27, + from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3408,13 +3456,7 @@ 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 datamatr.cpp:20: + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3431,13 +3473,9 @@ 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 datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3450,10 +3488,7 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h: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 configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3467,8 +3502,9 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h: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: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3485,9 +3521,7 @@ 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 tree.cpp:31: + from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3504,7 +3538,9 @@ 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 population.cpp:25: + from datamatr.h:23, + from sequencedata.h:27, + from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3548,7 +3584,7 @@ # 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 -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 + make -j20 check "TESTSUITEFLAGS=-j20 --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' @@ -4135,11 +4171,11 @@ 7 8 9 10 11 Initial ln Likelihood: -225.6424 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... -pass 1:+ 10.932 (branch= 2.26 scale= 0.50 omega= 0.00 rel rates= 8.17) -pass 2:+ 0.925 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) +pass 1:+ 10.931 (branch= 2.26 scale= 0.50 omega= 0.00 rel rates= 8.17) +pass 2:+ 0.924 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.733 (branch= 0.04 scale= 0.68 omega= 0.01 rel rates= 0.00) pass 4:+ 0.015 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.00) -lnL after optimization: -213.0379 +lnL after optimization: -213.0383 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** @@ -4625,13 +4661,13 @@ 7 8 9 10 11 Initial ln Likelihood: -13699.7841 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... -pass 1:+ 209.568 (branch= 7.95 scale= 0.00 alpha= 35.56 freqs= 28.70 rel rates= 62.31 pinv= 0.00 subset rates= 75.04) -pass 2:+ 77.795 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 11.10 rel rates= 3.26 pinv= 0.90 subset rates= 56.13) -pass 3:+ 48.928 (branch= 6.87 scale= 0.74 alpha= 4.62 freqs= 1.22 rel rates= 1.34 pinv= 0.01 subset rates= 34.13) -pass 4:+ 15.208 (branch= 0.00 scale= 0.76 alpha= 0.64 freqs= 1.21 rel rates= 0.55 pinv= 0.01 subset rates= 12.03) -pass 5:+ 5.795 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.01 subset rates= 4.91) -pass 6:+ 0.129 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) -lnL after optimization: -13342.3602 +pass 1:+ 209.508 (branch= 7.95 scale= 0.00 alpha= 35.56 freqs= 28.90 rel rates= 62.03 pinv= 0.19 subset rates= 74.88) +pass 2:+ 77.016 (branch= 1.74 scale= 0.00 alpha= 4.25 freqs= 11.29 rel rates= 3.50 pinv= 0.68 subset rates= 55.55) +pass 3:+ 50.073 (branch= 8.13 scale= 0.55 alpha= 4.79 freqs= 1.15 rel rates= 1.36 pinv= 0.01 subset rates= 34.08) +pass 4:+ 16.647 (branch= 1.54 scale= 0.00 alpha= 0.63 freqs= 1.21 rel rates= 1.36 pinv= 0.01 subset rates= 11.89) +pass 5:+ 6.281 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.12 rel rates= 1.30 pinv= 0.01 subset rates= 4.84) +pass 6:+ 0.125 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) +lnL after optimization: -13340.1342 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** @@ -5928,11 +5964,11 @@ pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) -pass 5:+ 0.158 (branch= 0.12 scale= 0.00 subset rates= 0.03) +pass 5:+ 0.157 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8622 +lnL after optimization: -474.8624 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** @@ -6068,7 +6104,7 @@ 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 3 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6218,7 +6254,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6515,7 +6551,7 @@ 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 23 seconds +Time used = 0 hours, 0 minutes and 50 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6667,7 +6703,7 @@ 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 19 seconds +Time used = 0 hours, 0 minutes and 35 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6840,51 +6876,51 @@ pass 1 : -3355.4759 (branch= 0.9931 alpha= 0.0078 pinv= 0.0071 eq freqs= 0.1960 rel rates= 1.3047 subset rates= 0.3862) pass 2 : -3354.0563 (branch= 0.5298 alpha= 0.0091 pinv= 0.0117 eq freqs= 0.0207 rel rates= 0.6834 subset rates= 0.1648) pass 3 : -3353.1967 (branch= 0.2868 alpha= 0.0000 pinv= 0.0083 eq freqs= 0.0152 rel rates= 0.4605 subset rates= 0.0888) -pass 4 : -3352.5780 (branch= 0.1724 alpha= 0.0025 pinv= 0.0159 eq freqs= 0.0063 rel rates= 0.3711 subset rates= 0.0506) -pass 5 : -3352.1370 (branch= 0.0837 alpha= 0.0059 pinv= 0.0162 eq freqs= 0.0022 rel rates= 0.3000 subset rates= 0.0330) -pass 6 : -3351.7981 (branch= 0.0484 alpha= 0.0068 pinv= 0.0163 eq freqs= 0.0007 rel rates= 0.2473 subset rates= 0.0193) -pass 7 : -3351.5299 (branch= 0.0312 alpha= 0.0090 pinv= 0.0157 eq freqs= 0.0006 rel rates= 0.2003 subset rates= 0.0114) -pass 8 : -3351.3148 (branch= 0.0227 alpha= 0.0097 pinv= 0.0150 eq freqs= 0.0006 rel rates= 0.1615 subset rates= 0.0055) -pass 9 : -3351.1430 (branch= 0.0127 alpha= 0.0096 pinv= 0.0141 eq freqs= 0.0004 rel rates= 0.1311 subset rates= 0.0038) -pass 10: -3351.0014 (branch= 0.0073 alpha= 0.0104 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1071 subset rates= 0.0027) -pass 11: -3350.8848 (branch= 0.0047 alpha= 0.0103 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0870 subset rates= 0.0016) -pass 12: -3350.7880 (branch= 0.0032 alpha= 0.0098 pinv= 0.0117 eq freqs= 0.0002 rel rates= 0.0709 subset rates= 0.0009) -pass 13: -3350.7083 (branch= 0.0021 alpha= 0.0093 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0577 subset rates= 0.0000) -pass 14: -3350.6394 (branch= 0.0005 alpha= 0.0090 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0486 subset rates= 0.0011) -pass 15: -3350.5826 (branch= 0.0008 alpha= 0.0083 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0394 subset rates= 0.0000) -pass 16: -3350.5339 (branch= 0.0002 alpha= 0.0076 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0335 subset rates= 0.0000) -pass 17: -3350.4925 (branch= 0.0001 alpha= 0.0073 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0274 subset rates= 0.0000) -pass 18: -3350.4569 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0230 subset rates= 0.0000) -pass 19: -3350.4263 (branch= 0.0000 alpha= 0.0058 pinv= 0.0053 eq freqs= 0.0001 rel rates= 0.0195 subset rates= 0.0000) +pass 4 : -3352.5812 (branch= 0.1724 alpha= 0.0025 pinv= 0.0159 eq freqs= 0.0063 rel rates= 0.3678 subset rates= 0.0506) +pass 5 : -3352.1335 (branch= 0.0836 alpha= 0.0059 pinv= 0.0162 eq freqs= 0.0020 rel rates= 0.3069 subset rates= 0.0331) +pass 6 : -3351.7942 (branch= 0.0548 alpha= 0.0068 pinv= 0.0164 eq freqs= 0.0009 rel rates= 0.2446 subset rates= 0.0158) +pass 7 : -3351.5261 (branch= 0.0336 alpha= 0.0083 pinv= 0.0159 eq freqs= 0.0005 rel rates= 0.2003 subset rates= 0.0095) +pass 8 : -3351.3125 (branch= 0.0179 alpha= 0.0100 pinv= 0.0150 eq freqs= 0.0007 rel rates= 0.1629 subset rates= 0.0071) +pass 9 : -3351.1406 (branch= 0.0111 alpha= 0.0103 pinv= 0.0140 eq freqs= 0.0006 rel rates= 0.1316 subset rates= 0.0044) +pass 10: -3351.0000 (branch= 0.0073 alpha= 0.0105 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1059 subset rates= 0.0027) +pass 11: -3350.8841 (branch= 0.0049 alpha= 0.0102 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0862 subset rates= 0.0016) +pass 12: -3350.7874 (branch= 0.0028 alpha= 0.0098 pinv= 0.0116 eq freqs= 0.0002 rel rates= 0.0710 subset rates= 0.0013) +pass 13: -3350.7077 (branch= 0.0020 alpha= 0.0094 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0576 subset rates= 0.0000) +pass 14: -3350.6388 (branch= 0.0005 alpha= 0.0090 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0485 subset rates= 0.0013) +pass 15: -3350.5822 (branch= 0.0010 alpha= 0.0082 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0391 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: -3350.4924 (branch= 0.0001 alpha= 0.0072 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0274 subset rates= 0.0000) +pass 18: -3350.4568 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0230 subset rates= 0.0000) +pass 19: -3350.4263 (branch= 0.0000 alpha= 0.0059 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0193 subset rates= 0.0000) pass 20: -3350.3999 (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= 0.0753 subset rates= 0.0000) +pass 30: -3350.2718 (branch= 0.0000 alpha= 0.0276 pinv= 0.0250 eq freqs= 0.0002 rel rates= 0.0753 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2422 (branch= 0.0000 alpha= 0.0065 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0168 subset rates= 0.0000) +pass 40: -3350.2423 (branch= 0.0000 alpha= 0.0066 pinv= 0.0061 eq freqs= 0.0001 rel rates= 0.0168 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2356 (branch= 0.0000 alpha= 0.0013 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 50: -3350.2357 (branch= 0.0000 alpha= 0.0013 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) 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) +pass 60: -3350.2341 (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: -3350.2338 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 70: -3350.2339 (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= 0.0001 subset rates= 0.0000) +pass 78: -3350.2337 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2336 -Time used = 0 hours, 0 minutes and 5 seconds +Final score = -3350.2338 +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -3350.2336 +Replicate 1 : -3350.2338 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 pinv -rep 1: 3.112 10.4 2.687 0.001 21.86 1 0.333 0.222 0.157 0.288 0.580 0.366 +rep 1: 3.108 10.39 2.682 0.001 21.82 1 0.333 0.222 0.157 0.288 0.580 0.366 Partition model subset 2: Model contains no estimated parameters @@ -6897,9 +6933,9 @@ Writing optimized trees and models to scr.g.dnaBnoZ.best.all.tre ***********TEST************** -***Score is 3350.23363 +***Score is 3350.23377 ***Expected is 3350.2345 -***SCORE DIFFERENCE IS -.00087 +***SCORE DIFFERENCE IS -.00073 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaBnoZ.conf *** Running scoring test ./scoring/g.dnaMix.conf @@ -7047,28 +7083,28 @@ Performing final optimizations... pass 1 : -3329.9920 (branch= 1.3745 alpha= 0.0217 pinv= 0.0099 eq freqs= 0.2403 rel rates= 0.7561 ins/del rates= 0.0754) pass 2 : -3329.0411 (branch= 0.3511 alpha= 0.0000 pinv= 0.0096 eq freqs= 0.0000 rel rates= 0.5271 ins/del rates= 0.0631) -pass 3 : -3328.4283 (branch= 0.1466 alpha= 0.0039 pinv= 0.0146 eq freqs= 0.0187 rel rates= 0.3867 ins/del rates= 0.0424) -pass 4 : -3327.9685 (branch= 0.0855 alpha= 0.0067 pinv= 0.0148 eq freqs= 0.0031 rel rates= 0.3207 ins/del rates= 0.0290) -pass 5 : -3327.6169 (branch= 0.0530 alpha= 0.0080 pinv= 0.0147 eq freqs= 0.0017 rel rates= 0.2561 ins/del rates= 0.0181) -pass 6 : -3327.3365 (branch= 0.0344 alpha= 0.0079 pinv= 0.0146 eq freqs= 0.0008 rel rates= 0.2111 ins/del rates= 0.0115) -pass 7 : -3327.1138 (branch= 0.0219 alpha= 0.0094 pinv= 0.0140 eq freqs= 0.0007 rel rates= 0.1690 ins/del rates= 0.0077) -pass 8 : -3326.9319 (branch= 0.0143 alpha= 0.0098 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.1388 ins/del rates= 0.0051) -pass 9 : -3326.7851 (branch= 0.0094 alpha= 0.0099 pinv= 0.0125 eq freqs= 0.0004 rel rates= 0.1113 ins/del rates= 0.0034) -pass 10: -3326.6639 (branch= 0.0063 alpha= 0.0097 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0903 ins/del rates= 0.0023) -pass 11: -3326.5636 (branch= 0.0042 alpha= 0.0095 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0735 ins/del rates= 0.0015) -pass 12: -3326.4810 (branch= 0.0028 alpha= 0.0090 pinv= 0.0099 eq freqs= 0.0002 rel rates= 0.0596 ins/del rates= 0.0010) -pass 13: -3326.4117 (branch= 0.0019 alpha= 0.0085 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0490 ins/del rates= 0.0007) -pass 14: -3326.3528 (branch= 0.0013 alpha= 0.0080 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0408 ins/del rates= 0.0005) -pass 15: -3326.3023 (branch= 0.0009 alpha= 0.0074 pinv= 0.0076 eq freqs= 0.0001 rel rates= 0.0342 ins/del rates= 0.0003) -pass 16: -3326.2594 (branch= 0.0006 alpha= 0.0069 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0283 ins/del rates= 0.0002) -pass 17: -3326.2227 (branch= 0.0004 alpha= 0.0064 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0235 ins/del rates= 0.0001) -pass 18: -3326.1910 (branch= 0.0002 alpha= 0.0057 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0201 ins/del rates= 0.0001) -pass 19: -3326.1634 (branch= 0.0001 alpha= 0.0052 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0000) -pass 20: -3326.1395 (branch= 0.0001 alpha= 0.0047 pinv= 0.0045 eq freqs= 0.0000 rel rates= 0.0146 ins/del rates= 0.0000) +pass 3 : -3328.4259 (branch= 0.1466 alpha= 0.0039 pinv= 0.0146 eq freqs= 0.0186 rel rates= 0.3891 ins/del rates= 0.0424) +pass 4 : -3327.9681 (branch= 0.0854 alpha= 0.0069 pinv= 0.0148 eq freqs= 0.0031 rel rates= 0.3185 ins/del rates= 0.0290) +pass 5 : -3327.6151 (branch= 0.0531 alpha= 0.0079 pinv= 0.0147 eq freqs= 0.0016 rel rates= 0.2576 ins/del rates= 0.0180) +pass 6 : -3327.3302 (branch= 0.0345 alpha= 0.0079 pinv= 0.0146 eq freqs= 0.0008 rel rates= 0.2156 ins/del rates= 0.0116) +pass 7 : -3327.1087 (branch= 0.0219 alpha= 0.0095 pinv= 0.0140 eq freqs= 0.0008 rel rates= 0.1676 ins/del rates= 0.0077) +pass 8 : -3326.9280 (branch= 0.0143 alpha= 0.0097 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.1378 ins/del rates= 0.0051) +pass 9 : -3326.7821 (branch= 0.0094 alpha= 0.0098 pinv= 0.0125 eq freqs= 0.0004 rel rates= 0.1105 ins/del rates= 0.0034) +pass 10: -3326.6617 (branch= 0.0063 alpha= 0.0097 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0895 ins/del rates= 0.0023) +pass 11: -3326.5618 (branch= 0.0042 alpha= 0.0094 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0731 ins/del rates= 0.0016) +pass 12: -3326.4795 (branch= 0.0028 alpha= 0.0090 pinv= 0.0099 eq freqs= 0.0002 rel rates= 0.0593 ins/del rates= 0.0010) +pass 13: -3326.4105 (branch= 0.0019 alpha= 0.0085 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0488 ins/del rates= 0.0007) +pass 14: -3326.3518 (branch= 0.0013 alpha= 0.0079 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0405 ins/del rates= 0.0005) +pass 15: -3326.3015 (branch= 0.0009 alpha= 0.0074 pinv= 0.0076 eq freqs= 0.0001 rel rates= 0.0340 ins/del rates= 0.0003) +pass 16: -3326.2590 (branch= 0.0005 alpha= 0.0070 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0278 ins/del rates= 0.0002) +pass 17: -3326.2225 (branch= 0.0004 alpha= 0.0063 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0234 ins/del rates= 0.0001) +pass 18: -3326.1908 (branch= 0.0002 alpha= 0.0057 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0200 ins/del rates= 0.0001) +pass 19: -3326.1633 (branch= 0.0002 alpha= 0.0052 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0000) +pass 20: -3326.1394 (branch= 0.0001 alpha= 0.0047 pinv= 0.0045 eq freqs= 0.0000 rel rates= 0.0145 ins/del rates= 0.0000) optimization up to ... -pass 30: -3326.0197 (branch= 0.0002 alpha= 0.0262 pinv= 0.0244 eq freqs= 0.0001 rel rates= 0.0688 ins/del rates= 0.0001) +pass 30: -3326.0197 (branch= 0.0002 alpha= 0.0262 pinv= 0.0243 eq freqs= 0.0002 rel rates= 0.0687 ins/del rates= 0.0000) optimization up to ... -pass 40: -3325.9908 (branch= 0.0000 alpha= 0.0068 pinv= 0.0064 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) +pass 40: -3325.9908 (branch= 0.0001 alpha= 0.0068 pinv= 0.0063 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) optimization up to ... pass 50: -3325.9841 (branch= 0.0000 alpha= 0.0015 pinv= 0.0014 eq freqs= 0.0000 rel rates= 0.0037 ins/del rates= 0.0000) optimization up to ... @@ -7076,10 +7112,10 @@ optimization up to ... pass 70: -3325.9823 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 76: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7092,7 +7128,7 @@ 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: 3.062 10.26 2.656 0.001 21.52 1 0.333 0.222 0.157 0.288 0.574 0.361 +rep 1: 3.061 10.26 2.655 0.001 21.52 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -7108,9 +7144,9 @@ Writing optimized trees and models to scr.g.dnaMix.best.all.tre ***********TEST************** -***Score is 3325.98220 +***Score is 3325.98219 ***Expected is 3325.98222 -***SCORE DIFFERENCE IS -.00002 +***SCORE DIFFERENCE IS -.00003 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaMix.conf *** Running scoring test ./scoring/n.G4.conf @@ -7241,7 +7277,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7564,7 +7600,7 @@ pass 16: -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 9 seconds +Time used = 0 hours, 0 minutes and 17 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7795,51 +7831,51 @@ pass 1 : -13309.3701 (branch= 2.8300 alpha= 0.8831 pinv= 0.0157 eq freqs= 0.2323 rel rates= 1.8499 subset rates= 0.6129) pass 2 : -13307.8643 (branch= 0.4301 alpha= 0.1996 pinv= 0.0131 eq freqs= 0.1261 rel rates= 0.6707 subset rates= 0.0662) pass 3 : -13307.2553 (branch= 0.1056 alpha= 0.0573 pinv= 0.0031 eq freqs= 0.0091 rel rates= 0.4215 subset rates= 0.0124) -pass 4 : -13306.8905 (branch= 0.0281 alpha= 0.0207 pinv= 0.0029 eq freqs= 0.0100 rel rates= 0.3008 subset rates= 0.0022) -pass 5 : -13306.6713 (branch= 0.0048 alpha= 0.0047 pinv= 0.0010 eq freqs= 0.0057 rel rates= 0.2010 subset rates= 0.0019) -pass 6 : -13306.5184 (branch= 0.0049 alpha= 0.0021 pinv= 0.0004 eq freqs= 0.0047 rel rates= 0.1407 subset rates= 0.0000) -pass 7 : -13306.4194 (branch= 0.0009 alpha= 0.0005 pinv= 0.0001 eq freqs= 0.0029 rel rates= 0.0946 subset rates= 0.0000) -pass 8 : -13306.3505 (branch= 0.0005 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0022 rel rates= 0.0651 subset rates= 0.0009) -pass 9 : -13306.3039 (branch= 0.0005 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0014 rel rates= 0.0444 subset rates= 0.0000) -pass 10: -13306.2727 (branch= 0.0002 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0010 rel rates= 0.0298 subset rates= 0.0000) -pass 11: -13306.2514 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0205 subset rates= 0.0000) -pass 12: -13306.2371 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0138 subset rates= 0.0000) -pass 13: -13306.2272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0095 subset rates= 0.0000) -pass 14: -13306.2205 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065 subset rates= 0.0000) -pass 15: -13306.2161 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0043 subset rates= 0.0000) -pass 16: -13306.2131 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0029 subset rates= 0.0000) -pass 17: -13306.2109 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0020 subset rates= 0.0000) -pass 18: -13306.2094 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0014 subset rates= 0.0000) -pass 19: -13306.2085 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) -pass 20: -13306.2077 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0007 subset rates= 0.0000) +pass 4 : -13306.8903 (branch= 0.0281 alpha= 0.0207 pinv= 0.0029 eq freqs= 0.0100 rel rates= 0.3008 subset rates= 0.0025) +pass 5 : -13306.6718 (branch= 0.0048 alpha= 0.0050 pinv= 0.0011 eq freqs= 0.0057 rel rates= 0.2008 subset rates= 0.0011) +pass 6 : -13306.5187 (branch= 0.0045 alpha= 0.0014 pinv= 0.0003 eq freqs= 0.0050 rel rates= 0.1405 subset rates= 0.0014) +pass 7 : -13306.4183 (branch= 0.0012 alpha= 0.0008 pinv= 0.0001 eq freqs= 0.0027 rel rates= 0.0954 subset rates= 0.0000) +pass 8 : -13306.3501 (branch= 0.0006 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0022 rel rates= 0.0651 subset rates= 0.0000) +pass 9 : -13306.3046 (branch= 0.0003 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0014 rel rates= 0.0437 subset rates= 0.0000) +pass 10: -13306.2736 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0010 rel rates= 0.0299 subset rates= 0.0000) +pass 11: -13306.2525 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0203 subset rates= 0.0000) +pass 12: -13306.2383 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0137 subset rates= 0.0000) +pass 13: -13306.2284 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0095 subset rates= 0.0000) +pass 14: -13306.2217 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0064 subset rates= 0.0001) +pass 15: -13306.2173 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0043 subset rates= 0.0000) +pass 16: -13306.2135 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0029 subset rates= 0.0008) +pass 17: -13306.2111 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0022 subset rates= 0.0000) +pass 18: -13306.2094 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0015 subset rates= 0.0001) +pass 19: -13306.2084 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) +pass 20: -13306.2077 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) optimization up to ... -pass 30: -13306.2062 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0014 subset rates= 0.0000) +pass 30: -13306.2063 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0014 subset rates= 0.0000) optimization up to ... -pass 37: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 38: -13306.2060 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0001) Looking for minimum length branches... -Final score = -13306.2061 -Time used = 0 hours, 0 minutes and 15 seconds +Final score = -13306.2060 +Time used = 0 hours, 0 minutes and 19 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13306.2061 +Replicate 1 : -13306.2060 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: 1.974 2.576 1.413 1.413 3.718 1 0.309 0.177 0.297 0.216 0.407 +rep 1: 1.975 2.577 1.414 1.414 3.721 1 0.309 0.177 0.297 0.216 0.407 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: 4.373 7.058 1.609 7.058 4.373 1 0.270 0.164 0.161 0.406 0.361 +rep 1: 4.374 7.059 1.609 7.059 4.374 1 0.270 0.164 0.161 0.406 0.361 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 4.939 3.386 0.4594 4.939 1 0.157 0.354 0.287 0.202 4.035 0.033 +rep 1: 1 4.936 3.385 0.4592 4.936 1 0.157 0.354 0.287 0.202 4.037 0.033 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) @@ -7849,9 +7885,9 @@ Writing optimized trees and models to scr.p.3diff.best.all.tre ***********TEST************** -***Score is 13306.20609 +***Score is 13306.20604 ***Expected is 13306.20608 -***SCORE DIFFERENCE IS .00001 +***SCORE DIFFERENCE IS -.00004 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.3diff.conf *** Running scoring test ./scoring/p.mk.conf @@ -8032,7 +8068,7 @@ pass 14: -474.1864 (branch= 0.0000) Looking for minimum length branches... Final score = -474.1864 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8243,7 +8279,7 @@ pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8452,7 +8488,7 @@ pass 13: -494.9700 (branch= 0.0000) Looking for minimum length branches... Final score = -494.9700 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8657,16 +8693,17 @@ pass 8 : -477.6886 (branch= 0.0015 subset rates= 0.0000) pass 9 : -477.6879 (branch= 0.0008 subset rates= 0.0000) pass 10: -477.6875 (branch= 0.0004 subset rates= 0.0000) -pass 11: -477.6872 (branch= 0.0002 subset rates= 0.0001) -pass 12: -477.6861 (branch= 0.0011 subset rates= 0.0000) -pass 13: -477.6857 (branch= 0.0004 subset rates= 0.0000) -pass 14: -477.6854 (branch= 0.0002 subset rates= 0.0000) -pass 15: -477.6848 (branch= 0.0001 subset rates= 0.0005) -pass 16: -477.6847 (branch= 0.0001 subset rates= 0.0000) -pass 17: -477.6847 (branch= 0.0000 subset rates= 0.0000) -pass 18: -477.6847 (branch= 0.0000 subset rates= 0.0000) +pass 11: -477.6869 (branch= 0.0002 subset rates= 0.0004) +pass 12: -477.6852 (branch= 0.0010 subset rates= 0.0007) +pass 13: -477.6849 (branch= 0.0003 subset rates= 0.0000) +pass 14: -477.6847 (branch= 0.0001 subset rates= 0.0000) +pass 15: -477.6847 (branch= 0.0001 subset rates= 0.0000) +pass 16: -477.6846 (branch= 0.0000 subset rates= 0.0000) +pass 17: -477.6846 (branch= 0.0000 subset rates= 0.0000) +pass 18: -477.6846 (branch= 0.0000 subset rates= 0.0000) +pass 19: -477.6846 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.6847 +Final score = -477.6846 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... @@ -8674,7 +8711,7 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -477.6847 +Replicate 1 : -477.6846 Parameter estimates: @@ -8689,15 +8726,15 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.917 0.629 1.903 2.809 +rep 1: 4.915 0.630 1.899 2.808 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkO.ssr.best.all.tre ***********TEST************** -***Score is 477.68467 +***Score is 477.68460 ***Expected is 477.6848 -***SCORE DIFFERENCE IS -.00013 +***SCORE DIFFERENCE IS -.00020 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkO.ssr.conf *** Running scoring test ./scoring/p.mkv.conf @@ -8878,7 +8915,7 @@ pass 14: -472.3906 (branch= 0.0000) Looking for minimum length branches... Final score = -472.3906 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9487,40 +9524,38 @@ pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) -pass 5:+ 0.158 (branch= 0.12 scale= 0.00 subset rates= 0.03) +pass 5:+ 0.157 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8622 -Current score = -474.8622 +lnL after optimization: -474.8624 +Current score = -474.8624 Performing final optimizations... -pass 1 : -474.7981 (branch= 0.0576 subset rates= 0.0066) -pass 2 : -474.6999 (branch= 0.0911 subset rates= 0.0071) -pass 3 : -474.6746 (branch= 0.0233 subset rates= 0.0020) -pass 4 : -474.6609 (branch= 0.0137 subset rates= 0.0000) -pass 5 : -474.6539 (branch= 0.0070 subset rates= 0.0000) -pass 6 : -474.6510 (branch= 0.0029 subset rates= 0.0000) -pass 7 : -474.6490 (branch= 0.0011 subset rates= 0.0009) -pass 8 : -474.6470 (branch= 0.0012 subset rates= 0.0008) -pass 9 : -474.6464 (branch= 0.0007 subset rates= 0.0000) -pass 10: -474.6460 (branch= 0.0004 subset rates= 0.0000) -pass 11: -474.6458 (branch= 0.0002 subset rates= 0.0000) -pass 12: -474.6457 (branch= 0.0001 subset rates= 0.0001) -pass 13: -474.6456 (branch= 0.0001 subset rates= 0.0000) -pass 14: -474.6455 (branch= 0.0000 subset rates= 0.0000) -pass 15: -474.6455 (branch= 0.0000 subset rates= 0.0000) -pass 16: -474.6455 (branch= 0.0000 subset rates= 0.0000) -pass 17: -474.6455 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.7936 (branch= 0.0575 subset rates= 0.0113) +pass 2 : -474.6948 (branch= 0.0955 subset rates= 0.0033) +pass 3 : -474.6697 (branch= 0.0251 subset rates= 0.0000) +pass 4 : -474.6594 (branch= 0.0104 subset rates= 0.0000) +pass 5 : -474.6525 (branch= 0.0054 subset rates= 0.0015) +pass 6 : -474.6494 (branch= 0.0031 subset rates= 0.0000) +pass 7 : -474.6473 (branch= 0.0021 subset rates= 0.0000) +pass 8 : -474.6466 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -474.6462 (branch= 0.0004 subset rates= 0.0000) +pass 10: -474.6460 (branch= 0.0002 subset rates= 0.0000) +pass 11: -474.6459 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.6458 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.6458 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.6458 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.6456 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... -Final score = -474.6455 -Time used = 0 hours, 0 minutes and 0 seconds +Final score = -474.6456 +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -474.6455 +Replicate 1 : -474.6456 Parameter estimates: @@ -9535,15 +9570,15 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.585 0.585 2.017 2.998 +rep 1: 4.582 0.587 2.016 2.988 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkvO.ssr.best.all.tre ***********TEST************** -***Score is 474.64547 +***Score is 474.64560 ***Expected is 474.6455633 -***SCORE DIFFERENCE IS -.0000933 +***SCORE DIFFERENCE IS .0000367 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkvO.ssr.conf *** ************************** @@ -9663,143 +9698,144 @@ Optimizing parameters... improved 1.330 lnL Optimizing branchlengths... improved 0.015 lnL 1500 -210.8785 0.010 1215 -2000 -210.6679 0.010 1215 -2500 -210.6043 0.010 1215 -3000 -210.5103 0.010 1215 -3500 -210.4074 0.010 1215 +2000 -210.6585 0.010 1215 +2500 -210.6112 0.010 1215 +3000 -210.5162 0.010 1215 Reached termination condition! last topological improvement at gen 1215 -Improvement over last 500 gen = 0.04852 -Current score = -210.3682 +Improvement over last 500 gen = 0.03350 +Current score = -210.5119 Performing final optimizations... -pass 1 : -210.0059 (branch= 0.0000 alpha= 0.0802 pinv= 0.2359 eq freqs= 0.0000 rel rates= 0.0462) -pass 2 : -209.4692 (branch= 0.0070 alpha= 0.3196 pinv= 0.1947 eq freqs= 0.0041 rel rates= 0.0113) -pass 3 : -209.3042 (branch= 0.0312 alpha= 0.1038 pinv= 0.0100 eq freqs= 0.0084 rel rates= 0.0117) -pass 4 : -209.2417 (branch= 0.0339 alpha= 0.0226 pinv= 0.0019 eq freqs= 0.0009 rel rates= 0.0032) -pass 5 : -209.1929 (branch= 0.0341 alpha= 0.0091 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0052) -pass 6 : -209.1660 (branch= 0.0130 alpha= 0.0045 pinv= 0.0007 eq freqs= 0.0010 rel rates= 0.0077) -pass 7 : -209.1440 (branch= 0.0080 alpha= 0.0023 pinv= 0.0002 eq freqs= 0.0005 rel rates= 0.0110) -pass 8 : -209.1280 (branch= 0.0045 alpha= 0.0005 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0105) -pass 9 : -209.1163 (branch= 0.0016 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0096) -pass 10: -209.1069 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0083) -pass 11: -209.0989 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0074) -pass 12: -209.0919 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0067) -pass 13: -209.0855 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) -pass 14: -209.0796 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) -pass 15: -209.0742 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) -pass 16: -209.0690 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) -pass 17: -209.0643 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) -pass 18: -209.0594 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 19: -209.0546 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) -pass 20: -209.0494 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) +pass 1 : -210.1434 (branch= 0.0000 alpha= 0.0976 pinv= 0.2247 eq freqs= 0.0000 rel rates= 0.0461) +pass 2 : -209.5389 (branch= 0.0000 alpha= 0.3281 pinv= 0.2512 eq freqs= 0.0028 rel rates= 0.0225) +pass 3 : -209.3295 (branch= 0.0347 alpha= 0.1440 pinv= 0.0168 eq freqs= 0.0070 rel rates= 0.0070) +pass 4 : -209.2576 (branch= 0.0482 alpha= 0.0145 pinv= 0.0019 eq freqs= 0.0011 rel rates= 0.0062) +pass 5 : -209.2201 (branch= 0.0237 alpha= 0.0068 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0067) +pass 6 : -209.1969 (branch= 0.0107 alpha= 0.0029 pinv= 0.0003 eq freqs= 0.0002 rel rates= 0.0091) +pass 7 : -209.1773 (branch= 0.0068 alpha= 0.0021 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0103) +pass 8 : -209.1596 (branch= 0.0043 alpha= 0.0010 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0116) +pass 9 : -209.1458 (branch= 0.0022 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0111) +pass 10: -209.1346 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) +pass 11: -209.1249 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0089) +pass 12: -209.1163 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0081) +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= 0.0048) optimization up to ... -pass 30: -208.9544 (branch= 0.0160 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0028 rel rates= 0.0756) +pass 30: -208.9996 (branch= 0.0075 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0584) optimization up to ... -pass 40: -208.7781 (branch= 0.0287 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0088 rel rates= 0.1369) +pass 40: -208.8388 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1219) optimization up to ... -pass 50: -208.6672 (branch= 0.0061 alpha= 0.0000 pinv= 0.0008 eq freqs= 0.0032 rel rates= 0.1009) +pass 50: -208.6967 (branch= 0.0133 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1216) optimization up to ... -pass 60: -208.6040 (branch= 0.0007 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0620) +pass 60: -208.6227 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0719) optimization up to ... -pass 70: -208.5600 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0436) +pass 70: -208.5735 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0487) optimization up to ... -pass 80: -208.5277 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0320) +pass 80: -208.5377 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0354) optimization up to ... -pass 90: -208.5028 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0248) +pass 90: -208.5106 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) optimization up to ... -pass 100: -208.4832 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0194) +pass 100: -208.4894 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) optimization up to ... -pass 110: -208.4675 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0157) +pass 110: -208.4724 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) optimization up to ... -pass 120: -208.4546 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0128) +pass 120: -208.4586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) optimization up to ... -pass 130: -208.4436 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0109) +pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) optimization up to ... -pass 140: -208.4345 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) +pass 140: -208.4374 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) optimization up to ... -pass 150: -208.4266 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) +pass 150: -208.4292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... -pass 160: -208.4199 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) +pass 160: -208.4221 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) optimization up to ... -pass 170: -208.4141 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) +pass 170: -208.4160 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) optimization up to ... -pass 180: -208.4090 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) +pass 180: -208.4107 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) optimization up to ... -pass 190: -208.4045 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) +pass 190: -208.4059 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... -pass 200: -208.4005 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) +pass 200: -208.4018 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0041) optimization up to ... -pass 210: -208.3968 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) +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: -208.3936 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) +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: -208.3906 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) +pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... -pass 240: -208.3879 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) +pass 240: -208.3888 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... -pass 250: -208.3855 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... -pass 260: -208.3833 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) +pass 260: -208.3840 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... -pass 270: -208.3812 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) +pass 270: -208.3819 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 280: -208.3793 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3799 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... -pass 290: -208.3775 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +pass 290: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... -pass 300: -208.3759 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 300: -208.3764 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 310: -208.3744 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) +pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 320: -208.3730 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) +pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 340: -208.3704 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 340: -208.3708 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 350: -208.3696 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 360: -208.3685 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 370: -208.3674 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 380: -208.3665 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +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: -208.3644 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 400: -208.3646 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 410: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +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: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +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: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 430: -208.3622 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +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: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 450: -208.3608 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 460: -208.3600 (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= 0.0006) optimization up to ... -pass 470: -208.3594 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +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: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) + optimization up to ... +pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... -pass 490: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 497: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... -Final score = -208.3585 -Time used = 0 hours, 0 minutes and 8 seconds +Final score = -208.3584 +Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.116, AG = 188.904, AT = 6.956, CG = 204.761, CT = 194.740, GT = 1.000 + AC = 122.591, AG = 189.174, AT = 6.994, CG = 205.391, CT = 195.428, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2035 0.2834 + (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 999.9000 + 999.8998 with an invariant (invariable) site category, proportion estimated 0.2781 Substitution rate categories under this model: @@ -9818,11 +9854,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3585 +Replicate 1 : -208.3584 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: 122.1 188.9 6.956 204.8 194.7 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.6 189.2 6.994 205.4 195.4 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -9958,50 +9994,50 @@ Improvement over last 500 gen = 0.03748 Current score = -211.2888 Performing final optimizations... -pass 1 : -208.9744 (branch= 0.0000 alpha= 0.7658 pinv= 1.4609 eq freqs= 0.0059 rel rates= 0.0818) -pass 2 : -208.6651 (branch= 0.0549 alpha= 0.2088 pinv= 0.0077 eq freqs= 0.0115 rel rates= 0.0264) -pass 3 : -208.5262 (branch= 0.0279 alpha= 0.0817 pinv= 0.0021 eq freqs= 0.0023 rel rates= 0.0249) -pass 4 : -208.4907 (branch= 0.0105 alpha= 0.0020 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0218) -pass 5 : -208.4703 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0195) -pass 6 : -208.4501 (branch= 0.0011 alpha= 0.0004 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0177) -pass 7 : -208.4330 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0166) -pass 8 : -208.4163 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0160) -pass 9 : -208.4019 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0142) -pass 10: -208.3886 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0131) -pass 11: -208.3767 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0117) -pass 12: -208.3659 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0108) -pass 13: -208.3560 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0099) -pass 14: -208.3467 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0093) -pass 15: -208.3381 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0085) -pass 16: -208.3302 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0079) -pass 17: -208.3228 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) -pass 18: -208.3159 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) -pass 19: -208.3095 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) -pass 20: -208.3034 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) - optimization up to ... -pass 30: -208.2582 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0450) - optimization up to ... -pass 40: -208.2302 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0279) - optimization up to ... -pass 50: -208.2111 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0190) - optimization up to ... -pass 60: -208.1973 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0139) - optimization up to ... -pass 70: -208.1868 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 1 : -209.0567 (branch= 0.0000 alpha= 0.7586 pinv= 1.3876 eq freqs= 0.0053 rel rates= 0.0806) +pass 2 : -208.6461 (branch= 0.0502 alpha= 0.3118 pinv= 0.0090 eq freqs= 0.0114 rel rates= 0.0282) +pass 3 : -208.5218 (branch= 0.0332 alpha= 0.0623 pinv= 0.0020 eq freqs= 0.0021 rel rates= 0.0247) +pass 4 : -208.4912 (branch= 0.0069 alpha= 0.0008 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0218) +pass 5 : -208.4694 (branch= 0.0013 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0003 rel rates= 0.0197) +pass 6 : -208.4487 (branch= 0.0013 alpha= 0.0006 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0186) +pass 7 : -208.4319 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0163) +pass 8 : -208.4157 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0157) +pass 9 : -208.4011 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0144) +pass 10: -208.3880 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0129) +pass 11: -208.3761 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0119) +pass 12: -208.3650 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0109) +pass 13: -208.3552 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) +pass 14: -208.3461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) +pass 15: -208.3376 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0085) +pass 16: -208.3297 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) +pass 17: -208.3223 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) +pass 18: -208.3156 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) +pass 19: -208.3091 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) +pass 20: -208.3031 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0059) + optimization up to ... +pass 30: -208.2580 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0450) + optimization up to ... +pass 40: -208.2301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0278) + optimization up to ... +pass 50: -208.2111 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) + optimization up to ... +pass 60: -208.1973 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) + optimization up to ... +pass 70: -208.1869 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... -pass 80: -208.1785 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) +pass 80: -208.1786 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... -pass 90: -208.1718 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) +pass 90: -208.1719 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... -pass 100: -208.1663 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) +pass 100: -208.1664 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... -pass 110: -208.1616 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) +pass 110: -208.1617 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) optimization up to ... pass 120: -208.1577 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... -pass 130: -208.1542 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 130: -208.1543 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... -pass 140: -208.1512 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) +pass 140: -208.1513 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 150: -208.1486 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... @@ -10052,13 +10088,13 @@ pass 372: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1244 -Time used = 0 hours, 0 minutes and 9 seconds +Time used = 0 hours, 0 minutes and 13 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 22.221, AG = 32.287, AT = 0.001, CG = 36.372, CT = 80.255, GT = 1.000 + AC = 22.224, AG = 32.291, AT = 0.001, CG = 36.376, CT = 80.264, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: @@ -10086,7 +10122,7 @@ 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: 22.22 32.29 0.001 36.37 80.25 1 0.221 0.344 0.216 0.218 999.900 0.338 +rep 1: 22.22 32.29 0.001 36.38 80.26 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL @@ -10226,56 +10262,56 @@ Performing final optimizations... pass 1 : -210.1101 (branch= 0.0000 alpha= 0.1171 pinv= 0.2670 eq freqs= 0.0000 rel rates= 0.1416) pass 2 : -209.4779 (branch= 0.0153 alpha= 0.3684 pinv= 0.2099 eq freqs= 0.0103 rel rates= 0.0282) -pass 3 : -209.3226 (branch= 0.0490 alpha= 0.0860 pinv= 0.0100 eq freqs= 0.0024 rel rates= 0.0079) -pass 4 : -209.2695 (branch= 0.0319 alpha= 0.0104 pinv= 0.0011 eq freqs= 0.0023 rel rates= 0.0074) -pass 5 : -209.2429 (branch= 0.0112 alpha= 0.0053 pinv= 0.0000 eq freqs= 0.0013 rel rates= 0.0088) -pass 6 : -209.2169 (branch= 0.0098 alpha= 0.0041 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0112) -pass 7 : -209.1938 (branch= 0.0086 alpha= 0.0024 pinv= 0.0002 eq freqs= 0.0011 rel rates= 0.0109) -pass 8 : -209.1714 (branch= 0.0063 alpha= 0.0021 pinv= 0.0000 eq freqs= 0.0010 rel rates= 0.0131) -pass 9 : -209.1535 (branch= 0.0045 alpha= 0.0006 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0119) -pass 10: -209.1400 (branch= 0.0021 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0108) -pass 11: -209.1291 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0096) -pass 12: -209.1197 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0086) -pass 13: -209.1114 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0079) -pass 14: -209.1039 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0072) -pass 15: -209.0971 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0066) -pass 16: -209.0907 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0062) -pass 17: -209.0847 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0058) -pass 18: -209.0790 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) -pass 19: -209.0737 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) -pass 20: -209.0686 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 3 : -209.3226 (branch= 0.0490 alpha= 0.0860 pinv= 0.0099 eq freqs= 0.0024 rel rates= 0.0079) +pass 4 : -209.2696 (branch= 0.0318 alpha= 0.0104 pinv= 0.0011 eq freqs= 0.0023 rel rates= 0.0074) +pass 5 : -209.2429 (branch= 0.0112 alpha= 0.0054 pinv= 0.0000 eq freqs= 0.0013 rel rates= 0.0088) +pass 6 : -209.2170 (branch= 0.0097 alpha= 0.0041 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0112) +pass 7 : -209.1934 (branch= 0.0086 alpha= 0.0024 pinv= 0.0002 eq freqs= 0.0011 rel rates= 0.0112) +pass 8 : -209.1711 (branch= 0.0062 alpha= 0.0022 pinv= 0.0001 eq freqs= 0.0010 rel rates= 0.0129) +pass 9 : -209.1529 (branch= 0.0054 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0121) +pass 10: -209.1396 (branch= 0.0019 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0108) +pass 11: -209.1288 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0096) +pass 12: -209.1194 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0087) +pass 13: -209.1112 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0078) +pass 14: -209.1038 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0071) +pass 15: -209.0969 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0067) +pass 16: -209.0905 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0062) +pass 17: -209.0845 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0059) +pass 18: -209.0788 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) +pass 19: -209.0735 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) +pass 20: -209.0685 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... -pass 30: -209.0034 (branch= 0.0068 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0011 rel rates= 0.0570) +pass 30: -209.0028 (branch= 0.0069 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0011 rel rates= 0.0574) optimization up to ... -pass 40: -208.8455 (branch= 0.0294 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0073 rel rates= 0.1197) +pass 40: -208.8446 (branch= 0.0294 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0073 rel rates= 0.1200) optimization up to ... -pass 50: -208.7005 (branch= 0.0143 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0061 rel rates= 0.1232) +pass 50: -208.6998 (branch= 0.0142 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0061 rel rates= 0.1231) optimization up to ... -pass 60: -208.6248 (branch= 0.0013 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0008 rel rates= 0.0734) +pass 60: -208.6244 (branch= 0.0013 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0008 rel rates= 0.0732) optimization up to ... -pass 70: -208.5751 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0492) +pass 70: -208.5748 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0490) optimization up to ... -pass 80: -208.5389 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0358) +pass 80: -208.5387 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0358) optimization up to ... -pass 90: -208.5114 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0273) +pass 90: -208.5113 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0272) optimization up to ... -pass 100: -208.4901 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0211) +pass 100: -208.4900 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0212) optimization up to ... -pass 110: -208.4731 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0169) +pass 110: -208.4730 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) optimization up to ... -pass 120: -208.4590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0139) +pass 120: -208.4590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) optimization up to ... pass 130: -208.4475 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) optimization up to ... -pass 140: -208.4378 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) +pass 140: -208.4377 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) optimization up to ... pass 150: -208.4294 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... -pass 160: -208.4224 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) +pass 160: -208.4223 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0071) optimization up to ... -pass 170: -208.4162 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0062) +pass 170: -208.4161 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) optimization up to ... -pass 180: -208.4108 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) +pass 180: -208.4108 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) optimization up to ... pass 190: -208.4061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... @@ -10295,9 +10331,9 @@ optimization up to ... 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: -208.3801 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3801 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 290: -208.3782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +pass 290: -208.3783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3766 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... @@ -10323,7 +10359,7 @@ 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) +pass 420: -208.3631 (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) optimization up to ... @@ -10339,21 +10375,21 @@ optimization up to ... pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... -pass 495: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) +pass 494: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... -Final score = -208.3585 -Time used = 0 hours, 0 minutes and 7 seconds +Final score = -208.3586 +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 121.965, AG = 188.215, AT = 6.958, CG = 204.349, CT = 194.441, GT = 1.000 + AC = 121.695, AG = 187.809, AT = 6.943, CG = 203.906, CT = 194.017, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 999.8998 + 999.9000 with an invariant (invariable) site category, proportion estimated 0.2781 Substitution rate categories under this model: @@ -10377,11 +10413,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3585 +Replicate 1 : -208.3586 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: 122 188.2 6.958 204.3 194.4 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 121.7 187.8 6.943 203.9 194 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -10528,7 +10564,7 @@ pass 9 : -209.1092 (branch= 0.0041 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0010 rel rates= 0.0100) pass 10: -209.0986 (branch= 0.0014 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0086) pass 11: -209.0902 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0074) -pass 12: -209.0831 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0066) +pass 12: -209.0831 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0065) pass 13: -209.0769 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0059) pass 14: -209.0714 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 15: -209.0662 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0050) @@ -10538,59 +10574,59 @@ pass 19: -209.0447 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 20: -209.0381 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0058) optimization up to ... -pass 30: -208.9191 (branch= 0.0216 alpha= 0.0000 pinv= 0.0008 eq freqs= 0.0045 rel rates= 0.0921) +pass 30: -208.9192 (branch= 0.0216 alpha= 0.0000 pinv= 0.0008 eq freqs= 0.0045 rel rates= 0.0920) optimization up to ... -pass 40: -208.7470 (branch= 0.0242 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0083 rel rates= 0.1376) +pass 40: -208.7470 (branch= 0.0241 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0083 rel rates= 0.1378) optimization up to ... pass 50: -208.6513 (branch= 0.0034 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0020 rel rates= 0.0899) optimization up to ... -pass 60: -208.5929 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0575) +pass 60: -208.5930 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0575) optimization up to ... -pass 70: -208.5519 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0406) +pass 70: -208.5520 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0406) optimization up to ... -pass 80: -208.5212 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0304) +pass 80: -208.5213 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0304) optimization up to ... -pass 90: -208.4976 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0234) +pass 90: -208.4976 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0235) optimization up to ... pass 100: -208.4790 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0185) optimization up to ... -pass 110: -208.4639 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0150) +pass 110: -208.4638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0150) optimization up to ... -pass 120: -208.4514 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0124) +pass 120: -208.4515 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) optimization up to ... -pass 130: -208.4410 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) +pass 130: -208.4410 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... -pass 140: -208.4320 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) +pass 140: -208.4321 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0088) optimization up to ... -pass 150: -208.4244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) +pass 150: -208.4245 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) optimization up to ... pass 160: -208.4179 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... pass 170: -208.4122 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... -pass 180: -208.4073 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 180: -208.4072 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... -pass 190: -208.4028 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) +pass 190: -208.4029 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... -pass 200: -208.3989 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) +pass 200: -208.3989 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... -pass 210: -208.3954 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) +pass 210: -208.3953 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3922 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... -pass 230: -208.3894 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) +pass 230: -208.3893 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... -pass 240: -208.3867 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) +pass 240: -208.3866 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 250: -208.3843 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 250: -208.3842 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... -pass 260: -208.3821 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) +pass 260: -208.3820 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... -pass 270: -208.3801 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) +pass 270: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 280: -208.3782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... -pass 290: -208.3765 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) +pass 290: -208.3764 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3748 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... @@ -10600,7 +10636,7 @@ optimization up to ... pass 330: -208.3706 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 340: -208.3694 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 340: -208.3693 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3682 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... @@ -10608,7 +10644,7 @@ optimization up to ... pass 370: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 380: -208.3651 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 380: -208.3651 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 390: -208.3642 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... @@ -10618,28 +10654,32 @@ optimization up to ... pass 420: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 430: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 430: -208.3610 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 440: -208.3604 (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= 0.0007) optimization up to ... pass 450: -208.3597 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 460: -208.3591 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 460: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) + optimization up to ... +pass 470: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... -pass 470: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 480: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 480: -208.3579 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 490: -208.3580 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 490: -208.3575 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) +pass 500: -208.3577 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) + optimization up to ... +pass 503: -208.3577 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... -Final score = -208.3575 -Time used = 0 hours, 0 minutes and 5 seconds +Final score = -208.3577 +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.825, AG = 189.980, AT = 6.991, CG = 205.972, CT = 195.928, GT = 1.000 + AC = 122.162, AG = 188.510, AT = 6.957, CG = 204.705, CT = 194.795, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2834 Rate Heterogeneity Model: @@ -10668,11 +10708,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3575 +Replicate 1 : -208.3577 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: 122.8 190 6.991 206 195.9 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.2 188.5 6.957 204.7 194.8 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -11516,21 +11556,21 @@ 7 8 9 10 11 Initial ln Likelihood: -225.6424 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... -pass 1:+ 10.932 (branch= 2.26 scale= 0.50 omega= 0.00 rel rates= 8.17) -pass 2:+ 0.925 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) +pass 1:+ 10.931 (branch= 2.26 scale= 0.50 omega= 0.00 rel rates= 8.17) +pass 2:+ 0.924 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.733 (branch= 0.04 scale= 0.68 omega= 0.01 rel rates= 0.00) pass 4:+ 0.015 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.00) -lnL after optimization: -213.0379 +lnL after optimization: -213.0383 gen current_lnL precision last_tree_imp -0 -213.0379 0.500 0 +0 -213.0383 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) - One estimated dN/dS ratio (aka omega) = 0.130445 + One estimated dN/dS ratio (aka omega) = 0.130420 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 2.468, AG = 4.008, AT = 0.588, CG = 2.683, CT = 2.283, GT = 1.000 + AC = 2.468, AG = 4.008, AT = 0.588, CG = 2.683, CT = 2.282, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -11564,11 +11604,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.2321 +Replicate 1 : -210.2322 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.130 1.000 2.468 4.008 0.588 2.683 2.283 1 +rep 1: 0.130 1.000 2.468 4.008 0.588 2.683 2.282 1 Treelengths: TL @@ -12399,15 +12439,15 @@ 7 8 9 10 11 Initial ln Likelihood: -13699.7841 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... -pass 1:+ 209.568 (branch= 7.95 scale= 0.00 alpha= 35.56 freqs= 28.70 rel rates= 62.31 pinv= 0.00 subset rates= 75.04) -pass 2:+ 77.795 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 11.10 rel rates= 3.26 pinv= 0.90 subset rates= 56.13) -pass 3:+ 48.928 (branch= 6.87 scale= 0.74 alpha= 4.62 freqs= 1.22 rel rates= 1.34 pinv= 0.01 subset rates= 34.13) -pass 4:+ 15.208 (branch= 0.00 scale= 0.76 alpha= 0.64 freqs= 1.21 rel rates= 0.55 pinv= 0.01 subset rates= 12.03) -pass 5:+ 5.795 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.01 subset rates= 4.91) -pass 6:+ 0.129 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) -lnL after optimization: -13342.3602 +pass 1:+ 209.508 (branch= 7.95 scale= 0.00 alpha= 35.56 freqs= 28.90 rel rates= 62.03 pinv= 0.19 subset rates= 74.88) +pass 2:+ 77.016 (branch= 1.74 scale= 0.00 alpha= 4.25 freqs= 11.29 rel rates= 3.50 pinv= 0.68 subset rates= 55.55) +pass 3:+ 50.073 (branch= 8.13 scale= 0.55 alpha= 4.79 freqs= 1.15 rel rates= 1.36 pinv= 0.01 subset rates= 34.08) +pass 4:+ 16.647 (branch= 1.54 scale= 0.00 alpha= 0.63 freqs= 1.21 rel rates= 1.36 pinv= 0.01 subset rates= 11.89) +pass 5:+ 6.281 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.12 rel rates= 1.30 pinv= 0.01 subset rates= 4.84) +pass 6:+ 0.125 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) +lnL after optimization: -13340.1342 gen current_lnL precision last_tree_imp -0 -13342.3602 0.500 0 +0 -13340.1342 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT @@ -12415,58 +12455,58 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.951, AG = 2.401, AT = 1.336, CG = 1.336, CT = 3.999, GT = 1.000 + AC = 1.951, AG = 2.401, AT = 1.337, CG = 1.337, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3134 0.1755 0.2988 0.2122 + (ACGT) 0.3133 0.1756 0.2989 0.2122 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3662 + 0.3651 Substitution rate categories under this model: rate proportion - 0.0122 0.2500 - 0.1561 0.2500 - 0.6920 0.2500 - 3.1397 0.2500 + 0.0120 0.2500 + 0.1552 0.2500 + 0.6905 0.2500 + 3.1423 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 3.969, AG = 6.053, AT = 1.216, CG = 6.053, CT = 3.969, GT = 1.000 + AC = 4.002, AG = 6.112, AT = 1.224, CG = 6.112, CT = 4.002, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2816 0.1661 0.1574 0.3949 + (ACGT) 0.2815 0.1660 0.1576 0.3948 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3384 + 0.3377 Substitution rate categories under this model: rate proportion - 0.0089 0.2500 - 0.1345 0.2500 - 0.6550 0.2500 - 3.2015 0.2500 + 0.0088 0.2500 + 0.1340 0.2500 + 0.6540 0.2500 + 3.2032 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 = 4.110, AT = 2.514, CG = 0.379, CT = 4.110, GT = 1.000 + AC = 1.000, AG = 4.475, AT = 2.816, CG = 0.436, CT = 4.475, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1593 0.3519 0.2841 0.2047 + (ACGT) 0.1595 0.3510 0.2837 0.2058 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1299 + 4.2180 with an invariant (invariable) site category, proportion estimated - 0.0283 + 0.0301 Substitution rate categories under this model: rate proportion - 0.0000 0.0283 - 0.4614 0.2429 - 0.7796 0.2429 - 1.0844 0.2429 - 1.6747 0.2429 + 0.0000 0.0301 + 0.4660 0.2425 + 0.7824 0.2425 + 1.0843 0.2425 + 1.6673 0.2425 Subset rate multipliers: - 0.54 0.33 2.14 + 0.54 0.32 2.14 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -12481,25 +12521,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13324.0761 +Replicate 1 : -13322.8959 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: 1.951 2.401 1.336 1.336 3.999 1 0.313 0.176 0.299 0.212 0.366 +rep 1: 1.951 2.401 1.337 1.337 3.999 1 0.313 0.176 0.299 0.212 0.365 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 3.969 6.053 1.216 6.053 3.969 1 0.282 0.166 0.157 0.395 0.338 +rep 1: 4.002 6.112 1.224 6.112 4.002 1 0.282 0.166 0.158 0.395 0.338 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 4.11 2.514 0.3789 4.11 1 0.159 0.352 0.284 0.205 4.130 0.028 +rep 1: 1 4.475 2.816 0.4357 4.475 1 0.160 0.351 0.284 0.206 4.218 0.030 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.696 0.538 0.326 2.136 +rep 1: 1.721 0.537 0.325 2.139 Saving final tree from best search rep (#1) to out.p.3diff.best.tre Inferring internal state probabilities on best tree... saving to file out.p.3diff.internalstates.log @@ -12672,13 +12712,13 @@ pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) -pass 5:+ 0.158 (branch= 0.12 scale= 0.00 subset rates= 0.03) +pass 5:+ 0.157 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8622 +lnL after optimization: -474.8624 gen current_lnL precision last_tree_imp -0 -474.8622 0.010 0 +0 -474.8624 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT @@ -12720,7 +12760,7 @@ Completed 1 replicate search(es) (of 5). Results: -Replicate 1 : -474.8614 (best) +Replicate 1 : -474.8616 (best) Parameter estimates across search replicates: @@ -12735,7 +12775,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.474 0.599 2.019 2.820 +rep 1: 4.474 0.599 2.019 2.819 Saving final tree from best search rep (#1) to out.p.mkvO.ssr.best.tre ####################################################### @@ -12827,7 +12867,7 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -474.8614 +Replicate 1 : -474.8616 Replicate 2 : -474.8505 (best) Parameter estimates across search replicates: @@ -12843,7 +12883,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.474 0.599 2.019 2.820 +rep 1: 4.474 0.599 2.019 2.819 rep 2: 4.516 0.599 2.014 2.839 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre @@ -12887,13 +12927,13 @@ pass 1:+ 116.111 (branch= 105.75 scale= 0.22 subset rates= 10.14) pass 2:+ 10.329 (branch= 5.57 scale= 0.02 subset rates= 4.75) pass 3:+ 2.693 (branch= 1.07 scale= 0.00 subset rates= 1.62) -pass 4:+ 0.939 (branch= 0.38 scale= 0.00 subset rates= 0.56) -pass 5:+ 0.207 (branch= 0.17 scale= 0.00 subset rates= 0.04) +pass 4:+ 0.940 (branch= 0.38 scale= 0.00 subset rates= 0.56) +pass 5:+ 0.206 (branch= 0.17 scale= 0.00 subset rates= 0.04) pass 6:+ 0.019 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8925 +lnL after optimization: -474.8928 gen current_lnL precision last_tree_imp -0 -474.8925 0.010 0 +0 -474.8928 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT @@ -12922,7 +12962,7 @@ no rate heterogeneity Subset rate multipliers: - 0.60 2.01 2.84 + 0.60 2.01 2.83 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 3 branches were collapsed. @@ -12938,9 +12978,9 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -474.8614 +Replicate 1 : -474.8616 Replicate 2 : -474.8505 (best) -Replicate 3 : -474.8831 +Replicate 3 : -474.8835 Parameter estimates across search replicates: @@ -12955,9 +12995,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.474 0.599 2.019 2.820 +rep 1: 4.474 0.599 2.019 2.819 rep 2: 4.516 0.599 2.014 2.839 -rep 3: 4.460 0.600 2.010 2.838 +rep 3: 4.460 0.600 2.011 2.835 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre @@ -12999,14 +13039,14 @@ optimizing: starting branch lengths, subset rates... pass 1:+ 155.944 (branch= 145.32 scale= 0.58 subset rates= 10.04) pass 2:+ 15.207 (branch= 10.68 scale= 0.00 subset rates= 4.52) -pass 3:+ 3.711 (branch= 2.16 scale= 0.00 subset rates= 1.55) -pass 4:+ 1.980 (branch= 1.40 scale= 0.00 subset rates= 0.58) -pass 5:+ 0.366 (branch= 0.33 scale= 0.00 subset rates= 0.04) +pass 3:+ 3.710 (branch= 2.16 scale= 0.00 subset rates= 1.55) +pass 4:+ 1.983 (branch= 1.40 scale= 0.00 subset rates= 0.58) +pass 5:+ 0.364 (branch= 0.33 scale= 0.00 subset rates= 0.03) pass 6:+ 0.111 (branch= 0.11 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8514 +lnL after optimization: -474.8511 gen current_lnL precision last_tree_imp -0 -474.8514 0.010 0 +0 -474.8511 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT @@ -13035,7 +13075,7 @@ no rate heterogeneity Subset rate multipliers: - 0.60 2.01 2.85 + 0.60 2.01 2.86 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 5 branches were collapsed. @@ -13051,10 +13091,10 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -474.8614 +Replicate 1 : -474.8616 Replicate 2 : -474.8505 -Replicate 3 : -474.8831 -Replicate 4 : -474.8500 (best) +Replicate 3 : -474.8835 +Replicate 4 : -474.8497 (best) Parameter estimates across search replicates: @@ -13069,10 +13109,10 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.474 0.599 2.019 2.820 +rep 1: 4.474 0.599 2.019 2.819 rep 2: 4.516 0.599 2.014 2.839 -rep 3: 4.460 0.600 2.010 2.838 -rep 4: 4.503 0.598 2.010 2.853 +rep 3: 4.460 0.600 2.011 2.835 +rep 4: 4.504 0.598 2.009 2.857 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre @@ -13114,14 +13154,14 @@ optimizing: starting branch lengths, subset rates... pass 1:+ 137.115 (branch= 125.84 scale= 0.86 subset rates= 10.41) pass 2:+ 12.972 (branch= 8.00 scale= 0.03 subset rates= 4.94) -pass 3:+ 2.469 (branch= 0.79 scale= 0.00 subset rates= 1.68) -pass 4:+ 0.826 (branch= 0.23 scale= 0.01 subset rates= 0.58) +pass 3:+ 2.470 (branch= 0.79 scale= 0.00 subset rates= 1.68) +pass 4:+ 0.825 (branch= 0.23 scale= 0.01 subset rates= 0.58) pass 5:+ 0.169 (branch= 0.13 scale= 0.00 subset rates= 0.04) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.9108 +lnL after optimization: -474.9109 gen current_lnL precision last_tree_imp -0 -474.9108 0.010 0 +0 -474.9109 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT @@ -13166,11 +13206,11 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -474.8614 +Replicate 1 : -474.8616 Replicate 2 : -474.8505 -Replicate 3 : -474.8831 -Replicate 4 : -474.8500 (best) -Replicate 5 : -474.9075 +Replicate 3 : -474.8835 +Replicate 4 : -474.8497 (best) +Replicate 5 : -474.9076 Parameter estimates across search replicates: @@ -13185,11 +13225,11 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.474 0.599 2.019 2.820 +rep 1: 4.474 0.599 2.019 2.819 rep 2: 4.516 0.599 2.014 2.839 -rep 3: 4.460 0.600 2.010 2.838 -rep 4: 4.503 0.598 2.010 2.853 -rep 5: 4.499 0.597 2.020 2.842 +rep 3: 4.460 0.600 2.011 2.835 +rep 4: 4.504 0.598 2.009 2.857 +rep 5: 4.499 0.597 2.020 2.841 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre @@ -13342,13 +13382,6 @@ 300 -90.7565 0.500 215 400 -90.4959 0.500 215 500 -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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13445,9 +13478,16 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 920, seed 1800203554, best lnL -88.945 +Bootstrap rep 1 (of 1) generation 594, seed 2088754582, best lnL -90.299 gen current_lnL precision last_tree_imp -920 -88.9446 0.010 879 +594 -90.2989 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 NOTE: ****Specified generation limit (1000) reached... @@ -13620,11 +13660,6 @@ 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 -600 -111.7788 0.500 84 -Optimization precision reduced - Optimizing parameters... improved 0.386 lnL - Optimizing branchlengths... improved 0.390 lnL -700 -110.8142 0.010 615 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13711,9 +13746,14 @@ STARTING RUN Restarting from checkpoint... - generation 792, seed 1346973797, best lnL -110.569 + generation 538, seed 1800801180, best lnL -111.801 gen current_lnL precision last_tree_imp -792 -110.5688 0.010 707 +538 -111.8013 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 0.010 707 900 -110.5555 0.010 707 1000 -110.5066 0.010 707 @@ -13897,7 +13937,6 @@ 1200 -111.6824 0.010 563 1300 -111.6822 0.010 563 1400 -111.6821 0.010 563 -1500 -111.6819 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13983,9 +14022,9 @@ STARTING RUN Restarting from checkpoint... - generation 1539, seed 410717808, best lnL -111.682 + generation 1443, seed 1928760388, best lnL -111.682 gen current_lnL precision last_tree_imp -1539 -111.6819 0.010 563 +1443 -111.6821 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -14009,14 +14048,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6819 +Replicate 1 : -111.6821 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.606 +rep 1: 2.604 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 @@ -14147,10 +14186,6 @@ 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 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14237,9 +14272,13 @@ STARTING RUN Restarting from checkpoint... - generation 88, seed 530483715, best lnL -205.387 + generation 48, seed 1451839081, best lnL -205.618 gen current_lnL precision last_tree_imp -88 -205.3871 0.500 76 +48 -205.6175 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... @@ -14427,6 +14466,9 @@ gen current_lnL precision last_tree_imp 0 -195.3999 0.500 0 10 -195.3553 0.500 0 +20 -195.3340 0.500 0 +30 -195.2776 0.500 0 +40 -195.2554 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14514,11 +14556,8 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 10, seed 1509658266, best lnL -195.355 +Bootstrap rep 1 (of 1) generation 40, seed 2068370778, best lnL -195.255 gen current_lnL precision last_tree_imp -10 -195.3553 0.500 0 -20 -195.3340 0.500 0 -30 -195.2776 0.500 0 40 -195.2554 0.500 0 50 -195.2137 0.500 0 60 -195.1629 0.500 0 @@ -14739,9 +14778,6 @@ Optimizing parameters... improved 0.831 lnL Optimizing branchlengths... improved 0.084 lnL 1100 -3352.7241 0.010 0 -1200 -3352.6772 0.010 0 -1300 -3352.5555 0.010 0 -1400 -3352.3163 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14845,83 +14881,74 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1464, seed 919707264, best lnL -3352.288 +Search rep 1 (of 2) generation 1159, seed 1382122805, best lnL -3352.724 gen current_lnL precision last_tree_imp -1464 -3352.2875 0.010 0 +1159 -3352.7237 0.010 0 +1200 -3352.6772 0.010 0 +1300 -3352.5555 0.010 0 +1400 -3352.3163 0.010 0 1500 -3352.2768 0.010 0 1600 -3352.1744 0.010 0 1700 -3352.1620 0.010 0 1800 -3352.0817 0.010 0 -1900 -3351.7340 0.010 0 -2000 -3351.6685 0.010 0 -2100 -3351.4843 0.010 0 -2200 -3351.3000 0.010 0 -2300 -3351.2527 0.010 0 -2400 -3351.2175 0.010 0 -2500 -3351.1254 0.010 0 -2600 -3351.0627 0.010 0 -2700 -3351.0625 0.010 0 -2800 -3351.0571 0.010 0 -2900 -3351.0137 0.010 0 -3000 -3351.0137 0.010 0 -3100 -3351.0009 0.010 0 -3200 -3350.9813 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.9788 +Current score = -3351.9318 Performing final optimizations... -pass 1 : -3350.9068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0110 eq freqs= 0.0070 rel rates= 0.0539 subset rates= 0.0000) -pass 2 : -3350.8273 (branch= 0.0000 alpha= 0.0162 pinv= 0.0168 eq freqs= 0.0000 rel rates= 0.0465 subset rates= 0.0000) -pass 3 : -3350.7544 (branch= 0.0038 alpha= 0.0178 pinv= 0.0151 eq freqs= 0.0030 rel rates= 0.0320 subset rates= 0.0011) -pass 4 : -3350.6925 (branch= 0.0067 alpha= 0.0137 pinv= 0.0145 eq freqs= 0.0000 rel rates= 0.0255 subset rates= 0.0016) -pass 5 : -3350.6360 (branch= 0.0064 alpha= 0.0131 pinv= 0.0134 eq freqs= 0.0003 rel rates= 0.0215 subset rates= 0.0018) -pass 6 : -3350.5876 (branch= 0.0036 alpha= 0.0114 pinv= 0.0124 eq freqs= 0.0003 rel rates= 0.0196 subset rates= 0.0013) -pass 7 : -3350.5459 (branch= 0.0028 alpha= 0.0105 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0169 subset rates= 0.0000) -pass 8 : -3350.5080 (branch= 0.0005 alpha= 0.0103 pinv= 0.0102 eq freqs= 0.0000 rel rates= 0.0156 subset rates= 0.0014) -pass 9 : -3350.4747 (branch= 0.0015 alpha= 0.0095 pinv= 0.0093 eq freqs= 0.0001 rel rates= 0.0129 subset rates= 0.0000) -pass 10: -3350.4457 (branch= 0.0002 alpha= 0.0085 pinv= 0.0084 eq freqs= 0.0000 rel rates= 0.0118 subset rates= 0.0000) -pass 11: -3350.4194 (branch= 0.0001 alpha= 0.0083 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0105 subset rates= 0.0000) -pass 12: -3350.3949 (branch= 0.0000 alpha= 0.0075 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0091 subset rates= 0.0010) -pass 13: -3350.3745 (branch= 0.0008 alpha= 0.0064 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0072 subset rates= 0.0000) -pass 14: -3350.3568 (branch= 0.0001 alpha= 0.0056 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0066 subset rates= 0.0000) -pass 15: -3350.3409 (branch= 0.0000 alpha= 0.0052 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0059 subset rates= 0.0000) -pass 16: -3350.3267 (branch= 0.0000 alpha= 0.0047 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0051 subset rates= 0.0000) -pass 17: -3350.3143 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0044 subset rates= 0.0000) -pass 18: -3350.3034 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0039 subset rates= 0.0000) -pass 19: -3350.2940 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0033 subset rates= 0.0000) -pass 20: -3350.2857 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2446 (branch= 0.0000 alpha= 0.0143 pinv= 0.0129 eq freqs= 0.0000 rel rates= 0.0138 subset rates= 0.0000) +pass 1 : -3351.6966 (branch= 0.0051 alpha= 0.0190 pinv= 0.0217 eq freqs= 0.0284 rel rates= 0.1550 subset rates= 0.0060) +pass 2 : -3351.4905 (branch= 0.0027 alpha= 0.0091 pinv= 0.0183 eq freqs= 0.0058 rel rates= 0.1702 subset rates= 0.0000) +pass 3 : -3351.3041 (branch= 0.0124 alpha= 0.0160 pinv= 0.0163 eq freqs= 0.0015 rel rates= 0.1369 subset rates= 0.0033) +pass 4 : -3351.1544 (branch= 0.0093 alpha= 0.0127 pinv= 0.0155 eq freqs= 0.0009 rel rates= 0.1101 subset rates= 0.0012) +pass 5 : -3351.0266 (branch= 0.0074 alpha= 0.0129 pinv= 0.0146 eq freqs= 0.0009 rel rates= 0.0908 subset rates= 0.0013) +pass 6 : -3350.9182 (branch= 0.0038 alpha= 0.0120 pinv= 0.0135 eq freqs= 0.0005 rel rates= 0.0774 subset rates= 0.0011) +pass 7 : -3350.8253 (branch= 0.0032 alpha= 0.0114 pinv= 0.0125 eq freqs= 0.0002 rel rates= 0.0656 subset rates= 0.0000) +pass 8 : -3350.7431 (branch= 0.0006 alpha= 0.0115 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0571 subset rates= 0.0017) +pass 9 : -3350.6737 (branch= 0.0019 alpha= 0.0104 pinv= 0.0104 eq freqs= 0.0002 rel rates= 0.0466 subset rates= 0.0000) +pass 10: -3350.6126 (branch= 0.0004 alpha= 0.0096 pinv= 0.0101 eq freqs= 0.0001 rel rates= 0.0398 subset rates= 0.0011) +pass 11: -3350.5613 (branch= 0.0011 alpha= 0.0086 pinv= 0.0085 eq freqs= 0.0001 rel rates= 0.0329 subset rates= 0.0000) +pass 12: -3350.5178 (branch= 0.0001 alpha= 0.0080 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0276 subset rates= 0.0000) +pass 13: -3350.4797 (branch= 0.0000 alpha= 0.0076 pinv= 0.0069 eq freqs= 0.0001 rel rates= 0.0235 subset rates= 0.0000) +pass 14: -3350.4457 (branch= 0.0000 alpha= 0.0068 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0200 subset rates= 0.0009) +pass 15: -3350.4177 (branch= 0.0007 alpha= 0.0058 pinv= 0.0055 eq freqs= 0.0001 rel rates= 0.0160 subset rates= 0.0000) +pass 16: -3350.3934 (branch= 0.0001 alpha= 0.0051 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0141 subset rates= 0.0000) +pass 17: -3350.3719 (branch= 0.0000 alpha= 0.0047 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0123 subset rates= 0.0000) +pass 18: -3350.3532 (branch= 0.0000 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0106 subset rates= 0.0000) +pass 19: -3350.3369 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0091 subset rates= 0.0000) +pass 20: -3350.3228 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0077 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2535 (branch= 0.0000 alpha= 0.0168 pinv= 0.0154 eq freqs= 0.0001 rel rates= 0.0370 subset rates= 0.0000) + optimization up to ... +pass 40: -3350.2377 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0086 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2354 (branch= 0.0000 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0033 subset rates= 0.0000) +pass 50: -3350.2341 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0022 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2335 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) +pass 60: -3350.2333 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2331 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 70: -3350.2332 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 66: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 75: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2331 +Final score = -3350.2332 Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.115, AG = 10.418, AT = 2.690, CG = 0.001, CT = 21.941, GT = 1.000 + AC = 3.114, AG = 10.414, AT = 2.690, CG = 0.001, CT = 21.919, 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 - 0.5768 + 0.5782 with an invariant (invariable) site category, proportion estimated - 0.3655 + 0.3660 Substitution rate categories under this model: rate proportion - 0.0000 0.3655 - 0.0484 0.1586 - 0.2991 0.1586 - 0.8690 0.1586 - 2.7835 0.1586 + 0.0000 0.3660 + 0.0486 0.1585 + 0.2999 0.1585 + 0.8698 0.1585 + 2.7817 0.1585 Model 2 Number of states = 2 (binary data) @@ -14946,20 +14973,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2332 (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: 3.115 10.42 2.69 0.001 21.94 1 0.333 0.222 0.157 0.288 0.577 0.365 +rep 1: 3.114 10.41 2.69 0.001 21.92 1 0.333 0.222 0.157 0.288 0.578 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.789 1.821 0.179 +rep 1: 0.789 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -15109,11 +15136,6 @@ 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15214,75 +15236,75 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 634, seed 1595951943, best lnL -3321.461 +Search rep 1 (of 2) generation 430, seed 1447050696, best lnL -3323.902 gen current_lnL precision last_tree_imp -634 -3321.4612 0.255 1 +430 -3323.9019 0.500 1 +500 -3323.6818 0.500 1 +600 -3323.3459 0.500 1 +Optimization precision reduced + Optimizing parameters... improved 1.812 lnL + Optimizing branchlengths... improved 0.023 lnL 700 -3321.3650 0.255 1 800 -3321.0295 0.255 1 900 -3321.0142 0.255 1 -1000 -3320.9667 0.255 1 -1100 -3320.8654 0.255 1 -Optimization precision reduced - Optimizing parameters... improved 0.578 lnL - Optimizing branchlengths... improved 0.060 lnL NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.1579 +Current score = -3320.9667 Performing final optimizations... -pass 1 : -3319.7763 (branch= 0.0378 alpha= 0.0094 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.2977 ins/del rates= 0.0205) -pass 2 : -3319.4541 (branch= 0.0457 alpha= 0.0058 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.2391 ins/del rates= 0.0154) -pass 3 : -3319.1922 (branch= 0.0313 alpha= 0.0099 pinv= 0.0153 eq freqs= 0.0026 rel rates= 0.1953 ins/del rates= 0.0075) -pass 4 : -3318.9736 (branch= 0.0217 alpha= 0.0107 pinv= 0.0145 eq freqs= 0.0014 rel rates= 0.1628 ins/del rates= 0.0075) -pass 5 : -3318.7961 (branch= 0.0156 alpha= 0.0103 pinv= 0.0138 eq freqs= 0.0007 rel rates= 0.1317 ins/del rates= 0.0054) -pass 6 : -3318.6465 (branch= 0.0106 alpha= 0.0099 pinv= 0.0130 eq freqs= 0.0006 rel rates= 0.1110 ins/del rates= 0.0045) -pass 7 : -3318.5202 (branch= 0.0066 alpha= 0.0104 pinv= 0.0121 eq freqs= 0.0006 rel rates= 0.0939 ins/del rates= 0.0027) -pass 8 : -3318.4139 (branch= 0.0046 alpha= 0.0091 pinv= 0.0113 eq freqs= 0.0001 rel rates= 0.0792 ins/del rates= 0.0020) -pass 9 : -3318.3246 (branch= 0.0031 alpha= 0.0092 pinv= 0.0104 eq freqs= 0.0002 rel rates= 0.0651 ins/del rates= 0.0013) -pass 10: -3318.2492 (branch= 0.0020 alpha= 0.0088 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0541 ins/del rates= 0.0009) -pass 11: -3318.1851 (branch= 0.0013 alpha= 0.0083 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0451 ins/del rates= 0.0006) -pass 12: -3318.1304 (branch= 0.0009 alpha= 0.0077 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0377 ins/del rates= 0.0004) -pass 13: -3318.0835 (branch= 0.0006 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0317 ins/del rates= 0.0002) -pass 14: -3318.0440 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0258 ins/del rates= 0.0001) -pass 15: -3318.0099 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0218 ins/del rates= 0.0001) -pass 16: -3317.9804 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0186 ins/del rates= 0.0000) -pass 17: -3317.9547 (branch= 0.0001 alpha= 0.0049 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0159 ins/del rates= 0.0000) -pass 18: -3317.9325 (branch= 0.0001 alpha= 0.0044 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0136 ins/del rates= 0.0000) -pass 19: -3317.9131 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0116 ins/del rates= 0.0000) -pass 20: -3317.8963 (branch= 0.0000 alpha= 0.0035 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0099 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8127 (branch= 0.0001 alpha= 0.0188 pinv= 0.0174 eq freqs= 0.0001 rel rates= 0.0473 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7929 (branch= 0.0001 alpha= 0.0046 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0109 ins/del rates= 0.0000) +pass 1 : -3320.2903 (branch= 0.0812 alpha= 0.0000 pinv= 0.0165 eq freqs= 0.0053 rel rates= 0.5483 ins/del rates= 0.0252) +pass 2 : -3319.8339 (branch= 0.0649 alpha= 0.0065 pinv= 0.0163 eq freqs= 0.0000 rel rates= 0.3481 ins/del rates= 0.0205) +pass 3 : -3319.4901 (branch= 0.0401 alpha= 0.0094 pinv= 0.0159 eq freqs= 0.0063 rel rates= 0.2586 ins/del rates= 0.0135) +pass 4 : -3319.2216 (branch= 0.0229 alpha= 0.0101 pinv= 0.0154 eq freqs= 0.0013 rel rates= 0.2097 ins/del rates= 0.0091) +pass 5 : -3318.9943 (branch= 0.0197 alpha= 0.0095 pinv= 0.0146 eq freqs= 0.0012 rel rates= 0.1744 ins/del rates= 0.0081) +pass 6 : -3318.8040 (branch= 0.0111 alpha= 0.0109 pinv= 0.0137 eq freqs= 0.0010 rel rates= 0.1489 ins/del rates= 0.0046) +pass 7 : -3318.6482 (branch= 0.0080 alpha= 0.0097 pinv= 0.0130 eq freqs= 0.0007 rel rates= 0.1209 ins/del rates= 0.0034) +pass 8 : -3318.5189 (branch= 0.0052 alpha= 0.0102 pinv= 0.0121 eq freqs= 0.0004 rel rates= 0.0991 ins/del rates= 0.0023) +pass 9 : -3318.4106 (branch= 0.0035 alpha= 0.0099 pinv= 0.0111 eq freqs= 0.0003 rel rates= 0.0819 ins/del rates= 0.0015) +pass 10: -3318.3189 (branch= 0.0023 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0678 ins/del rates= 0.0010) +pass 11: -3318.2433 (branch= 0.0015 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0549 ins/del rates= 0.0007) +pass 12: -3318.1798 (branch= 0.0010 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0451 ins/del rates= 0.0004) +pass 13: -3318.1256 (branch= 0.0007 alpha= 0.0077 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0376 ins/del rates= 0.0003) +pass 14: -3318.0799 (branch= 0.0004 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0308 ins/del rates= 0.0002) +pass 15: -3318.0407 (branch= 0.0003 alpha= 0.0067 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0257 ins/del rates= 0.0001) +pass 16: -3318.0068 (branch= 0.0002 alpha= 0.0060 pinv= 0.0057 eq freqs= 0.0001 rel rates= 0.0218 ins/del rates= 0.0001) +pass 17: -3317.9776 (branch= 0.0001 alpha= 0.0054 pinv= 0.0051 eq freqs= 0.0000 rel rates= 0.0185 ins/del rates= 0.0000) +pass 18: -3317.9523 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) +pass 19: -3317.9303 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0000) +pass 20: -3317.9112 (branch= 0.0000 alpha= 0.0039 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0114 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8162 (branch= 0.0001 alpha= 0.0211 pinv= 0.0194 eq freqs= 0.0001 rel rates= 0.0542 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7937 (branch= 0.0001 alpha= 0.0052 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0124 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7883 (branch= 0.0000 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0026 ins/del rates= 0.0000) +pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0006 ins/del rates= 0.0000) +pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 72: -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: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 17 seconds +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.063, AG = 10.258, AT = 2.655, CG = 0.001, CT = 21.525, GT = 1.000 + AC = 3.066, AG = 10.267, AT = 2.657, CG = 0.001, CT = 21.545, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5752 + 0.5746 with an invariant (invariable) site category, proportion estimated - 0.3614 + 0.3612 Substitution rate categories under this model: rate proportion - 0.0000 0.3614 - 0.0480 0.1596 - 0.2982 0.1596 - 0.8681 0.1596 - 2.7856 0.1596 + 0.0000 0.3612 + 0.0479 0.1597 + 0.2979 0.1597 + 0.8678 0.1597 + 2.7864 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15314,7 +15336,7 @@ 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: 3.063 10.26 2.655 0.001 21.52 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.066 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 @@ -15461,6 +15483,8 @@ 4200 -210.6740 0.010 1104 4400 -210.6493 0.010 1104 4600 -210.6257 0.010 1104 +4800 -210.5948 0.010 1104 +5000 -210.5740 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15540,13 +15564,9 @@ STARTING RUN Restarting from checkpoint... - generation 4697, seed 833467714, best lnL -210.610 + generation 5056, seed 224596228, best lnL -210.572 gen current_lnL precision last_tree_imp -4697 -210.6098 0.010 1104 -4700 -210.6098 0.010 1104 -4800 -210.5948 0.010 1104 -4900 -210.5781 0.010 1104 -5000 -210.5740 0.010 1104 +5056 -210.5715 0.010 1104 5100 -210.5710 0.010 1104 5200 -210.5693 0.010 1104 Reached termination condition! @@ -15713,41 +15733,31 @@ Optimization precision reduced Optimizing parameters... improved 2.192 lnL Optimizing branchlengths... improved 0.320 lnL -1000 -167.2069 0.010 843 -1200 -167.1476 0.010 843 -1400 -167.0486 0.010 843 -1600 -166.9641 0.010 843 -1800 -166.8222 0.010 843 -2000 -166.6787 0.010 843 -2200 -166.5887 0.010 843 -2400 -166.4578 0.010 843 -2600 -166.3861 0.010 843 -2800 -166.3656 0.010 843 -3000 -166.3069 0.010 843 -3200 -166.2786 0.010 843 -3400 -166.2098 0.010 843 -3600 -166.0618 0.010 843 -3800 -165.9520 0.010 843 -4000 -165.9339 0.010 843 -4200 -165.8875 0.010 843 -4400 -165.8799 0.010 843 -4600 -165.7808 0.010 843 -4800 -165.7681 0.010 843 -5000 -165.6807 0.010 843 -5200 -165.6629 0.010 843 -5400 -165.5971 0.010 843 -5600 -165.4762 0.010 843 -5800 -165.3720 0.010 843 -6000 -165.3449 0.010 843 -6200 -165.2640 0.010 843 -6400 -165.1346 0.010 843 -6600 -165.0582 0.010 843 -6800 -165.0555 0.010 843 -7000 -164.9208 0.010 843 -7200 -164.7998 0.010 843 -7400 -164.7200 0.010 7384 -7600 -164.6617 0.010 7384 -7800 -164.5208 0.010 7384 +1000 -167.2067 0.010 843 +1200 -167.1474 0.010 843 +1400 -167.0485 0.010 843 +1600 -166.9639 0.010 843 +1800 -166.8221 0.010 843 +2000 -166.6786 0.010 843 +2200 -166.5885 0.010 843 +2400 -166.4577 0.010 843 +2600 -166.3860 0.010 843 +2800 -166.3655 0.010 843 +3000 -166.3068 0.010 843 +3200 -166.2785 0.010 843 +3400 -166.2097 0.010 843 +3600 -166.0616 0.010 843 +3800 -165.9519 0.010 843 +4000 -165.9338 0.010 843 +4200 -165.8874 0.010 843 +4400 -165.8798 0.010 843 +4600 -165.7807 0.010 843 +4800 -165.7680 0.010 843 +5000 -165.6805 0.010 843 +5200 -165.6627 0.010 843 +5400 -165.5964 0.010 843 +5600 -165.4765 0.010 843 +5800 -165.3752 0.010 843 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15828,57 +15838,76 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 7841, seed 418168850, best lnL -164.514 +Bootstrap rep 1 (of 1) generation 5984, seed 38531214, best lnL -165.290 gen current_lnL precision last_tree_imp -7841 -164.5138 0.010 7384 -7900 -164.4744 0.010 7384 -8000 -164.4381 0.010 7384 -8100 -164.3291 0.010 7384 -8200 -164.2988 0.010 7384 -8300 -164.1852 0.010 7384 -8400 -164.1759 0.010 7384 -8500 -164.1671 0.010 7384 -8600 -164.1241 0.010 7384 -8700 -163.9937 0.010 7384 -8800 -163.9560 0.010 7384 -8900 -163.9223 0.010 7384 -9000 -163.8539 0.010 7384 -9100 -163.8505 0.010 7384 -9200 -163.8476 0.010 7384 -9300 -163.7792 0.010 7384 -9400 -163.7481 0.010 7384 -9500 -163.7087 0.010 7384 -9600 -163.6368 0.010 7384 -9700 -163.6118 0.010 7384 -9800 -163.5999 0.010 7384 -9900 -163.5962 0.010 7384 -10000 -163.5758 0.010 7384 - Optimizing parameters... improved 1.517 lnL - Optimizing branchlengths... improved 0.024 lnL +5984 -165.2904 0.010 843 +6000 -165.2854 0.010 843 +6100 -165.2628 0.010 6021 +6200 -165.2440 0.010 6021 +6300 -165.1486 0.010 6021 +6400 -165.1353 0.010 6021 +6500 -165.1253 0.010 6021 +6600 -165.0478 0.010 6021 +6700 -165.0437 0.010 6021 +6800 -165.0427 0.010 6021 +6900 -164.8436 0.010 6021 +7000 -164.8382 0.010 6021 +7100 -164.7889 0.010 6021 +7200 -164.6662 0.010 6021 +7300 -164.6616 0.010 6021 +7400 -164.6476 0.010 6021 +7500 -164.6471 0.010 6021 +7600 -164.5350 0.010 7573 +7700 -164.4033 0.010 7573 +7800 -164.3901 0.010 7573 +7900 -164.3594 0.010 7573 +8000 -164.3321 0.010 7573 +8100 -164.1709 0.010 7573 +8200 -164.1535 0.010 7573 +8300 -164.0536 0.010 7573 +8400 -164.0463 0.010 7573 +8500 -164.0048 0.010 7573 +8600 -163.9409 0.010 7573 +8700 -163.8404 0.010 7573 +8800 -163.8131 0.010 7573 +8900 -163.8022 0.010 7573 +9000 -163.7248 0.010 7573 +9100 -163.7135 0.010 7573 +9200 -163.7033 0.010 7573 +9300 -163.6572 0.010 7573 +9400 -163.6397 0.010 7573 +9500 -163.5643 0.010 7573 +9600 -163.5151 0.010 7573 +9700 -163.4696 0.010 7573 +9800 -163.4651 0.010 7573 +9900 -163.4586 0.010 7573 +10000 -163.4574 0.010 7573 + Optimizing parameters... improved 1.549 lnL + Optimizing branchlengths... improved 0.015 lnL NOTE: ****Specified generation limit (10000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.623, AG = 8.557, AT = 1.923, CG = 3.484, CT = 32.948, GT = 1.000 + AC = 0.785, AG = 10.721, AT = 2.724, CG = 4.252, CT = 45.306, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1298 0.4236 0.2357 0.2109 + (ACGT) 0.1323 0.4184 0.2444 0.2049 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 525.3875 + 525.5894 with an invariant (invariable) site category, proportion estimated - 0.3606 + 0.3494 Substitution rate categories under this model: rate proportion - 0.0000 0.3606 - 0.9451 0.1599 - 0.9853 0.1599 - 1.0136 0.1599 - 1.0560 0.1599 + 0.0000 0.3494 + 0.9451 0.1627 + 0.9853 0.1627 + 1.0136 0.1627 + 1.0560 0.1627 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 3 branches were collapsed. + No branches were short enough to be collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! @@ -15889,15 +15918,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -162.0348 +Replicate 1 : -161.8932 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 0.6227 8.557 1.923 3.484 32.95 1 0.130 0.424 0.236 0.211 525.388 0.361 +rep 1: 0.7855 10.72 2.724 4.252 45.31 1 0.132 0.418 0.244 0.205 525.589 0.349 Treelengths: TL -rep 1: 3.169 +rep 1: 3.343 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -16031,6 +16060,15 @@ 5400 -212.8139 0.010 530 5600 -212.7826 0.010 530 5800 -212.7400 0.010 530 +6000 -212.7022 0.010 530 +6200 -212.7004 0.010 530 +6400 -212.6999 0.010 530 +6600 -212.6826 0.010 530 +6800 -212.6807 0.010 530 +7000 -212.6763 0.010 530 +7200 -212.6756 0.010 530 +7400 -212.6501 0.010 530 +7600 -212.6274 0.010 530 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16110,25 +16148,23 @@ STARTING RUN Restarting from checkpoint... - generation 5800, seed 524168958, best lnL -212.740 + generation 7654, seed 936081400, best lnL -212.626 gen current_lnL precision last_tree_imp -5800 -212.7400 0.010 530 -5900 -212.7039 0.010 530 -6000 -212.7022 0.010 530 -6100 -212.7009 0.010 530 -6200 -212.7004 0.010 530 -6300 -212.7003 0.010 530 +7654 -212.6258 0.010 530 +7700 -212.6214 0.010 530 +7800 -212.6186 0.010 530 +7900 -212.6180 0.010 530 Reached termination condition! last topological improvement at gen 530 -Improvement over last 500 gen = 0.03965 +Improvement over last 500 gen = 0.03208 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.127, AG = 9.833, AT = 0.417, CG = 10.050, CT = 6.542, GT = 1.000 + AC = 6.252, AG = 11.222, AT = 0.471, CG = 11.704, CT = 7.757, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2228 0.2869 0.1842 0.3061 + (ACGT) 0.2199 0.2885 0.1846 0.3071 Rate Heterogeneity Model: no rate heterogeneity @@ -16141,15 +16177,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.7003 +Replicate 1 : -212.6180 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 5.127 9.833 0.4165 10.05 6.542 1 0.223 0.287 0.184 0.306 +rep 1: 6.252 11.22 0.471 11.7 7.757 1 0.220 0.288 0.185 0.307 Treelengths: TL -rep 1: 1.726 +rep 1: 1.717 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 @@ -16304,83 +16340,15 @@ 6000 -210.3074 0.010 5809 6200 -210.2931 0.010 5809 6400 -210.2229 0.010 5809 -6600 -210.2218 0.010 5809 -6800 -210.2089 0.010 5809 -7000 -210.2012 0.010 5809 -7200 -210.2009 0.010 5809 -7400 -210.1715 0.010 5809 -7600 -210.1495 0.010 5809 -7800 -210.1030 0.010 5809 -8000 -210.0996 0.010 5809 -8200 -210.0921 0.010 5809 -8400 -210.0384 0.010 5809 -8600 -209.9799 0.010 8491 -8800 -209.9639 0.010 8491 -9000 -209.9587 0.010 8491 -9200 -209.9408 0.010 8491 -9400 -209.9288 0.010 8491 -9600 -209.9140 0.010 8491 -9800 -209.9063 0.010 8491 -10000 -209.9022 0.010 8491 - Optimizing parameters... improved 0.499 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 2.427, AG = 4.433, AT = 0.045, CG = 4.623, CT = 8.877, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2434 0.3359 0.2135 0.2072 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 4.6841 - with an invariant (invariable) site category, proportion estimated - 0.3065 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3065 - 0.4884 0.1734 - 0.7960 0.1734 - 1.0838 0.1734 - 1.6318 0.1734 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. - - -NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with - a positive constraint, it is possible for a constrained branch itself to be collapsed. - If you care, be careful to check whether this has happened or turn off branch collapsing. - -Saving site likelihoods to file ch.n.const.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -209.4035 - -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: 2.427 4.433 0.04505 4.623 8.877 1 0.243 0.336 0.213 0.207 4.684 0.306 - -Treelengths: - TL -rep 1: 2.469 - -Saving final tree from best search rep (#1) to ch.n.const.best.tre -Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -16459,29 +16427,50 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 1232396621, best lnL -209.403 + generation 6455, seed 335717011, best lnL -210.223 gen current_lnL precision last_tree_imp -10001 -209.4035 0.010 8491 +6455 -210.2229 0.010 5809 +6500 -210.2223 0.010 5809 +6600 -210.2218 0.010 5809 +6700 -210.2094 0.010 5809 +6800 -210.2089 0.010 5809 +6900 -210.2040 0.010 5809 +7000 -210.2012 0.010 5809 +7100 -210.2009 0.010 5809 +7200 -210.2009 0.010 5809 +7300 -210.1715 0.010 5809 +7400 -210.1715 0.010 5809 +7500 -210.1609 0.010 5809 +7600 -210.1495 0.010 5809 +7700 -210.1129 0.010 5809 +7800 -210.1030 0.010 5809 +7900 -210.0996 0.010 5809 +8000 -210.0996 0.010 5809 +8100 -210.0990 0.010 5809 +8200 -210.0921 0.010 5809 +Reached termination condition! +last topological improvement at gen 5809 +Improvement over last 500 gen = 0.02075 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.427, AG = 4.433, AT = 0.045, CG = 4.623, CT = 8.877, GT = 1.000 + AC = 2.186, AG = 4.025, AT = 0.209, CG = 4.117, CT = 7.340, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2434 0.3359 0.2135 0.2072 + (ACGT) 0.2403 0.3378 0.2137 0.2082 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.6841 + 1.8434 with an invariant (invariable) site category, proportion estimated - 0.3065 + 0.2215 Substitution rate categories under this model: rate proportion - 0.0000 0.3065 - 0.4884 0.1734 - 0.7960 0.1734 - 1.0838 0.1734 - 1.6318 0.1734 + 0.0000 0.2215 + 0.2738 0.1946 + 0.6373 0.1946 + 1.0655 0.1946 + 2.0234 0.1946 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. @@ -16497,15 +16486,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.4035 +Replicate 1 : -210.0921 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: 2.427 4.433 0.04505 4.623 8.877 1 0.243 0.336 0.213 0.207 4.684 0.306 +rep 1: 2.186 4.025 0.2088 4.117 7.34 1 0.240 0.338 0.214 0.208 1.843 0.222 Treelengths: TL -rep 1: 2.469 +rep 1: 2.449 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 @@ -16713,15 +16702,6 @@ Optimizing branchlengths... improved 0.000 lnL 600 -13371.2064 0.402 0 700 -13371.0755 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16844,9 +16824,10 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1321, seed 95210831, best lnL -13370.509 +Bootstrap rep 1 (of 1) generation 714, seed 448124242, best lnL -13371.000 gen current_lnL precision last_tree_imp -1321 -13370.5094 0.304 0 +714 -13370.9999 0.402 0 +800 -13370.9489 0.402 0 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16854,55 +16835,55 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.598, AG = 2.495, AT = 1.208, CG = 1.208, CT = 4.135, GT = 1.000 + AC = 1.456, AG = 2.328, AT = 1.077, CG = 1.077, CT = 3.707, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3079 0.1814 0.3083 0.2024 + (ACGT) 0.3111 0.1852 0.3053 0.1984 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3640 + 0.3637 Substitution rate categories under this model: rate proportion - 0.0119 0.2500 - 0.1544 0.2500 - 0.6892 0.2500 - 3.1446 0.2500 + 0.0118 0.2500 + 0.1542 0.2500 + 0.6888 0.2500 + 3.1452 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 = 2.627, AG = 4.236, AT = 0.821, CG = 4.236, CT = 2.627, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2812 0.1772 0.1597 0.3819 + (ACGT) 0.2813 0.1775 0.1599 0.3813 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2460 + 0.2463 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0638 0.2500 - 0.4929 0.2500 - 3.4413 0.2500 + 0.0640 0.2500 + 0.4936 0.2500 + 3.4404 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 = 5.347, AT = 4.290, CG = 0.632, CT = 5.347, GT = 1.000 + AC = 1.000, AG = 5.382, AT = 4.420, CG = 0.634, CT = 5.382, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1555 0.3460 0.2768 0.2217 + (ACGT) 0.1554 0.3450 0.2777 0.2219 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1101 + 4.1086 with an invariant (invariable) site category, proportion estimated - 0.0486 + 0.0475 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 0.0475 + 0.4602 0.2381 + 0.7789 0.2381 + 1.0844 0.2381 + 1.6765 0.2381 Subset rate multipliers: 0.53 0.29 2.18 @@ -16919,25 +16900,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.5063 (TERMINATED PREMATURELY) +Replicate 1 : -13370.8929 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 1.598 2.495 1.208 1.208 4.135 1 0.308 0.181 0.308 0.202 0.364 +rep 1: 1.456 2.328 1.077 1.077 3.707 1 0.311 0.185 0.305 0.198 0.364 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 0.281 0.177 0.160 0.382 0.246 +rep 1: 2.627 4.236 0.8209 4.236 2.627 1 0.281 0.177 0.160 0.381 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 5.347 4.29 0.6325 5.347 1 0.155 0.346 0.277 0.222 4.110 0.049 +rep 1: 1 5.382 4.42 0.6343 5.382 1 0.155 0.345 0.278 0.222 4.109 0.047 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.763 0.530 0.287 2.183 +rep 1: 1.772 0.530 0.285 2.185 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -17113,6 +17094,24 @@ 800 -467.7483 0.010 76 900 -467.7471 0.010 76 1000 -467.7427 0.010 76 +1100 -467.7372 0.010 76 +1200 -467.7330 0.010 76 +1300 -467.7317 0.010 76 +1400 -467.7307 0.010 76 +1500 -467.7301 0.010 76 +1600 -467.7294 0.010 76 +1700 -467.7252 0.010 76 +1800 -467.7239 0.010 76 +1900 -467.7239 0.010 76 +2000 -467.7234 0.010 76 +2100 -467.7228 0.010 76 +2200 -467.7218 0.010 76 +2300 -467.7216 0.010 76 +2400 -467.7209 0.010 76 +2500 -467.7205 0.010 76 +2600 -467.7205 0.010 76 +2700 -467.7197 0.010 76 +2800 -467.7190 0.010 76 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17238,27 +17237,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 1065, seed 1771518790, best lnL -467.741 +Search rep 1 (of 5) generation 2829, seed 445679797, best lnL -467.719 gen current_lnL precision last_tree_imp -1065 -467.7412 0.010 76 -1100 -467.7372 0.010 76 -1200 -467.7330 0.010 76 -1300 -467.7317 0.010 76 -1400 -467.7307 0.010 76 -1500 -467.7301 0.010 76 -1600 -467.7294 0.010 76 -1700 -467.7252 0.010 76 -1800 -467.7239 0.010 76 -1900 -467.7239 0.010 76 -2000 -467.7234 0.010 76 -2100 -467.7228 0.010 76 -2200 -467.7218 0.010 76 -2300 -467.7216 0.010 76 -2400 -467.7209 0.010 76 -2500 -467.7205 0.010 76 -2600 -467.7205 0.010 76 -2700 -467.7197 0.010 76 -2800 -467.7190 0.010 76 +2829 -467.7189 0.010 76 2900 -467.7186 0.010 76 3000 -467.7184 0.010 76 3100 -467.7181 0.010 76 @@ -17287,7 +17268,7 @@ pass 15: -467.6797 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6797 -Time used so far = 0 hours, 0 minutes and 10 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17366,26 +17347,44 @@ 100 -467.8013 0.010 0 200 -467.7834 0.010 0 300 -467.7719 0.010 0 +400 -467.7466 0.010 0 +500 -467.7422 0.010 0 +600 -467.7394 0.010 0 +700 -467.7358 0.010 0 +800 -467.7328 0.010 0 +900 -467.7315 0.010 0 +1000 -467.7286 0.010 0 +1100 -467.7271 0.010 0 +1200 -467.7201 0.010 0 +1300 -467.7189 0.010 0 +1400 -467.7173 0.010 0 +1500 -467.7148 0.010 0 +1600 -467.7147 0.010 0 +1700 -467.7131 0.010 0 +1800 -467.7123 0.010 0 +1900 -467.7122 0.010 0 +2000 -467.7119 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7481 +Current score = -467.7119 Performing final optimizations... -pass 1 : -467.7354 (branch= 0.0127 subset rates= 0.0000) -pass 2 : -467.7033 (branch= 0.0321 subset rates= 0.0000) -pass 3 : -467.6939 (branch= 0.0094 subset rates= 0.0000) -pass 4 : -467.6849 (branch= 0.0090 subset rates= 0.0000) -pass 5 : -467.6816 (branch= 0.0033 subset rates= 0.0000) -pass 6 : -467.6801 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -467.6792 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -467.6789 (branch= 0.0002 subset rates= 0.0001) -pass 9 : -467.6786 (branch= 0.0003 subset rates= 0.0000) -pass 10: -467.6785 (branch= 0.0001 subset rates= 0.0000) -pass 11: -467.6784 (branch= 0.0000 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) +pass 1 : -467.7119 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.6922 (branch= 0.0197 subset rates= 0.0000) +pass 3 : -467.6898 (branch= 0.0024 subset rates= 0.0000) +pass 4 : -467.6852 (branch= 0.0046 subset rates= 0.0000) +pass 5 : -467.6816 (branch= 0.0036 subset rates= 0.0000) +pass 6 : -467.6804 (branch= 0.0012 subset rates= 0.0000) +pass 7 : -467.6796 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -467.6793 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -467.6791 (branch= 0.0002 subset rates= 0.0000) +pass 10: -467.6789 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6789 (branch= 0.0000 subset rates= 0.0000) +pass 12: -467.6789 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6788 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6788 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6788 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6784 -Time used so far = 0 hours, 0 minutes and 15 seconds +Final score = -467.6788 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -17413,7 +17412,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.18 + 0.79 1.48 2.16 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -17431,7 +17430,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -467.6797 -Replicate 2 : -467.6784 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -467.6788 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17447,7 +17446,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.838 0.789 1.477 2.150 -rep 2: 3.843 0.786 1.483 2.179 +rep 2: 3.840 0.788 1.479 2.162 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -17629,119 +17628,6 @@ 1500 -477.2601 0.010 555 1600 -477.2577 0.010 555 1700 -477.2572 0.010 555 -1800 -477.2565 0.010 555 -1900 -477.2564 0.010 555 -2000 -477.2546 0.010 555 -2100 -477.2536 0.010 555 -2200 -477.2522 0.010 555 -2300 -477.2519 0.010 555 -2400 -477.2514 0.010 555 -2500 -477.2508 0.010 555 -2600 -477.2508 0.010 555 -2700 -477.2503 0.010 555 -2800 -477.2502 0.010 555 -2900 -477.2501 0.010 555 -3000 -477.2501 0.010 555 -Reached termination condition! -last topological improvement at gen 555 -Improvement over last 500 gen = 0.00070 -Current score = -477.2501 -Performing final optimizations... -pass 1 : -477.2483 (branch= 0.0000 subset rates= 0.0018) -pass 2 : -477.2269 (branch= 0.0215 subset rates= 0.0000) -pass 3 : -477.2216 (branch= 0.0044 subset rates= 0.0009) -pass 4 : -477.2198 (branch= 0.0018 subset rates= 0.0000) -pass 5 : -477.2189 (branch= 0.0009 subset rates= 0.0000) -pass 6 : -477.2178 (branch= 0.0012 subset rates= 0.0000) -pass 7 : -477.2138 (branch= 0.0008 subset rates= 0.0032) -pass 8 : -477.2124 (branch= 0.0014 subset rates= 0.0000) -pass 9 : -477.2122 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2122 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2121 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.2119 (branch= 0.0000 subset rates= 0.0001) -pass 13: -477.2119 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.2119 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.2119 -Time used so far = 0 hours, 0 minutes and 5 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate 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: - 0.64 1.91 2.62 -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 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=1307257127 - -Initial ln Likelihood: -651.6393 -optimizing: starting branch lengths, subset rates... -pass 1:+ 150.861 (branch= 139.75 scale= 1.32 subset rates= 9.79) -pass 2:+ 13.825 (branch= 9.87 scale= 0.03 subset rates= 3.93) -pass 3:+ 7.730 (branch= 6.44 scale= 0.00 subset rates= 1.29) -pass 4:+ 1.235 (branch= 0.92 scale= 0.04 subset rates= 0.27) -pass 5:+ 0.048 (branch= 0.04 scale= 0.01 subset rates= 0.00) -pass 6:+ 0.081 (branch= 0.08 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.024 (branch= 0.01 scale= 0.00 subset rates= 0.01) -pass 8:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass 9:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8228 -gen current_lnL precision last_tree_imp -0 -477.8228 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17867,68 +17753,152 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 59, seed 1733370690, best lnL -477.811 +Search rep 1 (of 5) generation 1706, seed 515275693, best lnL -477.257 +gen current_lnL precision last_tree_imp +1706 -477.2572 0.010 555 +1800 -477.2565 0.010 555 +1900 -477.2564 0.010 555 +2000 -477.2546 0.010 555 +2100 -477.2536 0.010 555 +2200 -477.2522 0.010 555 +2300 -477.2519 0.010 555 +2400 -477.2514 0.010 555 +2500 -477.2508 0.010 555 +2600 -477.2508 0.010 555 +2700 -477.2503 0.010 555 +2800 -477.2502 0.010 555 +2900 -477.2501 0.010 555 +3000 -477.2501 0.010 555 +Reached termination condition! +last topological improvement at gen 555 +Improvement over last 500 gen = 0.00070 +Current score = -477.2501 +Performing final optimizations... +pass 1 : -477.2483 (branch= 0.0000 subset rates= 0.0018) +pass 2 : -477.2237 (branch= 0.0215 subset rates= 0.0032) +pass 3 : -477.2189 (branch= 0.0044 subset rates= 0.0004) +pass 4 : -477.2173 (branch= 0.0016 subset rates= 0.0000) +pass 5 : -477.2164 (branch= 0.0009 subset rates= 0.0000) +pass 6 : -477.2157 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -477.2147 (branch= 0.0010 subset rates= 0.0000) +pass 8 : -477.2127 (branch= 0.0005 subset rates= 0.0015) +pass 9 : -477.2126 (branch= 0.0001 subset rates= 0.0000) +pass 10: -477.2125 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2124 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.2124 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2124 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -477.2124 +Time used so far = 0 hours, 0 minutes and 10 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.64 1.90 2.64 +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 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=1307257127 + +Initial ln Likelihood: -651.6393 +optimizing: starting branch lengths, subset rates... +pass 1:+ 150.861 (branch= 139.75 scale= 1.32 subset rates= 9.79) +pass 2:+ 13.825 (branch= 9.87 scale= 0.03 subset rates= 3.93) +pass 3:+ 7.730 (branch= 6.44 scale= 0.00 subset rates= 1.29) +pass 4:+ 1.235 (branch= 0.92 scale= 0.04 subset rates= 0.27) +pass 5:+ 0.048 (branch= 0.04 scale= 0.01 subset rates= 0.00) +pass 6:+ 0.081 (branch= 0.08 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.024 (branch= 0.01 scale= 0.00 subset rates= 0.01) +pass 8:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 9:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -477.8228 gen current_lnL precision last_tree_imp -59 -477.8114 0.010 0 +0 -477.8228 0.010 0 100 -477.7920 0.010 0 200 -477.7401 0.010 179 300 -477.7261 0.010 179 -400 -477.6988 0.010 179 -500 -477.3458 0.010 496 -600 -477.3029 0.010 510 -700 -477.2985 0.010 510 -800 -477.2851 0.010 510 -900 -477.2775 0.010 510 -1000 -477.2743 0.010 510 -1100 -477.2726 0.010 510 -1200 -477.2713 0.010 510 -1300 -477.2708 0.010 510 -1400 -477.2690 0.010 510 -1500 -477.2686 0.010 510 -1600 -477.2682 0.010 510 -1700 -477.2659 0.010 510 -1800 -477.2652 0.010 510 -1900 -477.2634 0.010 510 -2000 -477.2631 0.010 510 -2100 -477.2605 0.010 510 -2200 -477.2601 0.010 510 -2300 -477.2592 0.010 510 -2400 -477.2590 0.010 510 -2500 -477.2586 0.010 510 -2600 -477.2586 0.010 510 -2700 -477.2584 0.010 510 -2800 -477.2581 0.010 510 -2900 -477.2571 0.010 510 -3000 -477.2519 0.010 510 -3100 -477.2510 0.010 510 -3200 -477.2508 0.010 510 -3300 -477.2504 0.010 510 -3400 -477.2503 0.010 510 -3500 -477.2501 0.010 510 -3600 -477.2490 0.010 510 -3700 -477.2490 0.010 510 -3800 -477.2485 0.010 510 -3900 -477.2481 0.010 510 -4000 -477.2480 0.010 510 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.2480 +Current score = -477.7086 Performing final optimizations... -pass 1 : -477.2426 (branch= 0.0000 subset rates= 0.0055) -pass 2 : -477.2256 (branch= 0.0149 subset rates= 0.0020) -pass 3 : -477.2168 (branch= 0.0088 subset rates= 0.0000) -pass 4 : -477.2160 (branch= 0.0008 subset rates= 0.0000) -pass 5 : -477.2155 (branch= 0.0005 subset rates= 0.0000) -pass 6 : -477.2151 (branch= 0.0005 subset rates= 0.0000) -pass 7 : -477.2134 (branch= 0.0007 subset rates= 0.0010) -pass 8 : -477.2127 (branch= 0.0006 subset rates= 0.0001) -pass 9 : -477.2123 (branch= 0.0004 subset rates= 0.0000) -pass 10: -477.2122 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2122 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.2121 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2121 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.6995 (branch= 0.0068 subset rates= 0.0023) +pass 2 : -477.6526 (branch= 0.0441 subset rates= 0.0028) +pass 3 : -477.6259 (branch= 0.0266 subset rates= 0.0001) +pass 4 : -477.6157 (branch= 0.0102 subset rates= 0.0000) +pass 5 : -477.6123 (branch= 0.0033 subset rates= 0.0000) +pass 6 : -477.6111 (branch= 0.0012 subset rates= 0.0000) +pass 7 : -477.6101 (branch= 0.0010 subset rates= 0.0000) +pass 8 : -477.6096 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -477.6094 (branch= 0.0002 subset rates= 0.0000) +pass 10: -477.6093 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.6093 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.6092 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.6090 (branch= 0.0000 subset rates= 0.0002) +pass 14: -477.6088 (branch= 0.0001 subset rates= 0.0000) +pass 15: -477.6088 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.6088 (branch= 0.0000 subset rates= 0.0000) +pass 17: -477.6088 (branch= 0.0000 subset rates= 0.0000) +pass 18: -477.6087 (branch= 0.0000 subset rates= 0.0000) +pass 19: -477.6087 (branch= 0.0000 subset rates= 0.0000) +pass 20: -477.6087 (branch= 0.0000 subset rates= 0.0000) + optimization up to ... +pass 24: -477.6087 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.2121 -Time used so far = 0 hours, 0 minutes and 14 seconds +Final score = -477.6087 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -17956,9 +17926,9 @@ no rate heterogeneity Subset rate multipliers: - 0.64 1.90 2.61 + 0.63 1.92 2.67 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. >>>Terminated Search rep 2 (of 5)<<< @@ -17973,8 +17943,8 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -477.2119 (best) -Replicate 2 : -477.2121 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -477.2124 (best) +Replicate 2 : -477.6087 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17989,8 +17959,8 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.671 0.643 1.908 2.618 -rep 2: 4.667 0.644 1.904 2.613 +rep 1: 4.671 0.643 1.902 2.636 +rep 2: 4.839 0.635 1.923 2.668 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### @@ -18178,20 +18148,6 @@ 1800 -425.5972 0.010 365 1900 -425.5954 0.010 365 2000 -425.5950 0.010 365 -2100 -425.5942 0.010 365 -2200 -425.5913 0.010 365 -2300 -425.5899 0.010 365 -2400 -425.5893 0.010 365 -2500 -425.5891 0.010 365 -2600 -425.5890 0.010 365 -2700 -425.5888 0.010 365 -2800 -425.5883 0.010 365 -2900 -425.5869 0.010 365 -3000 -425.5868 0.010 365 -3100 -425.5859 0.010 365 -3200 -425.5858 0.010 365 -3300 -425.5850 0.010 365 -3400 -425.5843 0.010 365 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18320,9 +18276,23 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3492, seed 1337381527, best lnL -425.584 +Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 2019, seed 1366645766, best lnL -425.594 gen current_lnL precision last_tree_imp -3492 -425.5843 0.010 365 +2019 -425.5945 0.010 365 +2100 -425.5942 0.010 365 +2200 -425.5913 0.010 365 +2300 -425.5899 0.010 365 +2400 -425.5893 0.010 365 +2500 -425.5891 0.010 365 +2600 -425.5890 0.010 365 +2700 -425.5888 0.010 365 +2800 -425.5883 0.010 365 +2900 -425.5869 0.010 365 +3000 -425.5868 0.010 365 +3100 -425.5859 0.010 365 +3200 -425.5858 0.010 365 +3300 -425.5850 0.010 365 +3400 -425.5843 0.010 365 3500 -425.5843 0.010 365 3600 -425.5841 0.010 365 3700 -425.5839 0.010 365 @@ -18333,21 +18303,21 @@ Improvement over last 500 gen = 0.00044 Current score = -425.5839 Performing final optimizations... -pass 1 : -425.5730 (branch= 0.0000 subset rates= 0.0109) -pass 2 : -425.5586 (branch= 0.0144 subset rates= 0.0000) -pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0000) -pass 4 : -425.5509 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -425.5505 (branch= 0.0004 subset rates= 0.0000) +pass 1 : -425.5750 (branch= 0.0000 subset rates= 0.0089) +pass 2 : -425.5585 (branch= 0.0144 subset rates= 0.0020) +pass 3 : -425.5515 (branch= 0.0070 subset rates= 0.0000) +pass 4 : -425.5508 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -425.5504 (branch= 0.0004 subset rates= 0.0000) pass 6 : -425.5498 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -425.5494 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5488 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -425.5487 (branch= 0.0001 subset rates= 0.0000) -pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 7 : -425.5493 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.5490 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0002 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0000 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 7 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18390,7 +18360,7 @@ pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) -pass 4:+ 1.686 (branch= 1.66 scale= 0.02 subset rates= 0.01) +pass 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) @@ -18401,43 +18371,36 @@ pass12:+ 0.042 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass13:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass14:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.2276 +lnL after optimization: -439.2271 gen current_lnL precision last_tree_imp -0 -439.2276 0.010 0 -100 -428.8676 0.010 98 -200 -428.0499 0.010 164 -300 -427.6003 0.010 249 -400 -427.5649 0.010 249 -500 -427.4911 0.010 499 -600 -427.3864 0.010 511 -700 -425.7188 0.010 668 -800 -425.6951 0.010 722 -900 -425.6795 0.010 722 -1000 -425.6689 0.010 722 -1100 -425.6640 0.010 722 -1200 -425.6430 0.010 722 -1300 -425.6381 0.010 722 -1400 -425.6345 0.010 722 -1500 -425.6341 0.010 722 +0 -439.2271 0.010 0 +100 -428.8679 0.010 98 +200 -428.0498 0.010 164 +300 -427.6002 0.010 249 +400 -427.5647 0.010 249 +500 -427.4910 0.010 499 +600 -427.3863 0.010 511 +700 -425.7187 0.010 668 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.6341 +Current score = -425.6960 Performing final optimizations... -pass 1 : -425.6001 (branch= 0.0064 subset rates= 0.0275) -pass 2 : -425.5711 (branch= 0.0280 subset rates= 0.0010) -pass 3 : -425.5598 (branch= 0.0113 subset rates= 0.0000) -pass 4 : -425.5549 (branch= 0.0048 subset rates= 0.0000) -pass 5 : -425.5520 (branch= 0.0026 subset rates= 0.0004) -pass 6 : -425.5496 (branch= 0.0023 subset rates= 0.0000) -pass 7 : -425.5493 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5490 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -425.5488 (branch= 0.0002 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: -425.5486 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.6680 (branch= 0.0220 subset rates= 0.0061) +pass 2 : -425.6062 (branch= 0.0521 subset rates= 0.0097) +pass 3 : -425.5818 (branch= 0.0113 subset rates= 0.0131) +pass 4 : -425.5694 (branch= 0.0125 subset rates= 0.0000) +pass 5 : -425.5617 (branch= 0.0077 subset rates= 0.0000) +pass 6 : -425.5605 (branch= 0.0011 subset rates= 0.0000) +pass 7 : -425.5601 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.5599 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -425.5596 (branch= 0.0002 subset rates= 0.0000) +pass 10: -425.5595 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.5595 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5590 (branch= 0.0000 subset rates= 0.0005) +pass 13: -425.5590 (branch= 0.0000 subset rates= 0.0000) +pass 14: -425.5590 (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 14 seconds +Final score = -425.5590 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -18465,7 +18428,7 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.53 1.12 + 0.87 1.54 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 branches were collapsed. @@ -18483,7 +18446,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -425.5486 (best) -Replicate 2 : -425.5486 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -425.5590 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18498,8 +18461,8 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.038 0.868 1.530 1.121 -rep 2: 3.038 0.869 1.528 1.121 +rep 1: 3.038 0.868 1.531 1.122 +rep 2: 3.024 0.866 1.539 1.124 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre @@ -18659,46 +18622,33 @@ pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) -pass 5:+ 0.158 (branch= 0.12 scale= 0.00 subset rates= 0.03) +pass 5:+ 0.157 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8622 +lnL after optimization: -474.8624 gen current_lnL precision last_tree_imp -0 -474.8622 0.010 0 +0 -474.8624 0.010 0 100 -474.7511 0.010 68 -200 -474.7181 0.010 68 -300 -474.6977 0.010 68 +200 -474.7182 0.010 68 +300 -474.6978 0.010 68 400 -474.6394 0.010 329 -500 -474.1564 0.010 455 -600 -474.1360 0.010 560 -700 -474.0348 0.010 653 -800 -474.0229 0.010 653 -900 -474.0144 0.010 653 -1000 -474.0143 0.010 653 -1100 -474.0135 0.010 653 -1200 -474.0077 0.010 653 -1300 -474.0014 0.010 653 -1400 -473.9965 0.010 653 -1500 -473.9958 0.010 653 -1600 -473.9945 0.010 653 -1700 -473.9894 0.010 653 -1800 -473.9877 0.010 653 -1900 -473.9867 0.010 653 -2000 -473.9852 0.010 653 -2100 -473.9830 0.010 653 -2200 -473.9824 0.010 653 -2300 -473.9816 0.010 653 -2400 -473.9807 0.010 653 -2500 -473.9801 0.010 653 -2600 -473.9795 0.010 653 -2700 -473.9790 0.010 653 -2800 -473.9779 0.010 653 -2900 -473.9776 0.010 653 -3000 -473.9775 0.010 653 -3100 -473.9771 0.010 653 -3200 -473.9769 0.010 653 -3300 -473.9766 0.010 653 +500 -474.1553 0.010 455 +600 -474.1358 0.010 560 +700 -474.0415 0.010 653 +800 -474.0256 0.010 653 +900 -474.0163 0.010 653 +1000 -474.0079 0.010 653 +1100 -474.0062 0.010 653 +1200 -474.0018 0.010 653 +1300 -474.0004 0.010 653 +1400 -473.9972 0.010 653 +1500 -473.9932 0.010 653 +1600 -473.9890 0.010 653 +1700 -473.9880 0.010 653 +1800 -473.9876 0.010 653 +1900 -473.9835 0.010 653 +2000 -473.9824 0.010 653 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18824,35 +18774,43 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 3399, seed 317086130, best lnL -473.976 +Search rep 1 (of 5) generation 2052, seed 698314396, best lnL -473.982 gen current_lnL precision last_tree_imp -3399 -473.9762 0.010 653 -3400 -473.9762 0.010 653 -3500 -473.9761 0.010 653 -3600 -473.9761 0.010 653 -3700 -473.9759 0.010 653 +2052 -473.9824 0.010 653 +2100 -473.9820 0.010 653 +2200 -473.9804 0.010 653 +2300 -473.9801 0.010 653 +2400 -473.9787 0.010 653 +2500 -473.9787 0.010 653 +2600 -473.9778 0.010 653 +2700 -473.9774 0.010 653 +2800 -473.9763 0.010 653 +2900 -473.9761 0.010 653 +3000 -473.9761 0.010 653 +3100 -473.9758 0.010 653 +3200 -473.9758 0.010 653 +3300 -473.9754 0.010 653 Reached termination condition! last topological improvement at gen 653 -Improvement over last 500 gen = 0.00096 -Current score = -473.9759 +Improvement over last 500 gen = 0.00094 +Current score = -473.9754 Performing final optimizations... -pass 1 : -473.9758 (branch= 0.0001 subset rates= 0.0000) -pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0016) -pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9550 (branch= 0.0009 subset rates= 0.0000) -pass 5 : -473.9525 (branch= 0.0007 subset rates= 0.0018) -pass 6 : -473.9521 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -473.9516 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9734 (branch= 0.0000 subset rates= 0.0020) +pass 2 : -473.9552 (branch= 0.0178 subset rates= 0.0004) +pass 3 : -473.9552 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9552 (branch= 0.0000 subset rates= 0.0000) +pass 5 : -473.9539 (branch= 0.0013 subset rates= 0.0000) +pass 6 : -473.9530 (branch= 0.0008 subset rates= 0.0001) +pass 7 : -473.9521 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -473.9515 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -473.9513 (branch= 0.0001 subset rates= 0.0000) +pass 10: -473.9508 (branch= 0.0001 subset rates= 0.0004) +pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9507 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 6 seconds +Final score = -473.9507 +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18880,7 +18838,7 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.81 + 0.59 2.07 2.80 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -18915,68 +18873,45 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=74284197 +Starting with seed=2125680066 -Initial ln Likelihood: -646.1143 +Initial ln Likelihood: -649.8224 optimizing: starting branch lengths, subset rates... -pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) -pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) -pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) -pass 4:+ 2.490 (branch= 1.89 scale= 0.00 subset rates= 0.60) -pass 5:+ 0.684 (branch= 0.61 scale= 0.02 subset rates= 0.05) -pass 6:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) +pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) +pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) +pass 4:+ 2.345 (branch= 1.67 scale= 0.00 subset rates= 0.67) +pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) +pass 6:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8185 +lnL after optimization: -474.8071 gen current_lnL precision last_tree_imp -0 -474.8185 0.010 0 -100 -474.7244 0.010 55 -200 -474.7128 0.010 55 -300 -474.7037 0.010 55 -400 -474.6654 0.010 339 -500 -474.5695 0.010 496 -600 -474.0703 0.010 585 -700 -474.0481 0.010 585 -800 -474.0412 0.010 585 -900 -474.0316 0.010 585 -1000 -474.0282 0.010 585 -1100 -474.0225 0.010 585 -1200 -474.0142 0.010 585 -1300 -474.0116 0.010 585 -1400 -474.0080 0.010 585 -1500 -474.0041 0.010 585 -1600 -474.0016 0.010 585 -1700 -474.0010 0.010 585 -1800 -473.9994 0.010 585 -1900 -473.9983 0.010 585 -2000 -473.9971 0.010 585 -2100 -473.9968 0.010 585 -2200 -473.9964 0.010 585 -2300 -473.9963 0.010 585 -2400 -473.9952 0.010 585 -2500 -473.9949 0.010 585 -2600 -473.9933 0.010 585 -2700 -473.9932 0.010 585 -2800 -473.9932 0.010 585 -2900 -473.9930 0.010 585 +0 -474.8071 0.010 0 +100 -474.7912 0.010 0 +200 -474.7022 0.010 123 +300 -474.5642 0.010 272 +400 -474.5191 0.010 272 +500 -474.5075 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -473.9930 +Current score = -474.5034 Performing final optimizations... -pass 1 : -473.9930 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -473.9680 (branch= 0.0192 subset rates= 0.0058) -pass 3 : -473.9549 (branch= 0.0058 subset rates= 0.0072) -pass 4 : -473.9549 (branch= 0.0000 subset rates= 0.0000) -pass 5 : -473.9538 (branch= 0.0004 subset rates= 0.0008) -pass 6 : -473.9519 (branch= 0.0019 subset rates= 0.0000) -pass 7 : -473.9513 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -473.9512 (branch= 0.0001 subset rates= 0.0000) -pass 9 : -473.9511 (branch= 0.0001 subset rates= 0.0000) -pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4803 (branch= 0.0232 subset rates= 0.0000) +pass 2 : -474.4561 (branch= 0.0242 subset rates= 0.0000) +pass 3 : -474.4450 (branch= 0.0110 subset rates= 0.0000) +pass 4 : -474.4363 (branch= 0.0087 subset rates= 0.0000) +pass 5 : -474.4323 (branch= 0.0040 subset rates= 0.0000) +pass 6 : -474.4313 (branch= 0.0010 subset rates= 0.0000) +pass 7 : -474.4305 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -474.4293 (branch= 0.0007 subset rates= 0.0005) +pass 9 : -474.4287 (branch= 0.0006 subset rates= 0.0000) +pass 10: -474.4285 (branch= 0.0002 subset rates= 0.0000) +pass 11: -474.4284 (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) Looking for minimum length branches... -Final score = -473.9508 +Final score = -474.4284 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -19005,9 +18940,9 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.81 + 0.59 2.03 2.91 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. >>>Terminated Search rep 2 (of 5)<<< @@ -19022,8 +18957,8 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -473.9508 -Replicate 2 : -473.9508 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -473.9507 (best) +Replicate 2 : -474.4284 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19038,10 +18973,10 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.351 0.587 2.066 2.813 -rep 2: 4.350 0.587 2.067 2.812 +rep 1: 4.349 0.588 2.067 2.803 +rep 2: 4.598 0.588 2.034 2.906 -Saving final tree from best search rep (#2) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -19057,7 +18992,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j42 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j20 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' @@ -19106,11 +19041,11 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. -dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -19118,12 +19053,14 @@ 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/128431/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/128431/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/3778595 and its subdirectories -I: Current time: Wed Feb 11 23:54:43 -12 2026 -I: pbuilder-time-stamp: 1770897283 +I: removing directory /srv/workspace/pbuilder/128431 and its subdirectories +I: Current time: Fri Jan 10 19:51:23 +14 2025 +I: pbuilder-time-stamp: 1736488283